From 2d33a5144ac6c263059e00dcebe5b66ffcb7e11a Mon Sep 17 00:00:00 2001 From: ajfriedman22 Date: Wed, 4 Sep 2024 14:04:48 -0600 Subject: [PATCH 01/68] Add deafult swapping function --- ensemble_md/cli/run_REXEE.py | 2 + ensemble_md/replica_exchange_EE.py | 174 +++- ensemble_md/utils/coordinate_swap.py | 1325 ++++++++++++++++++++++++++ 3 files changed, 1491 insertions(+), 10 deletions(-) create mode 100644 ensemble_md/utils/coordinate_swap.py diff --git a/ensemble_md/cli/run_REXEE.py b/ensemble_md/cli/run_REXEE.py index 1581b490..bba96f09 100644 --- a/ensemble_md/cli/run_REXEE.py +++ b/ensemble_md/cli/run_REXEE.py @@ -99,6 +99,8 @@ def main(): os.mkdir(f'{REXEE.working_dir}/sim_{i}/iteration_0') MDP = REXEE.initialize_MDP(i) MDP.write(f"{REXEE.working_dir}/sim_{i}/iteration_0/expanded.mdp", skipempty=True) + if REXEE.modify_coords == 'default' and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): + REXEE.process_top() # 2-2. Run the first set of simulations REXEE.run_REXEE(0) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index 99b7fcbb..c40ea635 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -29,6 +29,7 @@ import ensemble_md from ensemble_md.utils import utils from ensemble_md.utils import gmx_parser +from ensemble_md.utils import coordinate_swap from ensemble_md.utils.exceptions import ParameterError comm = MPI.COMM_WORLD @@ -157,6 +158,8 @@ def set_params(self, analysis): optional_args = { "add_swappables": None, "modify_coords": None, + "resname_list": None, + "swap_rep_pattern": None, "nst_sim": None, "proposal": 'exhaustive', "w_combine": False, @@ -254,11 +257,15 @@ def set_params(self, analysis): raise ParameterError(f"The parameter '{i}' should be a boolean variable.") params_list = ['add_swappables', 'df_ref'] + if self.resname_list is not None: + params_list.append('resname_list') for i in params_list: if getattr(self, i) is not None and not isinstance(getattr(self, i), list): raise ParameterError(f"The parameter '{i}' should be a list.") params_dict = ['mdp_args', 'grompp_args', 'runtime_args'] + if self.swap_rep_pattern is not None: + params_dict.append('swap_rep_pattern') for i in params_dict: if getattr(self, i) is not None and not isinstance(getattr(self, i), dict): raise ParameterError(f"The parameter '{i}' should be a dictionary.") @@ -441,17 +448,24 @@ def set_params(self, analysis): # 7-12. External module for coordinate modification if self.modify_coords is not None: - module_file = os.path.basename(self.modify_coords) - module_dir = os.path.dirname(self.modify_coords) - if module_dir not in sys.path: - sys.path.append(module_dir) # so that the module can be imported - module_name = os.path.splitext(module_file)[0] - module = importlib.import_module(module_name) - if not hasattr(module, module_name): - err_msg = f'The module for coordinate manipulation (specified through the parameter) must have a function with the same name as the module, i.e., {module_name}.' # noqa: E501 - raise ParameterError(err_msg) + if self.modify_coords.lower == 'default': + if self.swap_rep_pattern is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): + raise Exception('swap_rep_pattern option must be filled in if using default swapping function and not swap guide') + if self.resname_list is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): + raise Exception('resname_list option must be filled in if using default swapping function and not swap guide') + self.modify_coords_fn = self.default_coords_fn else: - self.modify_coords_fn = getattr(module, module_name) + module_file = os.path.basename(self.modify_coords) + module_dir = os.path.dirname(self.modify_coords) + if module_dir not in sys.path: + sys.path.append(module_dir) # so that the module can be imported + module_name = os.path.splitext(module_file)[0] + module = importlib.import_module(module_name) + if not hasattr(module, module_name): + err_msg = f'The module for coordinate manipulation (specified through the parameter) must have a function with the same name as the module, i.e., {module_name}.' # noqa: E501 + raise ParameterError(err_msg) + else: + self.modify_coords_fn = getattr(module, module_name) else: self.modify_coords_fn = None @@ -1496,3 +1510,143 @@ def run_REXEE(self, n, swap_pattern=None): # want it to start parsing the dhdl file (in the if condition of if rank == 0) of simulation 3 being run by # rank 3 that has not been generated, which will lead to an I/O error. comm.barrier() + + def default_coords_fn(self, molA_file_name: str, molB_file_name: str): + """ + Swap coordinates between two GRO files + + Parameters + ---------- + molA_file_name : str + GRO file name for the moleucle to be swapped + molB_file_name : str + GRO file name for the other moleucle to be swapped + Return + ------ + None + """ + # Step 1: Load necessary files + import mdtraj as md + import pandas as pd + + #Determine name for transformed residue + molA_dir = molA_file_name.rsplit('/', 1)[0] + '/' + molB_dir = molB_file_name.rsplit('/', 1)[0] + '/' + + #Load trajectory trr for higher precison coordinates + molA = md.load_trr(f'{molA_dir}/traj.trr', top=molA_file_name).slice(-1) #Load last frame of trr trajectory + molB = md.load_trr(f'{molB_dir}/traj.trr', top=molB_file_name).slice(-1) + + #Load the coordinate swapping map + connection_map = pd.read_csv('residue_connect.csv') + swap_map = pd.read_csv('residue_swap_map.csv') + + # Step 2: Read the GRO input coordinate files and open temporary Output files + molA_file = open(molA_file_name, 'r').readlines() #open input file + molB_new_file_name = 'B_hybrid_swap.gro' + molB_new = open(molB_new_file_name, 'w') + molB_file = open(molB_file_name, 'r').readlines() #open input file + molA_new_file_name = 'A_hybrid_swap.gro' + molA_new = open(molA_new_file_name, 'w') + + # Step 3: Determine atoms for alignment and swapping + nameA = coordinate_swap.deter_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) + nameB = coordinate_swap.deter_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) + df_atom_swap = coordinate_swap.deter_common(molA_file, molB_file, nameA, nameB) + + # Step 4: Fix break if present for solvated systems only + if len(molA.topology.select('water')) != 0: + A_dimensions = coordinate_swap.get_dimensions(molA_file) + B_dimensions = coordinate_swap.get_dimensions(molB_file) + molA = coordinate_swap.fix_break(molA, nameA, A_dimensions, connection_map[connection_map['Resname'] == nameA]) + molB = coordinate_swap.fix_break(molB, nameB, B_dimensions, connection_map[connection_map['Resname'] == nameB]) + + # Step 5: Determine coordinates of atoms which need to be reconstructed as we swap coordinates between molecules + miss_B = df_atom_swap[(df_atom_swap['Swap']=='B2A') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() + miss_A = df_atom_swap[(df_atom_swap['Swap']=='A2B') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() + if len(miss_B) != 0: + df_atom_swap = coordinate_swap.get_miss_coord(molB, molA, nameB, nameA, df_atom_swap, 'B2A', swap_map[(swap_map['Swap A'] == nameA) & (swap_map['Swap B'] == nameB)]) + if len(miss_A) != 0: + df_atom_swap = coordinate_swap.get_miss_coord(molA, molB, nameA, nameB, df_atom_swap, 'A2B', swap_map[(swap_map['Swap A'] == nameB) & (swap_map['Swap B'] == nameA)]) + + #Reprint preamble text + line_start = coordinate_swap.print_preamble(molA_file, molB_new, len(miss_B), len(miss_A)) + + #Print new coordinates to file for molB + coordinate_swap.write_new_file(df_atom_swap, 'A2B', 'B2A', line_start, molA_file, molB_new, nameA, nameB, copy.deepcopy(molA.xyz[0]), miss_A) + + #Print new coordinates to file + #Reprint preamble text + line_start = coordinate_swap.print_preamble(molB_file, molA_new, len(miss_A), len(miss_B)) + + #Print new coordinates for molA + coordinate_swap.write_new_file(df_atom_swap, 'B2A', 'A2B', line_start, molB_file, molA_new, nameB, nameA, copy.deepcopy(molB.xyz[0]), miss_B) + + #Rename temp files + os.rename('A_hybrid_swap.gro', molB_dir + '/confout.gro') + os.rename('B_hybrid_swap.gro', molA_dir + '/confout.gro') + + def process_top(self): + """ + Process the input topologies in order to determine the atoms for alignment in the default GRO swapping function. + Output as csv files to prevent needing to re-run this step. + + Parameters + ---------- + None + Return + ------ + None + """ + import pandas as pd + + if not os.path.exists('residue_connect.csv'): + df_top = pd.DataFrame() + for f, file_name in enumerate(self.top): + #Read file + input = coordinate_swap.read_top(file_name, self.resname_list[f]) + + #Determine the atom names corresponding to the atom numbers + start_line, atom_name, state = coordinate_swap.get_names(input) + + #Determine the connectivity of all atoms + connect_1, connect_2, state_1, state_2 = [], [], [], [] #Atom 1 and atom 2 which are connected and which state they are dummy atoms + for l, line in enumerate(input[start_line:]): + line_sep = line.split(' ') + if line_sep[0] == ';': + continue + if line_sep[0] == '\n': + break + while '' in line_sep: + line_sep.remove('') + connect_1.append(atom_name[int(line_sep[0])-1]) + connect_2.append(atom_name[int(line_sep[1])-1]) + state_1.append(state[int(line_sep[0])-1]) + state_2.append(state[int(line_sep[1])-1]) + df = pd.DataFrame({'Resname': self.resname_list[f], 'Connect 1': connect_1, 'Connect 2': connect_2, 'State 1': state_1, 'State 2': state_2}) + df_top = pd.concat([df_top, df]) + df_top.to_csv('residue_connect.csv') + else: + df_top = pd.read_csv('residue_connect.csv') + + if not os.path.exists('residue_swap_map.csv'): + df_map = pd.DataFrame() + + for swap in self.swap_rep_pattern: + #Determine atoms not present in both molecules + X, Y = swap.keys() + for A, B in zip([X, Y], [Y, X]): + input_A = coordinate_swap.read_top(self.top_files[A], self.resname_list[A]) + start_line, A_name, state = coordinate_swap.get_names(input_A) + input_B = coordinate_swap.read_top(self.top_files[B], self.resname_list[B]) + start_line, B_name, state = coordinate_swap.get_names(input_B) + + A_only = [x for x in A_name if x not in B_name] + B_only = [x for x in B_name if x not in A_name] + + #Seperate real to dummy switches + df = coordinate_swap.deter_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, swap[A]) + + df_map = pd.concat([df_map, df]) + + df_map.to_csv('residue_swap_map.csv') \ No newline at end of file diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py new file mode 100644 index 00000000..90d2b658 --- /dev/null +++ b/ensemble_md/utils/coordinate_swap.py @@ -0,0 +1,1325 @@ +import mdtraj as md +import re +import numpy as np +import os +from itertools import product +import pandas as pd +import copy + +def get_dimensions(file): + """ + Determine the dimensions of the cubic box based on the input GRO file + + Parameters + ---------- + file : List of strings + containing all of the lines in the input gro file + + Returns + ------- + [x, y, z] : List of floats + X, Y, and Z coordinates for the periodic box + """ + box_raw = file[-1].split(' ') + while '' in box_raw: + box_raw.remove('') + + return [float(box_raw[0]), float(box_raw[1]), float(box_raw[2])] + +def deter_common(molA_file, molB_file, nameA : str, nameB : str): + """ + Determine the atoms which are common, which are switched between dummy and real atoms, and which are unique between the two molecule + + Parameters + ---------- + molA_file : List of strings + Lines of the GRO file for molecule A + molB_file : List of strings + Lines of the GRO file for molecule B + nameA : str + The name of the residue being altered in molecule A + nameB : str + The name of the residue being altered in molecule B + + Returns + ------- + df : pandas DataFrame + Containing the atoms which are not the same between the two molecules and how they are changed + """ + #Gather atom names from each file + nameA_list, lineA_list, nameB_list, lineB_list = [], [], [], [] + for l, line in enumerate(molA_file): + split_line = line.split(' ') + while("" in split_line): split_line.remove("") + if len(line[1]) > 5: + split_line = sep_merge(split_line) + if nameA in split_line[0]: + nameA_list.append(split_line[1]) + lineA_list.append(l) + + for l, line in enumerate(molB_file): + split_line = line.split(' ') + while("" in split_line): split_line.remove("") + if len(line[1]) > 5: + split_line = sep_merge(split_line) + if nameB in split_line[0]: + nameB_list.append(split_line[1]) + lineB_list.append(l) + + #Determine the atom names present in both molecules + common_atoms_all = list(set(nameA_list) & set(nameB_list)) + + #Determine the swaps for each transformation + df_A2B = deter_R2D_D2R_miss(nameA_list, nameB_list, common_atoms_all, lineA_list, 'A2B') + df_B2A = deter_R2D_D2R_miss(nameB_list, nameA_list, common_atoms_all, lineB_list, 'B2A') + + #Add D2R + df = pd.concat([df_A2B, df_B2A]) + df.reset_index(inplace=True) + return df + +def deter_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap): + """ + Determine which atoms are swapped between dummy and real states and which are missing + + Parameters + ---------- + name_list : str + List of all the atom names for the atoms in the molecule of interest + name_other_list : str + List of all the atom names for the atoms that the molecule of interest is swapping with + common_atoms : str + List of all the atom names for atoms known to be common between the two molecules + Line_list : int + List of the line in the file which corresponds to each atom name in the molecule of interest + swap : str + The direction of the swap based on the molecules identified as A and B + + Returns + ------- + df : pandas DataFrame + For each atom that is not in the common list the dataframe gives the name of the atom, the atom number, the atom element, whether the atom is switchin between dummy and real or missing, the swap direction (same as input), whether the final atom type is real or dummy + """ + #Determine atoms unique to either molecule + names, an_num, elements, directions, swaps, lines, final_type = [], [], [], [], [], [], [] + for a, atom in enumerate(name_list): + element = atom.strip('0123456789') + real_element = element.strip('DV') + num = atom.strip('ABCDEFGHIJKLMNOPQRSTUVWXYZ') + if atom not in common_atoms: + names.append(atom) + an_num.append(num) + swaps.append(swap) + lines.append(line_list[a]) + if 'C' in element: + elements.append('C') + else: + elements.append('H') + if f'D{atom}' in name_other_list or f'{element}V{num}' in name_other_list: + directions.append('R2D') + final_type.append('dummy') + elif f'{real_element}{num}' in name_other_list: + directions.append('D2R') + final_type.append('real') + else: + directions.append('miss') + if 'V' in atom or 'DC' in atom: + final_type.append('dummy') + else: + final_type.append('real') + return pd.DataFrame({'Name': names, 'Atom Name Number': an_num, 'Element': elements, 'Direction': directions, 'Swap': swaps, 'File line': lines, 'Final Type': final_type}) + +def fix_break(mol, resname, box_dimensions, atom_connect_all): + """ + Determine if there are any breaks across periodic boundary conditions in the residue of interest and shift the molecule across those boudaries to make it whole + + Parameters + ---------- + mol : mdtraj Trajectory object + Trajectory object for the molecule or interest + resname : str + Name of the residue of interest for coordinate swapping + box_dimensions : list + Dimensions of the periodic box for the system of interest + atom_connect_all : pd.DataFrame + DataFrame which contains the name of all atoms which are connected to one another in the residue of interest + + Returns + ------- + mol : mdtraj Trajecotry object + Trajectory with all breaks in the necessary portions of the molecule fixed + + """ + mol_top = mol.topology + + atom_connect = [] + for i, row in atom_connect_all.iterrows(): + atom_connect.append([row['Connect 1'], row['Connect 2']]) + + atom_pairs = [] + for atoms in atom_connect: + atom_pairs.append(list(mol_top.select(f"resname {resname} and (name {atoms[0]} or name {atoms[1]})"))) + + #Find any broken bonds + broken_pairs = check_break(mol, atom_pairs) + + if len(broken_pairs) == 0: + print('No breaks found') + return mol + else: + print('Fixing break') + + iter = 0 #Keep track of while loop iterations + shift_atom = [] + while len(broken_pairs) > 0: + #Prevent infinite loop + if iter > len(atom_pairs): + raise Exception('Break could not be fixed') + iter += 1 + + #Fix this break + mol, Fixed, shift_atom = perform_shift_1D(mol, box_dimensions, broken_pairs, atom_pairs, shift_atom) + if Fixed: + broken_pairs = check_break(mol, atom_pairs) + continue + else: + mol, Fixed = perform_shift_2D(mol, box_dimensions, broken_pairs, shift_atom) + if Fixed: + broken_pairs = check_break(mol, atom_pairs) + continue + else: + mol, Fixed = perform_shift_3D(mol, box_dimensions, broken_pairs, shift_atom) + if Fixed: + broken_pairs = check_break(mol, atom_pairs) + continue + else: + raise Exception('Break could not be fixed') + + return mol + +def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): + """ + Shift across the periodic boundaries in 1D + + Parameters + ---------- + mol : mdtraj Trajectory object + Trajecotry with the original coordinates prior to the fhist + box_dimensions : list of floats + Dimensions of the periodic boundary box + broken_pairs_init : int + which pairs of atoms were found to be broken + prev_shift_atom : int + Which atoms have already been shifted so we don't undo what we've done + + Returns + ------- + mol : mdtraj Trajectory object + Trajectory with the new coordintes + Fixed : bool + Was the break actually fixed + prev_shift_atom : int + Which atoms have already been shifted so we don't undo what we've done + """ + atom_pair = broken_pairs_init[0] + broken_atom = atom_pair[1] + if broken_atom in prev_shift_atom: + broken_atom = atom_pair[0] + Fixed = False + for x in range(3): #Loop through x, y, and z + for shift_dir in [1, -1]: + mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) #positive shift + dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) + if dist_check > 0.2: #Didn't work so reverse and try again + mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] - (shift_dir[0] * box_dimensions[x]) + else: #Yay fixed break + Fixed = True + break + if Fixed: + break + if Fixed: + prev_shift_atom.append(broken_atom) + return mol, Fixed, prev_shift_atom + +def perform_shift_2D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): + """ + Shift across the periodic boundaries in 2D + + Parameters + ---------- + mol : mdtraj Trajectory object + Trajecotry with the original coordinates prior to the fhist + box_dimensions : list of floats + Dimensions of the periodic boundary box + broken_pairs_init : int + which pairs of atoms were found to be broken + prev_shift_atom : int + Which atoms have already been shifted so we don't undo what we've done + + Returns + ------- + mol : mdtraj Trajectory object + Trajectory with the new coordintes + Fixed : bool + Was the break actually fixed + prev_shift_atom : int + Which atoms have already been shifted so we don't undo what we've done + """ + atom_pair = broken_pairs_init[0] + broken_atom = atom_pair[1] + if broken_atom in prev_shift_atom: + broken_atom = atom_pair[0] + Fixed = False + shift_combos = product([0, 1, 2], [0, 1, 2]) + for pair in shift_combos: #Loop through x, y, and z + for shift_dir in product([1, -1], [1,-1]): #Try all combos of shift direction + x, y = pair + mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) #positive shift + mol.xyz[0,broken_atom,y] = mol.xyz[0,broken_atom,y] + (shift_dir[1] * box_dimensions[y]) + dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) + if dist_check > 0.2: #Didn't work so reverse and try again + mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] - (shift_dir[0] * box_dimensions[x]) + mol.xyz[0,broken_atom,y] = mol.xyz[0,broken_atom,y] - (shift_dir[1] * box_dimensions[y]) + else: #Yay fixed break + Fixed = True + break + if Fixed: + break + if Fixed: + prev_shift_atom.append(broken_atom) + return mol, Fixed + +def perform_shift_3D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): + """ + Shift across the periodic boundaries in 3D + + Parameters + ---------- + mol : mdtraj Trajectory object + Trajecotry with the original coordinates prior to the fhist + box_dimensions : list of floats + Dimensions of the periodic boundary box + broken_pairs_init : int + which pairs of atoms were found to be broken + prev_shift_atom : int + Which atoms have already been shifted so we don't undo what we've done + + Returns + ------- + mol : mdtraj Trajectory object + Trajectory with the new coordintes + Fixed : bool + Was the break actually fixed + prev_shift_atom : int + Which atoms have already been shifted so we don't undo what we've done + """ + atom_pair = broken_pairs_init[0] + broken_atom = atom_pair[1] + if broken_atom in prev_shift_atom: + broken_atom = atom_pair[0] + Fixed = False + for shift_dir in product([1, -1], [1,-1], [1, -1]): #Try all combos of shift direction + mol.xyz[0,broken_atom,0] = mol.xyz[0,broken_atom,0] + (shift_dir[0] * box_dimensions[0]) + mol.xyz[0,broken_atom,1] = mol.xyz[0,broken_atom,1] + (shift_dir[1] * box_dimensions[1]) + mol.xyz[0,broken_atom,2] = mol.xyz[0,broken_atom,2] + (shift_dir[2] * box_dimensions[2]) + dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) + if dist_check > 0.2: #Didn't work so reverse and try again + mol.xyz[0,broken_atom,0] = mol.xyz[0,broken_atom,0] - (shift_dir[0] * box_dimensions[0]) + mol.xyz[0,broken_atom,1] = mol.xyz[0,broken_atom,1] - (shift_dir[1] * box_dimensions[1]) + mol.xyz[0,broken_atom,2] = mol.xyz[0,broken_atom,2] - (shift_dir[2] * box_dimensions[2]) + else: #Yay fixed break + Fixed = True + break + if Fixed: + prev_shift_atom.append(broken_atom) + return mol, Fixed + +def check_break(mol, atom_pairs): + """ + Determine whether a break is present between the atom pairs of interest + + Parameters + ---------- + mol : mdtraj Trajectory object + Trajectory to examine for breaks + atom_pairs : int + The atom number pairs which should be connected in the residue of interest + + Returns + ------- + broken_pairs : int + which pairs of atoms have breaks across the periodic boundary + """ + dist = md.compute_distances(mol, atom_pairs=atom_pairs, periodic=False) + broken_pairs = [] + for i, d in enumerate(dist[0]): + if d > 0.2: + broken_pairs.append(atom_pairs[i]) + return broken_pairs + +def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, df_swap): + """ + Get coordinates for the missing atoms after the conformational swap + + Parameters + ---------- + mol_align : mdtraj Trajectory object + trajectory for the molecule being aligned + mol_ref : mdtraj Trajectory object + trajectory for the reference molecule + name_align : str + resname for the molecule which is being aligned + name_ref : str + resname for the molecule which has the reference coordinates + df_atom_swap : pandas DataFrame + For each atom that is not in the common list the dataframe gives the name of the atom, the atom number, the atom element, whether the atom is switchin between dummy and real or missing, the swap direction (same as input), whether the final atom type is real or dummy + dir : str + swapping direction + df_swap : pandas DataFrame + For each missing atoms + + Returns + ------- + df_atom_swap : pandas DataFrame + Same dataframe as the input, but with coordinates for the missing atoms + """ + #Create a new column for coordinates if one does not exist + if 'X Coordinates' not in df_atom_swap.columns: + df_atom_swap['X Coordinates'] = np.NaN + df_atom_swap['Y Coordinates'] = np.NaN + df_atom_swap['Z Coordinates'] = np.NaN + + if len(df_swap.index) == 0: + return df_atom_swap + + for i, row in df_swap.iterrows(): + conn_align = [row['Anchor Atom Name A'], row['Alignment Atom A']] + conn_ref = [row['Anchor Atom Name B'], row['Alignment Atom B']] + geom_fix_select = [row['Missing Atom Name'][0], row['Anchor Atom Name A'], row['Angle Atom A']] + miss_names_select = row['Missing Atom Name'] + #Limit to region of interest + align_select = [] + for a in conn_align + miss_names_select + geom_fix_select: + atom = mol_align.topology.select(f'resname {name_align} and name {a}')[0] + if atom not in align_select: + align_select.append(atom) + align_select.sort() + ref_select = mol_ref.topology.select(f'resname {name_ref} and (name {conn_ref[0]} or name {conn_ref[1]} or name {geom_fix_select[-1]})') + + mol_ref_select = copy.deepcopy(mol_ref.atom_slice(ref_select)) + mol_align_select = copy.deepcopy(mol_align.atom_slice(align_select)) + + #Select atoms in connection bond + conn0_align = mol_align_select.topology.select(f'resname {name_align} and name {conn_align[0]}')[0] + conn1_align = mol_align_select.topology.select(f'resname {name_align} and name {conn_align[1]}')[0] + conn0_ref = mol_ref_select.topology.select(f'resname {name_ref} and name {conn_ref[0]}')[0] + conn1_ref = mol_ref_select.topology.select(f'resname {name_ref} and name {conn_ref[1]}')[0] + + #Step 1: Perform translation to align point 1 + shift_vec = mol_ref_select.xyz[0,conn0_ref,:] - mol_align_select.xyz[0,conn0_align,:] + for a in range(mol_align_select.n_atoms): + mol_align_select.xyz[0,a,:] = mol_align_select.xyz[0,a,:] + shift_vec + + #Step 2: Perform rotational motion to line up point 2 + ref_vec = mol_ref_select.xyz[0,conn1_ref,:] - mol_ref_select.xyz[0,conn0_ref,:] #defing 0-1 vector in ref + align_vec = mol_align_select.xyz[0,conn1_align,:] - mol_ref_select.xyz[0,conn0_ref,:] #defing 0-1 vector in align + axis_rot = np.cross(ref_vec/np.linalg.norm(ref_vec), (align_vec/np.linalg.norm(align_vec))) #Perpendicular vector to ref and align vectors + theta = find_rotation_angle(mol_align_select.xyz[0,conn1_align,:], mol_ref_select.xyz[0,conn0_ref,:], mol_ref_select.xyz[0,conn1_ref,:], axis_rot) + + for a in range(mol_align_select.n_atoms): + if a != conn0_align: + mol_align_select.xyz[0,a,:] = rotate_point_around_axis(mol_align_select.xyz[0,a,:], mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta) + + #Step 3: Rotate around 0-1 bond to get the correct angle for connecting atom + angle_atoms = [mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[0]}')[0], + mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0], + mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[2]}')[0]] + internal_angle = compute_angle([mol_align.xyz[0,angle_atoms[0],:], mol_align.xyz[0,angle_atoms[1],:], mol_align.xyz[0,angle_atoms[2],:]]) + change_atoms = mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[0]}') + axis_rot = mol_align_select.xyz[0,conn0_align,:] - mol_align_select.xyz[0,conn1_align,:] + axis_rot = axis_rot / np.linalg.norm(axis_rot) + + #Determine angle of rotation to get the right internal angle + min_dev_angle = 3 + init_coords = mol_align_select.xyz[0,change_atoms,:][0].copy() + constant_coords = [mol_align_select.xyz[0,mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0],:], + mol_ref_select.xyz[0,mol_ref_select.topology.select(f'resname {name_ref} and name {geom_fix_select[2]}')[0],:]] + for theta in np.linspace(0, 2*np.pi, num=10): + new_coors = np.zeros((3,3)) + new_coors[0,:] = rotate_point_around_axis(init_coords, mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta) + new_coors[1:,:] = constant_coords + iangle = compute_angle(new_coors) + if abs(iangle - internal_angle) < min_dev_angle: + theta_min = theta + min_dev_angle = abs(iangle - internal_angle) + if min_dev_angle < 0.05: + break + #Perform the rotation + for a in range(mol_align_select.n_atoms): + if a != conn0_align: + mol_align_select.xyz[0,a,:] = rotate_point_around_axis(mol_align_select.xyz[0,a,:], mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta_min) + + #Add coordinates to df + for r in range(len(df_atom_swap.index)): + if df_atom_swap.iloc[r]['Direction'] == 'miss' and df_atom_swap.iloc[r]['Swap'] == dir: + for name in miss_names_select: + if df_atom_swap.iloc[r]['Name'] == name: + a = mol_align_select.topology.select(f'name {name}') + df_atom_swap.at[r, 'X Coordinates'] = mol_align_select.xyz[0,a,0] + df_atom_swap.at[r, 'Y Coordinates'] = mol_align_select.xyz[0,a,1] + df_atom_swap.at[r, 'Z Coordinates'] = mol_align_select.xyz[0,a,2] + continue + + return df_atom_swap + +def process_line(mol_file, i): + """ + Seperate the line by spaces and correct for when the atom number merges the atom name + + Parameters + ---------- + mol_file : list of str + Reading the lines of the input gro file + i : int + The iterator for the line in the file + + Returns + ------- + line : str + Line i in the file + prev_line : str + Line i-1 in the file + """ + #Load previous line to determine identity of previous atom + prev_line = mol_file[i-1].split(' ') + while("" in prev_line): prev_line.remove("") + + #Load current line in file and seperate + line = mol_file[i].split(' ') + while("" in line): line.remove("") + + #Control for atom name and atom number merging + if len(line[1]) > 5: + line = sep_merge(line) + if i > 2 and len(prev_line[1]) > 5: + prev_line = sep_merge(prev_line) + + return line, prev_line + +def print_preamble(old_file, new_file, num_add_names, num_rm_names): + """ + Print the preamble of the gro file before the atom specifications begin + + Parameters + ---------- + old_file : list of str + + new_file : list of str + + num_add_names : int + Number of atoms to be added to the pre-swap molecule + num_rm_names : int + Number of atoms to be removed to the post-swap molecule + + Returns + ------- + line_start : int + The line number to start when you continue to read the file + """ + for i in range(len(old_file)): + if not re.match(r'[ \t]', old_file[i]) and not re.match('^[0-9]+$', old_file[i]): + new_file.write(old_file[i]) + else: + num_atom = int(float(old_file[i]) + num_add_names - num_rm_names) + new_file.write(f'{num_atom}\n') + line_start = i + 1 + break + return line_start + +def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB=None): + """ + Write a line in the file in which some parameter needs changed and maintain spacing + + Parameters + ---------- + mol_new : File object + The new file that is being written to + raw_line : str + The unseperated and unchanged line + Line : List of str + + atom_num : int + The new atom number to be assigned to the atom in this line + vel : list of float + The velocities to be assigned to the atom in this line + coor : list of float + The coordinates for the atom in this line + resnun : int + The new residue number if it changes else leave deafult of None + nameB : str + The new residue name if if changes from what was in the previous file else leave deafult of None + + Returns + ------- + None + """ + coor = ["{:.7f}".format(coor[0]), "{:.7f}".format(coor[1]), "{:.7f}".format(coor[2])] + if len(line) == 9: + if nameB == None: + mol_new.write(line[0].rjust(8, ' ') + line[1].rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + else: + mol_new.write(f'{resnum}{nameB}'.rjust(8, ' ') + line[1].rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + elif len(line) == 8: #Atom name and number blend together because of number size so they need seperated + if 'HW1' in line[1]: + atom_name = 'HW1' + elif 'HW2' in line[1]: + atom_name = 'HW2' + else: + atom_name = re.sub(r'[0-9]', '', line[1]) + + if nameB == None: + mol_new.write(line[0].rjust(8, ' ') + atom_name.rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + else: + mol_new.write(f'{resnum}{nameB}'.rjust(8, ' ') + atom_name.rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + else: + mol_new.write(raw_line) + +def deter_res(mol_top, resname_options): + """ + Determine which of the potential residues of interest are in this molecule + + Parameters + ---------- + mol_top : mdtraj topology + The molecule topology + resname_options : list of str + The potential residue names which may be in the moleucle + + Returns + ------- + resname : str + The name of the residue of interest which is in the molecule + """ + for name in resname_options: + if len(mol_top.select(f"resname {name}")) != 0: + print('check') + resname = name + break + return resname + +def add_atom(mol_new, resnum, resname, df, vel, atom_num): + """ + Add a new atom to the GRO file + + Parameters + ---------- + mol_new : file + The temporary file for the new GRO + resnum : int + The residue number of the atom being added + resname : str + The name of the residue which the atom being added belongs to + df : pandas.DataFrame + The master dataframe which contains the coordinates for the atom being added + vel : list of float + The velocity to assign to the atom being added + atom_num : int + The atom number to assign to the atom being added + + Returns + ------- + atom_num : int + The atom number for the next atom in the file + """ + name_new = df['Name'].to_list()[0] + #Reformat coordiantes + x_init = df['X Coordinates'].to_list() + y_init = df['Y Coordinates'].to_list() + z_init = df['Z Coordinates'].to_list() + x_temp = np.round(x_init[0], decimals=7) + x = format(x_temp, '.7f') + y_temp = np.round(y_init[0], decimals=7) + y = format(y_temp, '.7f') + z_temp = np.round(z_init[0], decimals=7) + z = format(z_temp, '.7f') + #Write line for new atom + mol_new.write(f'{resnum}{resname}'.rjust(8, ' ') + name_new.rjust(7, ' ') + str(atom_num).rjust(5, ' ') + str(x).rjust(12, ' ') + str(y).rjust(12, ' ') + + str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + atom_num += 1 + return atom_num + +def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): + """ + Add an atom to the file which is switching between dummy and real state or vice versa + + Parameters + ---------- + mol_new : file + The temporary file for the new GRO + resnum : int + The residue number of the atom being added + resname : str + The name of the residue which the atom being added belongs to + df : pandas.DataFrame + The master dataframe which contains the coordinates for the atom being added + vel : list of float + The velocity to assign to the atom being added + atom_num : int + The atom number to assign to the atom being added + orig_coords : list of float + The coordinates for the atom being added + + Returns + ------- + line_num : int + Since the atom may be added in a different order than it was in the previous file save the line number so that we skip it when we come to it + """ + #Get the name for the atom we are writting + name_orig = df['Name'].to_list()[0] + + #Determine the new atom name based on whether the new atom should be real or dummy + final_state = df['Final Type'].to_list()[0] + if final_state == 'dummy': + element = name_orig.strip('0123456789') + atom_name_num = name_orig.strip('DCVH') + #Add D or C + if element == 'C': + name_new = f'D{element}{atom_name_num}' + else: + name_new = f'{element}V{atom_name_num}' + else: + if 'DC' in name_orig: + name_new = name_orig.replace('DC', 'C') + else: + name_new = name_orig.replace('HV', 'H') + + #These may be added out of order so lets make sure we have the right coordinates + line_num = df['File line'].to_list()[0] + c = line_num - 2 + orig_coor = orig_coords[c] + x, y, z = ["{:.7f}".format(orig_coor[0]), "{:.7f}".format(orig_coor[1]), "{:.7f}".format(orig_coor[2])] + + #Write line + mol_new.write(f'{resnum}{resname}'.rjust(8, ' ') + name_new.rjust(7, ' ') + str(atom_num).rjust(5, ' ') + str(x).rjust(12, ' ') + str(y).rjust(12, ' ') + + str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + return line_num + +def sep_merge(line): + """ + Seperate two GRO file columns which no longer have a space sperating them + + Parameters + ---------- + line : list of str + The line contents seperated by spaces + + Returns + ------- + temp_line : list of str + The line contents with the merged columns + """ + temp_line = [line[0]] + merged = [*line[1]] + atom_name = "".join(merged[:-5]) + atom_num = "".join(merged[-5:]) + temp_line.append(atom_name) + temp_line.append(atom_num) + for n in line[2:]: + temp_line.append(n) + return temp_line + +def rotate_point_around_axis(point, vertex, axis, angle): + """ + Rotate a 3D point around an aritrary axis + + Parameters + ---------- + point : np.array shape (1,3) + The starting point prior to rotation + start : np.array shape (1,3) + The vertex of the axis of rotation + axis : np.array shape (1,3) + The axis of rotation + angle : float + The angle to rotate + + Returns + ------- + rotated point : np.array shape (1,3) + The new rotated point + """ + #Transformation matrix to origin + T = np.eye(4) + T[0:3,3] = -vertex + #Reverse the transformation to origin + T_r = np.eye(4) + T_r[0:3,3] = vertex + #Normalize rotational axis + axis = axis / np.linalg.norm(axis) + a, b, c = axis + d = np.sqrt(b**2+c**2) + + # Rotation about the x axis + Rx = [[1, 0, 0, 0], [0, c/d, -b/d, 0], [0, b/d, c/d, 0], [0, 0, 0, 1]] + Rx_r = [[1, 0, 0, 0], [0, c/d, b/d, 0], [0, -b/d, c/d, 0], [0, 0, 0, 1]] + + #Rotation about the y axis + Ry = [[d, 0, -a, 0], [0, 1, 0, 0], [a, 0, d, 0], [0, 0, 0, 1]] + Ry_r = [[d, 0, a, 0], [0, 1, 0, 0], [-a, 0, d, 0], [0, 0, 0, 1]] + + #Rotation about the z axis + Rz = [[np.cos(angle), np.sin(angle), 0, 0], [-np.sin(angle), np.cos(angle), 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]] + + #Initial position + x0, y0, z0 = point + init_arry = [x0, y0, z0, 1] + + #Perform the transofmration + final_arry = T_r@Rx_r@Ry_r@Rz@Ry@Rx@T@init_arry + + #Get the corrdinates for the rotated point + rotated_point = final_arry[0:3] + + return rotated_point + +def find_rotation_angle(initial_point, vertex, rotated_point, axis): + """ + Determine the angle of rotation around an arbitrary axis in 3D space. + + Parameters + ---------- + initial_point: A numpy array + the initial point coordinates + rotated_point: A numpy array + the rotated point coordinates + axis: A numpy array + the axis of rotation + + Returns + ------- + angle: int + The angle of rotation in radians. + """ + # Normalize axis and seperate coordinates + u, v, w = axis / np.linalg.norm(axis) + x0, y0, z0 = initial_point + a, b, c = vertex + + #Determine the rotated point with the same bond length as the initial point + rotated_point_axis = rotated_point - vertex + norm_rot_point_vec = rotated_point_axis / np.linalg.norm(rotated_point_axis) + final_bond_length = np.sqrt((x0-a)**2 + (y0-b)**2 + (z0-c)**2) + rotated_point_standard = vertex + final_bond_length*norm_rot_point_vec + x, y, z = rotated_point_standard #Change to point with same bond length along this vector + + Q = np.sqrt(v**2+w**2) + B = ((w/Q)*(y0-b)) - ((v/Q)*(z0-c)) + A = Q*(x0-a) - u*(((v/Q)*(y0-b)) + ((w/Q)*(z0-c))) + C = u*(x0-a) + Q*(((v/Q)*(y0-b)) + ((w/Q)*(z0-c))) + L = np.arctan2(B,A) + + # Determine the rotational angle to line-up point + cos_arg = (x-a-u*C)/(Q*np.sqrt(A**2+B**2)) + if cos_arg > 1 or cos_arg < -1: + if abs(cos_arg - 1) < .0001: + cos_arg = 1 + elif abs(cos_arg + 1) < .0001: + cos_arg = -1 + else: + raise Exception(f'Invalid arccos argument: {(x-a-u*C)/(Q*np.sqrt(A**2+B**2))}') + arc_cos = np.arccos(cos_arg) + angle = L + arc_cos + + #Test point + new_pt = rotate_point_around_axis(initial_point, vertex, axis / np.linalg.norm(axis), angle) + if abs(new_pt[1] - y) < 0.0001: + return angle + else: + arc_cos = 2*np.pi - arc_cos + angle = L + arc_cos + if angle > 2*np.pi: + angle = angle - 2*np.pi + + return angle + +def compute_angle(coords): + """ + Compute the angle between two vectors + + Parameters + ---------- + coords : np.array + Four points which define two vectors to compute the angle between + + Return + ------ + angle : int + Angle in radians between the two points + """ + vec1 = coords[0] - coords[1] + vec2 = coords[2] - coords[1] + + angle = np.dot(vec1, vec2)/(np.linalg.norm(vec1)*np.linalg.norm(vec2)) + + return angle + +def add_or_swap(df_select, file_new, resnum, resname, vel, atom_num, orig_coor, skip_line, R_o_D_num, pick): + """ + Determine if the atom needs added or swapped between real and dummy state and then add the atom to the new file + + Parameters + ---------- + df_select : pd.DataFrame + + file_new : File + The temporary file for the new GRO + resnum : int + The residue number of the atom being added + resname : str + The name of the residue which the atom being added belongs to + vel : list of float + The velocity to assign to the atom being added + atom_num : int + The atom number to assign to the atom being added + orig_coords : list of float + The coordinates for the atom being added + skip_line : list of str + List of line numbers that should be skipped when we come across them while reading the file + R_o_D_num : list of str + list of atoms that need added + pick : int + Index in the list to add now + Return + ------ + skip_line : list of int + Updated list of line numbers that should be skipped when we come across them while reading the file + R_o_D_num_new : + Updated list of atoms that need added + """ + c = df_select.index.values.tolist() + if df_select.loc[c[0], 'Direction'] == 'miss': #Add atom if missing + add_atom(file_new, resnum, resname, df_select, vel, atom_num) + else: #Swap from dummy to real + line = dummy_real_swap(file_new, resnum, resname, df_select, vel, atom_num, orig_coor) #Add the dummy atom from A as a real atom in B and save the line so it can be skipped later + skip_line.append(line) + R_o_D_num_new = np.delete(R_o_D_num, pick) #Atom no longer needs added + return skip_line, R_o_D_num_new + +def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, old_res_name, new_res_name, orig_coords, miss): + """ + Write a new GRO file + + Parameters + ---------- + df_atom_swap : pd.DataFrame + Master dataframe containing info on the atoms which will change before and after the swap + swap : + Swapping direction + r_swap : + Reverse of the swapping direction + line_start : int + The line number where we start reading the file + orig_file : List of str + Pre-swap file to read from + new_file : File + Temporary file to write new coordinates + old_res_name : str + Residue name from before the swap + new_res_name : str + Residue name for after the swap + orig_coords : np.array + Coordinates for all atoms in the system before the swap + miss : list of str + Residues which are needed after the swap which are not present before the swap + + Return + ------ + None + """ + #Add vero velocity to all atoms + vel = ['0.000', '0.000', '0.000\n'] + + atom_num_A, atom_num_B = 0, 0 + skip_line = [] + df_interest = df_atom_swap[((df_atom_swap['Swap'] == swap) & ((df_atom_swap['Direction'] == 'R2D') | (df_atom_swap['Direction'] == 'D2R'))) | ((df_atom_swap['Swap'] == r_swap) & (df_atom_swap['Direction'] == 'miss'))] + R_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) + D_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) + R_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) + D_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) + R_C_num.sort() + D_C_num.sort() + R_H_num.sort() + D_H_num.sort() + for i in range(line_start, len(orig_file)-1): + #Some atoms are added out of order from file A and thus must be skipped when they come up + if i in skip_line: + atom_num_A += 1 + continue + #Iterate atom number to keep track of file progress + atom_num_B += 1 + + #Process input lines + line, prev_line = process_line(orig_file, i) + + #Seperate resname from resnumber + res_i = [*line[0]] + prev_res_i = [*prev_line[0]] + + resname = "".join(res_i[-3:]) + resnum = "".join(res_i[0:int(len(res_i)-3)]) + prev_resname = "".join(prev_res_i[-3:]) + + #Determine how to write line based on contents + if resname != old_res_name and prev_resname != old_res_name: #Change only atom number and velocities if atoms not in residue of interest + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A]) + elif resname == old_res_name: #Atom manipulation required for acyl chain + #determine the number for the atom being written in the current line + current_num = int(line[1].strip('CVHDSON')) + current_element = line[1].strip('0123456789') + if line[1] in miss: #Do not write coordinates if atoms are not present in B + atom_num_B -= 1 + atom_num_A += 1 + continue + elif (current_element == 'C' and current_num in D_C_num) or (current_element == 'H' and current_num in D_H_num): #Skip this line for now as we will add it in later + atom_num_B -= 1 + atom_num_A += 1 + continue + elif (current_element == 'C' and (current_num > R_C_num).any()): #We need to add an atom or move an atom to a new line position + while (current_num > R_C_num).any(): + #Either add atom or perform swap + pick = np.where(current_num > R_C_num)[0][0] + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[pick])) & (df_interest['Element'] == 'C')] + skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, pick) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + elif (len(R_C_num) != 0 and current_element == 'H'): #Add remaining real heavy atoms if all heavy atoms have been written + while len(R_C_num) != 0: + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[0])) & (df_interest['Element'] == 'C')] + skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, 0) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + elif current_element == 'H' and (current_num > R_H_num).any(): #Add real Hs in proper order + while (current_num > R_H_num).any(): + #Either add atom or perform swap + pick = np.where(current_num > R_H_num)[0][0] + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[pick])) & (df_interest['Element'] == 'H')] + skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, pick) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + elif len(R_H_num) != 0 and (current_element == 'DC' or current_element == 'HV'): #Add remaining real Hs if all H atoms have been written + while len(R_H_num) != 0: + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] + skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) + atom_num_B += 1 + if current_element == 'DC': + while (current_num > D_C_num).any(): + #Either add atom or perform swap + pick = np.where(current_num > D_C_num)[0][0] + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + elif current_element == 'DC' and (current_num > D_C_num).any(): #Add dummy Cs in correct order + while (current_num > D_C_num).any(): + #Either add atom or perform swap + pick = np.where(current_num > D_C_num)[0][0] + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + elif len(D_C_num) != 0 and current_element == 'HV': #Add remaining dummy Cs after real Hs + while len(D_C_num) != 0: + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + elif current_element == 'HV' and (current_num > D_H_num).any(): #Add dummy Hs in proper order + while (current_num > D_H_num).any(): + #Either add atom or perform swap + pick = np.where(current_num > D_H_num)[0][0] + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] + skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) + atom_num_B += 1 + if i not in skip_line: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + else: + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) + elif resname != old_res_name and prev_resname == old_res_name: #Add dummy atoms at the end of the residue + while len(R_H_num) != 0: + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] + skip_line, R_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) + atom_num_B += 1 + while len(D_C_num) != 0: + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] + skip_line, D_C_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) + atom_num_B += 1 + while len(D_H_num) != 0: + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] + skip_line, D_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) + atom_num_B += 1 + line, prev_line = process_line(orig_file, i) + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A]) + else: + print(f'Warning line {i+1} not written') + atom_num_A += 1 + + if len(R_H_num) != 0: #If we hit end of coordinates without adding Hs add them now + while len(R_H_num) != 0: + atom_num_B += 1 + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] + skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) + + if len(D_C_num) != 0: #If we hit end of coordinates without adding Cs add them now + while len(D_C_num) != 0: + atom_num_B += 1 + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) + + if len(D_H_num) != 0: #If we hit end of coordinates without adding Hs add them now + while len(D_H_num) != 0: + atom_num_B += 1 + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] + skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) + + #Add Box dimensions to file + new_file.write(orig_file[-1]) + new_file.close() + +def swap_name(init_atom_names, new_resname, df_top): + """ + Determine the corresponding atom name in new molecule + + Parameters + ---------- + init_atom_names : list of str + Atom name in the original molecule + new_resname : str + Resname for the new molecule + df_top : pd.DataFrame + Dataframe containing the connectivity between the atoms in each molecule + + Return + ------ + new_atom_names : list of str + Atom names in the new molecule + """ + #Find all atom names in new moleucle + new_names = set(df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 2'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 2'].to_list()) + new_atom_names = [] + for atom in init_atom_names: + if atom in new_names: + new_atom_names.append(atom) + continue + atom_num = re.findall(r'[0-9]+', atom)[0] + atom_identifier = re.findall(r'[a-zA-Z]+', atom)[0] + if 'D' in atom_identifier: + atom_identifier = atom_identifier.strip('D') + if 'V' in atom_identifier: + atom_identifier = atom_identifier.strip('V') + if f'{atom_identifier}V{atom_num}' in new_names: + new_atom_names.append(f'{atom_identifier}V{atom_num}') + elif f'{atom_identifier}{atom_num}' in new_names: + new_atom_names.append(f'{atom_identifier}{atom_num}') + elif f'D{atom_identifier}{atom_num}' in new_names: + new_atom_names.append(f'D{atom_identifier}{atom_num}') + else: + raise Exception(f'Compatible atom could not be found for {atom}') + return new_atom_names + +def get_names(input): + """ + Determine the names of all atoms in the topology and which lambda state for which they are dummy atoms + + Parameters + ---------- + input : List of str + Read the lines of the input topology + + Return + ------ + start_line : int + The next line to start reading from the topology + atom_name : list of str + All atom names in the topology + state : list of int + The state that the atom is a dummy atom (lambda=0, lambda=1, or -1 if nevver dummy) + """ + atom_section = False + atom_name, state = [], [] + for l, line in enumerate(input): + if atom_section: + line_sep = line.split(' ') + if line_sep[0] == ';': + continue + while '' in line_sep: + line_sep.remove('') + if line_sep[0] == '\n': + start_line = l+2 + break + atom_name.append(line_sep[4]) + if len(line_sep) < 10: + state.append(-1) + elif float(line_sep[6]) == 0: + state.append(0) + elif float(line_sep[9]) == 0: + state.append(1) + else: + state.append(-1) + if line == '[ atoms ]\n': + atom_section = True + return start_line, atom_name, state + +def deter_connection(main_only, other_only, main_name, other_name, df_top, main_state): + """ + Determine the connectivity of the missing atoms in the topology + + Parameters + ---------- + main_only : list of str + All atoms which can be found only in the molecule of interest + other_only : list of str + All atoms which can be found only in the other molecule + main_name : str + resname for the molecule of interest + other_name : str + resname for the other molecule + df_top : pd.DataFrame + Connectivity of the atoms in each molecule + main_state : list of int + Which lambda state are each atom in the molecule of interest in the dummy state + Return + ------ + df : pd.DataFrame + Dataframes contains the missing atoms, the real anchor atom that connects them, and the atom to be used to determine the angle to place the missing atoms + """ + miss, D2R, R2D = [],[],[] + align_atom, angle_atom = [], [] + for atom in main_only: + element = atom.strip('0123456789') + real_element = element.strip('DV') + num = atom.strip('ABCDEFGHIJKLMNOPQRSTUVWXYZ') + + if f'D{atom}' in other_only or f'{element}V{num}' in other_only: + D2R.append(atom) + elif f'{real_element}{num}' in other_only: + R2D.append(atom) + else: + miss.append(atom) + df_select = df_top[df_top['Resname']==main_name] + #Seperate into each seperate functional group to be added + anchor_atoms = [] + + for m_atom in miss: + #Find what atoms the missing atom connects to + connected_atoms = [] + for a in df_select[df_select['Connect 1'] == m_atom]['Connect 2'].values: + connected_atoms.append(a) + for a in df_select[df_select['Connect 2'] == m_atom]['Connect 1'].values: + connected_atoms.append(a) + + #If the atom connects to non-missing atoms than keep these as anchors + for a in connected_atoms: + if a not in miss: + anchor_atoms.append(a) + + #Seperate missing atoms connected to each anchor + miss_sep, align_atoms, angle_atoms = [],[],[] + for anchor in anchor_atoms: + miss_anchor = [] + + #Which missing atoms are connected to the anchor + search = True + included_atoms = [anchor] + while search == True: + found_atoms = list(df_select[(df_select['Connect 1'].isin(included_atoms)) & (df_select['Connect 2'].isin(miss))]['Connect 2'].values) + list(df_select[(df_select['Connect 2'].isin(included_atoms)) & (df_select['Connect 1'].isin(miss))]['Connect 1'].values) + if len(found_atoms) == 0: + search = False + else: + for atom in found_atoms: + miss_anchor.append(atom) + included_atoms.append(atom) + miss.remove(atom) + included_atoms.remove(anchor) + miss_sep.append(included_atoms) + + #Find atoms connected to the anchor which are real in main state, but dummy when the atoms we are building are real + align_atom = list(df_select[(df_select['Connect 1'] == anchor) & (df_select['State 2'] != main_state) & (df_select['State 2'] != -1)]['Connect 2'].values) + list(df_select[(df_select['Connect 2'] == anchor) & (df_select['State 1'] != main_state) & (df_select['State 1'] != -1)]['Connect 1'].values) + align_atoms.append(align_atom[0]) + + #Find the atom to use for matching the angle to ensure that the dummy atom is added in the correct orientation + ignore_atoms = anchor_atoms + included_atoms + align_atom + angle_atom = list(df_select[(df_select['Connect 1'] == anchor) & (~df_select['Connect 2'].isin(ignore_atoms))]['Connect 2'].values) + list(df_select[(df_select['Connect 2'] == anchor) & (~df_select['Connect 1'].isin(ignore_atoms))]['Connect 1'].values) + angle_atoms.append(angle_atom[-1]) + + #Now let's figure out what these atoms are called in the other molecule + anchor_atoms_B = swap_name(anchor_atoms, other_name, df_top) + angle_atoms_B = swap_name(angle_atoms, other_name, df_top) + align_atoms_B = swap_name(align_atoms, other_name, df_top) + df = pd.DataFrame({'Swap A': main_name, 'Swap B': other_name, 'Connecting Atom Name A': anchor_atoms, 'Anchor Atom Name B': anchor_atoms_B, 'Alignment Atom A': align_atoms, 'Alignment Atom B': align_atoms_B, 'Angle Atom A': angle_atoms, 'Angle Atom B': angle_atoms_B}) + df['Missing Atom Name'] = np.NaN + df['Missing Atom Name'] = df['Missing Atom Name'].astype(object) + df['Missing Atom Name'] = miss_sep + + return df + +def read_top(file_name, resname): + """ + Read the topology to find the file containing the molecule of interest + + Parameters + ---------- + file_name : str + Name for the topology file + resname : str + Name of the residue of interest we are searching for + + Return + ------ + input_file : list of str + Contents of the topology file which contains the residue of interest + """ + input_file = open(file_name).readlines() + itp_files = [] + atom_sect = True + for line in input_file: + if line == '[ atoms ]\n': + atom_sect = True + if atom_sect: + if line == '\n': + atom_sect = False + line_sep = line.split(' ') + while '' in line_sep: + line_sep.remove('') + if len(line_sep) > 4 and line_sep[3] == resname: + return input_file + if '#include' in line: + line_sep = line.split(' ') + while '' in line_sep: + line_sep.remove('') + itp_files.append(line_sep[-1].strip('\n""')) + for file in itp_files: + if os.path.exists(file): + input_file = open(file).readlines() + atom_sect = False + for line in input_file: + if line == '[ atoms ]\n': + atom_sect = True + if atom_sect: + if line == '\n': + break + line_sep = line.split(' ') + while '' in line_sep: + line_sep.remove('') + if len(line_sep) > 4 and line_sep[3] == resname: + return input_file + raise Exception(f'Residue {resname} can not be found in {file_name}') From ee7cc4578c154bf0ad7d8ad96777f550c12ddbb6 Mon Sep 17 00:00:00 2001 From: Anika Friedman <74794503+ajfriedman22@users.noreply.github.com> Date: Thu, 5 Sep 2024 12:23:21 -0600 Subject: [PATCH 02/68] Update replica_exchange_EE.py --- ensemble_md/replica_exchange_EE.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index c40ea635..476dc867 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -259,13 +259,13 @@ def set_params(self, analysis): params_list = ['add_swappables', 'df_ref'] if self.resname_list is not None: params_list.append('resname_list') + if self.swap_rep_pattern is not None: + params_list.append('swap_rep_pattern') for i in params_list: if getattr(self, i) is not None and not isinstance(getattr(self, i), list): raise ParameterError(f"The parameter '{i}' should be a list.") params_dict = ['mdp_args', 'grompp_args', 'runtime_args'] - if self.swap_rep_pattern is not None: - params_dict.append('swap_rep_pattern') for i in params_dict: if getattr(self, i) is not None and not isinstance(getattr(self, i), dict): raise ParameterError(f"The parameter '{i}' should be a dictionary.") @@ -1649,4 +1649,4 @@ def process_top(self): df_map = pd.concat([df_map, df]) - df_map.to_csv('residue_swap_map.csv') \ No newline at end of file + df_map.to_csv('residue_swap_map.csv') From a9f46a2d5cee1f5f400ca02daa477ff1b1587a94 Mon Sep 17 00:00:00 2001 From: Anika Date: Mon, 9 Sep 2024 14:08:39 -0600 Subject: [PATCH 03/68] Fix Errors --- ensemble_md/replica_exchange_EE.py | 50 ++++++++++++++-------------- ensemble_md/utils/coordinate_swap.py | 29 ++++++++++------ 2 files changed, 44 insertions(+), 35 deletions(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index 476dc867..a6f5d5d1 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -448,7 +448,7 @@ def set_params(self, analysis): # 7-12. External module for coordinate modification if self.modify_coords is not None: - if self.modify_coords.lower == 'default': + if self.modify_coords == 'default': if self.swap_rep_pattern is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): raise Exception('swap_rep_pattern option must be filled in if using default swapping function and not swap guide') if self.resname_list is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): @@ -1565,9 +1565,9 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): miss_B = df_atom_swap[(df_atom_swap['Swap']=='B2A') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() miss_A = df_atom_swap[(df_atom_swap['Swap']=='A2B') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() if len(miss_B) != 0: - df_atom_swap = coordinate_swap.get_miss_coord(molB, molA, nameB, nameA, df_atom_swap, 'B2A', swap_map[(swap_map['Swap A'] == nameA) & (swap_map['Swap B'] == nameB)]) + df_atom_swap = coordinate_swap.get_miss_coord(molB, molA, nameB, nameA, df_atom_swap, 'B2A', swap_map[(swap_map['Swap A'] == nameB) & (swap_map['Swap B'] == nameA)]) if len(miss_A) != 0: - df_atom_swap = coordinate_swap.get_miss_coord(molA, molB, nameA, nameB, df_atom_swap, 'A2B', swap_map[(swap_map['Swap A'] == nameB) & (swap_map['Swap B'] == nameA)]) + df_atom_swap = coordinate_swap.get_miss_coord(molA, molB, nameA, nameB, df_atom_swap, 'A2B', swap_map[(swap_map['Swap A'] == nameA) & (swap_map['Swap B'] == nameB)]) #Reprint preamble text line_start = coordinate_swap.print_preamble(molA_file, molB_new, len(miss_B), len(miss_A)) @@ -1604,25 +1604,25 @@ def process_top(self): df_top = pd.DataFrame() for f, file_name in enumerate(self.top): #Read file - input = coordinate_swap.read_top(file_name, self.resname_list[f]) + input_file = coordinate_swap.read_top(file_name, self.resname_list[f]) - #Determine the atom names corresponding to the atom numbers - start_line, atom_name, state = coordinate_swap.get_names(input) + #Determine the atom names corresponding to the atom numbers + start_line, atom_name, state = coordinate_swap.get_names(input_file) - #Determine the connectivity of all atoms - connect_1, connect_2, state_1, state_2 = [], [], [], [] #Atom 1 and atom 2 which are connected and which state they are dummy atoms - for l, line in enumerate(input[start_line:]): - line_sep = line.split(' ') - if line_sep[0] == ';': - continue - if line_sep[0] == '\n': - break - while '' in line_sep: - line_sep.remove('') - connect_1.append(atom_name[int(line_sep[0])-1]) - connect_2.append(atom_name[int(line_sep[1])-1]) - state_1.append(state[int(line_sep[0])-1]) - state_2.append(state[int(line_sep[1])-1]) + #Determine the connectivity of all atoms + connect_1, connect_2, state_1, state_2 = [], [], [], [] #Atom 1 and atom 2 which are connected and which state they are dummy atoms + for l, line in enumerate(input_file[start_line:]): + line_sep = line.split(' ') + if line_sep[0] == ';': + continue + if line_sep[0] == '\n': + break + while '' in line_sep: + line_sep.remove('') + connect_1.append(atom_name[int(line_sep[0])-1]) + connect_2.append(atom_name[int(line_sep[1])-1]) + state_1.append(state[int(line_sep[0])-1]) + state_2.append(state[int(line_sep[1])-1]) df = pd.DataFrame({'Resname': self.resname_list[f], 'Connect 1': connect_1, 'Connect 2': connect_2, 'State 1': state_1, 'State 2': state_2}) df_top = pd.concat([df_top, df]) df_top.to_csv('residue_connect.csv') @@ -1631,21 +1631,21 @@ def process_top(self): if not os.path.exists('residue_swap_map.csv'): df_map = pd.DataFrame() - for swap in self.swap_rep_pattern: #Determine atoms not present in both molecules - X, Y = swap.keys() + X, Y = [int(swap[0][0]), int(swap[1][0])] + lam = {X: int(swap[0][1]), Y: int(swap[1][1])} for A, B in zip([X, Y], [Y, X]): - input_A = coordinate_swap.read_top(self.top_files[A], self.resname_list[A]) + input_A = coordinate_swap.read_top(self.top[A], self.resname_list[A]) start_line, A_name, state = coordinate_swap.get_names(input_A) - input_B = coordinate_swap.read_top(self.top_files[B], self.resname_list[B]) + input_B = coordinate_swap.read_top(self.top[B], self.resname_list[B]) start_line, B_name, state = coordinate_swap.get_names(input_B) A_only = [x for x in A_name if x not in B_name] B_only = [x for x in B_name if x not in A_name] #Seperate real to dummy switches - df = coordinate_swap.deter_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, swap[A]) + df = coordinate_swap.deter_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, lam[A]) df_map = pd.concat([df_map, df]) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 90d2b658..f1abc48b 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -395,8 +395,8 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, for i, row in df_swap.iterrows(): conn_align = [row['Anchor Atom Name A'], row['Alignment Atom A']] conn_ref = [row['Anchor Atom Name B'], row['Alignment Atom B']] - geom_fix_select = [row['Missing Atom Name'][0], row['Anchor Atom Name A'], row['Angle Atom A']] - miss_names_select = row['Missing Atom Name'] + miss_names_select = row['Missing Atom Name'].split(' ') + geom_fix_select = [miss_names_select[0], row['Anchor Atom Name A'], row['Angle Atom A']] #Limit to region of interest align_select = [] for a in conn_align + miss_names_select + geom_fix_select: @@ -404,7 +404,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, if atom not in align_select: align_select.append(atom) align_select.sort() - ref_select = mol_ref.topology.select(f'resname {name_ref} and (name {conn_ref[0]} or name {conn_ref[1]} or name {geom_fix_select[-1]})') + ref_select = mol_ref.topology.select(f"resname {name_ref} and (name {conn_ref[0]} or name {conn_ref[1]} or name {row['Angle Atom B']})") mol_ref_select = copy.deepcopy(mol_ref.atom_slice(ref_select)) mol_align_select = copy.deepcopy(mol_align.atom_slice(align_select)) @@ -443,7 +443,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, min_dev_angle = 3 init_coords = mol_align_select.xyz[0,change_atoms,:][0].copy() constant_coords = [mol_align_select.xyz[0,mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0],:], - mol_ref_select.xyz[0,mol_ref_select.topology.select(f'resname {name_ref} and name {geom_fix_select[2]}')[0],:]] + mol_ref_select.xyz[0,mol_ref_select.topology.select(f"resname {name_ref} and name {row['Angle Atom B']}")[0],:]] for theta in np.linspace(0, 2*np.pi, num=10): new_coors = np.zeros((3,3)) new_coors[0,:] = rotate_point_around_axis(init_coords, mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta) @@ -606,7 +606,6 @@ def deter_res(mol_top, resname_options): """ for name in resname_options: if len(mol_top.select(f"resname {name}")) != 0: - print('check') resname = name break return resname @@ -978,7 +977,10 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A]) elif resname == old_res_name: #Atom manipulation required for acyl chain #determine the number for the atom being written in the current line - current_num = int(line[1].strip('CVHDSON')) + if len(line[1]) > 1: + current_num = int(line[1].strip('CVHDSON')) + else: + current_num = np.NaN current_element = line[1].strip('0123456789') if line[1] in miss: #Do not write coordinates if atoms are not present in B atom_num_B -= 1 @@ -1265,10 +1267,17 @@ def deter_connection(main_only, other_only, main_name, other_name, df_top, main_ anchor_atoms_B = swap_name(anchor_atoms, other_name, df_top) angle_atoms_B = swap_name(angle_atoms, other_name, df_top) align_atoms_B = swap_name(align_atoms, other_name, df_top) - df = pd.DataFrame({'Swap A': main_name, 'Swap B': other_name, 'Connecting Atom Name A': anchor_atoms, 'Anchor Atom Name B': anchor_atoms_B, 'Alignment Atom A': align_atoms, 'Alignment Atom B': align_atoms_B, 'Angle Atom A': angle_atoms, 'Angle Atom B': angle_atoms_B}) - df['Missing Atom Name'] = np.NaN - df['Missing Atom Name'] = df['Missing Atom Name'].astype(object) - df['Missing Atom Name'] = miss_sep + df = pd.DataFrame({'Swap A': main_name, 'Swap B': other_name, 'Anchor Atom Name A': anchor_atoms, 'Anchor Atom Name B': anchor_atoms_B, 'Alignment Atom A': align_atoms, 'Alignment Atom B': align_atoms_B, 'Angle Atom A': angle_atoms, 'Angle Atom B': angle_atoms_B}) + miss_sep_reformat = [] + for missing in miss_sep: + if isinstance(missing, list): + missing_reformat = missing[0] + for atom in missing[1:]: + missing_reformat += f' {atom}' + else: + missing_reformat = missing + miss_sep_reformat.append(missing_reformat) + df['Missing Atom Name'] = miss_sep_reformat return df From 90976c5d7df7dc2820e63d254739f0acebee8215 Mon Sep 17 00:00:00 2001 From: Anika Date: Mon, 9 Sep 2024 18:43:48 -0600 Subject: [PATCH 04/68] Fix minor error --- ensemble_md/replica_exchange_EE.py | 3 ++- ensemble_md/utils/coordinate_swap.py | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index a6f5d5d1..520434e2 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -1553,7 +1553,8 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): nameA = coordinate_swap.deter_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) nameB = coordinate_swap.deter_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) df_atom_swap = coordinate_swap.deter_common(molA_file, molB_file, nameA, nameB) - + df_atom_swap.to_csv('swap_test.csv') + # Step 4: Fix break if present for solvated systems only if len(molA.topology.select('water')) != 0: A_dimensions = coordinate_swap.get_dimensions(molA_file) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index f1abc48b..4590bdf0 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -677,6 +677,7 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): line_num : int Since the atom may be added in a different order than it was in the previous file save the line number so that we skip it when we come to it """ + print(df) #Get the name for the atom we are writting name_orig = df['Name'].to_list()[0] @@ -982,6 +983,7 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, else: current_num = np.NaN current_element = line[1].strip('0123456789') + print(line[1]) if line[1] in miss: #Do not write coordinates if atoms are not present in B atom_num_B -= 1 atom_num_A += 1 From 5532d43f447612679e0230d4e77cc6fa783fe00e Mon Sep 17 00:00:00 2001 From: Anika Date: Mon, 9 Sep 2024 18:44:33 -0600 Subject: [PATCH 05/68] Fix comment typo --- ensemble_md/utils/coordinate_swap.py | 1 - 1 file changed, 1 deletion(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 4590bdf0..d24f7a40 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -983,7 +983,6 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, else: current_num = np.NaN current_element = line[1].strip('0123456789') - print(line[1]) if line[1] in miss: #Do not write coordinates if atoms are not present in B atom_num_B -= 1 atom_num_A += 1 From 12d695974f921ef0e86cebc2c5f095e2d6580aac Mon Sep 17 00:00:00 2001 From: Anika Date: Tue, 10 Sep 2024 10:55:56 -0600 Subject: [PATCH 06/68] Remove unnessary prints --- ensemble_md/replica_exchange_EE.py | 1 - ensemble_md/utils/coordinate_swap.py | 1 - 2 files changed, 2 deletions(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index 520434e2..1d4c18e3 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -1553,7 +1553,6 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): nameA = coordinate_swap.deter_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) nameB = coordinate_swap.deter_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) df_atom_swap = coordinate_swap.deter_common(molA_file, molB_file, nameA, nameB) - df_atom_swap.to_csv('swap_test.csv') # Step 4: Fix break if present for solvated systems only if len(molA.topology.select('water')) != 0: diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index d24f7a40..f1abc48b 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -677,7 +677,6 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): line_num : int Since the atom may be added in a different order than it was in the previous file save the line number so that we skip it when we come to it """ - print(df) #Get the name for the atom we are writting name_orig = df['Name'].to_list()[0] From 71e3d8f7783dfffdbf88216d80cc55b629bda99d Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 01:57:30 +0800 Subject: [PATCH 07/68] Tweaked README.md and fixed linting errors for run_REXEE.py and replica_exchange_EE.py --- README.md | 15 +++-- ensemble_md/cli/run_REXEE.py | 2 +- ensemble_md/replica_exchange_EE.py | 92 +++++++++++++++--------------- 3 files changed, 57 insertions(+), 52 deletions(-) diff --git a/README.md b/README.md index d7c4cf5f..20df541a 100644 --- a/README.md +++ b/README.md @@ -12,16 +12,21 @@ Ensemble Molecular Dynamics [![Downloads](https://static.pepy.tech/badge/ensemble-md)](https://pepy.tech/project/ensemble-md) -`ensemble_md` is a Python package that provides methods for setting up, running, and analyzing GROMACS simulation ensembles. Currently, the package implements all the necessary algorithms for running synchronous replica exchange (REX) of expanded ensembles (EE), abbreviated as REXEE, as well as its multi-topology (MT) variation, MT-REXEE. Our future work includes implementing asynchronous REXEE and other possible variations of the REXEE method. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest) and our [JCTC paper](https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c00484). +`ensemble_md` is a Python package that provides methods for setting up, running, and analyzing GROMACS simulation ensembles. Currently, the package implements all the necessary algorithms for running synchronous replica exchange (REX) of expanded ensembles (EE), abbreviated as REXEE, as well as its multi-topology (MT) variation, MT-REXEE. Our future work includes implementing asynchronous REXEE and other possible variations of the REXEE method. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest) and our papers (listed in the next section). -### Reference +### References If you use any components of the Python package `ensemble_md` or the REXEE method in your research, please cite the following paper: -Hsu, W. T., & Shirts, M. R. (2024). Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. *Journal of Chemical Theory and Computation*. 20.14 (2024): 6062-6081. doi: [10.1021/acs.jctc.4c00484](https://doi.org/10.1021/acs.jctc.4c00484) +> Hsu, W. T., & Shirts, M. R. (2024). Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. *Journal of Chemical Theory and Computation*. 20.14 (2024): 6062-6081. doi: [10.1021/acs.jctc.4c00484](https://doi.org/10.1021/acs.jctc.4c00484) -### Copyright +If you use the MT-REXEE method in your research, please cite the following paper: -Copyright (c) 2022, Wei-Tse Hsu +> Friedman, A. J., Hsu, W. T., & Shirts, M. R. (2024). Multiple Topology Replica Exchange of Expanded Ensembles (MT-REXEE) for Multidimensional Alchemical Calculations. arXiv preprint arXiv:2408.11038. doi: [10.48550/arXiv.2408.11038]( +https://doi.org/10.48550/arXiv.2408.11038) + +### Authors +- Wei-Tse Hsu, University of Colorado, Boulder (weitse.hsu@colorado.edu) +- Anika Friedman, University of Colorado, Boulder (anika.friedman@colorado.edu) ### Acknowledgements diff --git a/ensemble_md/cli/run_REXEE.py b/ensemble_md/cli/run_REXEE.py index bba96f09..7f537880 100644 --- a/ensemble_md/cli/run_REXEE.py +++ b/ensemble_md/cli/run_REXEE.py @@ -99,7 +99,7 @@ def main(): os.mkdir(f'{REXEE.working_dir}/sim_{i}/iteration_0') MDP = REXEE.initialize_MDP(i) MDP.write(f"{REXEE.working_dir}/sim_{i}/iteration_0/expanded.mdp", skipempty=True) - if REXEE.modify_coords == 'default' and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): + if REXEE.modify_coords == 'default' and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): # noqa: E501 REXEE.process_top() # 2-2. Run the first set of simulations diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index 1d4c18e3..081031f2 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -449,10 +449,10 @@ def set_params(self, analysis): # 7-12. External module for coordinate modification if self.modify_coords is not None: if self.modify_coords == 'default': - if self.swap_rep_pattern is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): - raise Exception('swap_rep_pattern option must be filled in if using default swapping function and not swap guide') - if self.resname_list is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): - raise Exception('resname_list option must be filled in if using default swapping function and not swap guide') + if self.swap_rep_pattern is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): # noqa: E501 + raise Exception('swap_rep_pattern option must be filled in if using default swapping function and not swap guide') # noqa: E501 + if self.resname_list is None and (not os.path.exists('residue_connect.csv') or not os.path.exists('residue_swap_map.csv')): # noqa: E501 + raise Exception('resname_list option must be filled in if using default swapping function and not swap guide') # noqa: E501 self.modify_coords_fn = self.default_coords_fn else: module_file = os.path.basename(self.modify_coords) @@ -1510,7 +1510,7 @@ def run_REXEE(self, n, swap_pattern=None): # want it to start parsing the dhdl file (in the if condition of if rank == 0) of simulation 3 being run by # rank 3 that has not been generated, which will lead to an I/O error. comm.barrier() - + def default_coords_fn(self, molA_file_name: str, molB_file_name: str): """ Swap coordinates between two GRO files @@ -1528,24 +1528,24 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): # Step 1: Load necessary files import mdtraj as md import pandas as pd - - #Determine name for transformed residue + + # Determine name for transformed residue molA_dir = molA_file_name.rsplit('/', 1)[0] + '/' molB_dir = molB_file_name.rsplit('/', 1)[0] + '/' - #Load trajectory trr for higher precison coordinates - molA = md.load_trr(f'{molA_dir}/traj.trr', top=molA_file_name).slice(-1) #Load last frame of trr trajectory + # Load trajectory trr for higher precison coordinates + molA = md.load_trr(f'{molA_dir}/traj.trr', top=molA_file_name).slice(-1) # Load last frame of trr trajectory molB = md.load_trr(f'{molB_dir}/traj.trr', top=molB_file_name).slice(-1) - #Load the coordinate swapping map + # Load the coordinate swapping map connection_map = pd.read_csv('residue_connect.csv') swap_map = pd.read_csv('residue_swap_map.csv') # Step 2: Read the GRO input coordinate files and open temporary Output files - molA_file = open(molA_file_name, 'r').readlines() #open input file + molA_file = open(molA_file_name, 'r').readlines() # open input file molB_new_file_name = 'B_hybrid_swap.gro' molB_new = open(molB_new_file_name, 'w') - molB_file = open(molB_file_name, 'r').readlines() #open input file + molB_file = open(molB_file_name, 'r').readlines() # open input file molA_new_file_name = 'A_hybrid_swap.gro' molA_new = open(molA_new_file_name, 'w') @@ -1558,38 +1558,38 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): if len(molA.topology.select('water')) != 0: A_dimensions = coordinate_swap.get_dimensions(molA_file) B_dimensions = coordinate_swap.get_dimensions(molB_file) - molA = coordinate_swap.fix_break(molA, nameA, A_dimensions, connection_map[connection_map['Resname'] == nameA]) - molB = coordinate_swap.fix_break(molB, nameB, B_dimensions, connection_map[connection_map['Resname'] == nameB]) + molA = coordinate_swap.fix_break(molA, nameA, A_dimensions, connection_map[connection_map['Resname'] == nameA]) # noqa: E501 + molB = coordinate_swap.fix_break(molB, nameB, B_dimensions, connection_map[connection_map['Resname'] == nameB]) # noqa: E501 - # Step 5: Determine coordinates of atoms which need to be reconstructed as we swap coordinates between molecules - miss_B = df_atom_swap[(df_atom_swap['Swap']=='B2A') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() - miss_A = df_atom_swap[(df_atom_swap['Swap']=='A2B') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() + # Step 5: Determine coordinates of atoms which need to be reconstructed as we swap coordinates between molecules # noqa: E501 + miss_B = df_atom_swap[(df_atom_swap['Swap'] == 'B2A') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() # noqa: E501 + miss_A = df_atom_swap[(df_atom_swap['Swap'] == 'A2B') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() # noqa: E501 if len(miss_B) != 0: - df_atom_swap = coordinate_swap.get_miss_coord(molB, molA, nameB, nameA, df_atom_swap, 'B2A', swap_map[(swap_map['Swap A'] == nameB) & (swap_map['Swap B'] == nameA)]) + df_atom_swap = coordinate_swap.get_miss_coord(molB, molA, nameB, nameA, df_atom_swap, 'B2A', swap_map[(swap_map['Swap A'] == nameB) & (swap_map['Swap B'] == nameA)]) # noqa: E501 if len(miss_A) != 0: - df_atom_swap = coordinate_swap.get_miss_coord(molA, molB, nameA, nameB, df_atom_swap, 'A2B', swap_map[(swap_map['Swap A'] == nameA) & (swap_map['Swap B'] == nameB)]) - - #Reprint preamble text + df_atom_swap = coordinate_swap.get_miss_coord(molA, molB, nameA, nameB, df_atom_swap, 'A2B', swap_map[(swap_map['Swap A'] == nameA) & (swap_map['Swap B'] == nameB)]) # noqa: E501 + + # Reprint preamble text line_start = coordinate_swap.print_preamble(molA_file, molB_new, len(miss_B), len(miss_A)) - #Print new coordinates to file for molB - coordinate_swap.write_new_file(df_atom_swap, 'A2B', 'B2A', line_start, molA_file, molB_new, nameA, nameB, copy.deepcopy(molA.xyz[0]), miss_A) - - #Print new coordinates to file - #Reprint preamble text + # Print new coordinates to file for molB + coordinate_swap.write_new_file(df_atom_swap, 'A2B', 'B2A', line_start, molA_file, molB_new, nameA, nameB, copy.deepcopy(molA.xyz[0]), miss_A) # noqa: E501 + + # Print new coordinates to file + # Reprint preamble text line_start = coordinate_swap.print_preamble(molB_file, molA_new, len(miss_A), len(miss_B)) - - #Print new coordinates for molA - coordinate_swap.write_new_file(df_atom_swap, 'B2A', 'A2B', line_start, molB_file, molA_new, nameB, nameA, copy.deepcopy(molB.xyz[0]), miss_B) - #Rename temp files + # Print new coordinates for molA + coordinate_swap.write_new_file(df_atom_swap, 'B2A', 'A2B', line_start, molB_file, molA_new, nameB, nameA, copy.deepcopy(molB.xyz[0]), miss_B) # noqa: E501 + + # Rename temp files os.rename('A_hybrid_swap.gro', molB_dir + '/confout.gro') os.rename('B_hybrid_swap.gro', molA_dir + '/confout.gro') def process_top(self): """ - Process the input topologies in order to determine the atoms for alignment in the default GRO swapping function. - Output as csv files to prevent needing to re-run this step. + Process the input topologies in order to determine the atoms for alignment in the default GRO swapping + function. Output as csv files to prevent needing to re-run this step. Parameters ---------- @@ -1603,15 +1603,15 @@ def process_top(self): if not os.path.exists('residue_connect.csv'): df_top = pd.DataFrame() for f, file_name in enumerate(self.top): - #Read file + # Read file input_file = coordinate_swap.read_top(file_name, self.resname_list[f]) - #Determine the atom names corresponding to the atom numbers + # Determine the atom names corresponding to the atom numbers start_line, atom_name, state = coordinate_swap.get_names(input_file) - - #Determine the connectivity of all atoms - connect_1, connect_2, state_1, state_2 = [], [], [], [] #Atom 1 and atom 2 which are connected and which state they are dummy atoms - for l, line in enumerate(input_file[start_line:]): + + # Determine the connectivity of all atoms + connect_1, connect_2, state_1, state_2 = [], [], [], [] # Atom 1 and atom 2 which are connected and which state they are dummy atoms # noqa: E501 + for l, line in enumerate(input_file[start_line:]): # noqa: E741 line_sep = line.split(' ') if line_sep[0] == ';': continue @@ -1623,7 +1623,7 @@ def process_top(self): connect_2.append(atom_name[int(line_sep[1])-1]) state_1.append(state[int(line_sep[0])-1]) state_2.append(state[int(line_sep[1])-1]) - df = pd.DataFrame({'Resname': self.resname_list[f], 'Connect 1': connect_1, 'Connect 2': connect_2, 'State 1': state_1, 'State 2': state_2}) + df = pd.DataFrame({'Resname': self.resname_list[f], 'Connect 1': connect_1, 'Connect 2': connect_2, 'State 1': state_1, 'State 2': state_2}) # noqa: E501 df_top = pd.concat([df_top, df]) df_top.to_csv('residue_connect.csv') else: @@ -1632,7 +1632,7 @@ def process_top(self): if not os.path.exists('residue_swap_map.csv'): df_map = pd.DataFrame() for swap in self.swap_rep_pattern: - #Determine atoms not present in both molecules + # Determine atoms not present in both molecules X, Y = [int(swap[0][0]), int(swap[1][0])] lam = {X: int(swap[0][1]), Y: int(swap[1][1])} for A, B in zip([X, Y], [Y, X]): @@ -1640,13 +1640,13 @@ def process_top(self): start_line, A_name, state = coordinate_swap.get_names(input_A) input_B = coordinate_swap.read_top(self.top[B], self.resname_list[B]) start_line, B_name, state = coordinate_swap.get_names(input_B) - + A_only = [x for x in A_name if x not in B_name] B_only = [x for x in B_name if x not in A_name] - - #Seperate real to dummy switches - df = coordinate_swap.deter_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, lam[A]) - + + # Seperate real to dummy switches + df = coordinate_swap.deter_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, lam[A]) # noqa: E501 + df_map = pd.concat([df_map, df]) - + df_map.to_csv('residue_swap_map.csv') From f85d9146804db263e659efc80aafe28b41b48c1d Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 15:21:05 +0800 Subject: [PATCH 08/68] Some work on tweaking the docstrings in coordinate_swap.py --- ensemble_md/replica_exchange_EE.py | 6 +- ensemble_md/utils/coordinate_swap.py | 430 ++++++++++++++------------- 2 files changed, 233 insertions(+), 203 deletions(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index 081031f2..703057dc 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -1550,9 +1550,9 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): molA_new = open(molA_new_file_name, 'w') # Step 3: Determine atoms for alignment and swapping - nameA = coordinate_swap.deter_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) - nameB = coordinate_swap.deter_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) - df_atom_swap = coordinate_swap.deter_common(molA_file, molB_file, nameA, nameB) + nameA = coordinate_swap.identify_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) + nameB = coordinate_swap.identify_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) + df_atom_swap = coordinate_swap.find_common(molA_file, molB_file, nameA, nameB) # Step 4: Fix break if present for solvated systems only if len(molA.topology.select('water')) != 0: diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index f1abc48b..76f53710 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -1,52 +1,71 @@ -import mdtraj as md +#################################################################### +# # +# ensemble_md, # +# a python package for running GROMACS simulation ensembles # +# # +# Written by # +# - Anika Friedman # +# - Wei-Tse Hsu # +# Copyright (c) 2022 University of Colorado Boulder # +# # +#################################################################### +""" +The :obj:`.coordinate_swap` module provides functions for swapping coordinates +in a MT-REXEE simulation. +""" +import os import re +import copy +import mdtraj as md import numpy as np -import os -from itertools import product import pandas as pd -import copy +from itertools import product + def get_dimensions(file): """ - Determine the dimensions of the cubic box based on the input GRO file + Determines the dimensions of the cubic box based on the input GRO file. Parameters ---------- - file : List of strings - containing all of the lines in the input gro file + file : list + A list of strings containing all of the lines in the input GRO file. Returns ------- - [x, y, z] : List of floats - X, Y, and Z coordinates for the periodic box + dim_vector : list + A list of floats containing the dimensions of the cubic box. """ box_raw = file[-1].split(' ') while '' in box_raw: box_raw.remove('') - - return [float(box_raw[0]), float(box_raw[1]), float(box_raw[2])] -def deter_common(molA_file, molB_file, nameA : str, nameB : str): + dim_vector = [float(i) for i in box_raw] + return dim_vector + +def find_common(molA_file, molB_file, nameA, nameB): """ - Determine the atoms which are common, which are switched between dummy and real atoms, and which are unique between the two molecule + Determine the atoms which are common, which are switched between dummy and real atoms, + and which are unique between the two input molecules. Parameters ---------- - molA_file : List of strings - Lines of the GRO file for molecule A - molB_file : List of strings - Lines of the GRO file for molecule B + molA_file : list + A list of strings containing lines of the GRO file for molecule A. + molB_file : list + A list of strings containing lines of the GRO file for molecule B. nameA : str - The name of the residue being altered in molecule A + The name of the residue being altered in molecule A. nameB : str - The name of the residue being altered in molecule B + The name of the residue being altered in molecule B. Returns ------- - df : pandas DataFrame - Containing the atoms which are not the same between the two molecules and how they are changed + df : pandas.DataFrame + A pandas DataFrame containing the atoms which are not the same between the two molecules + and how they are changed. """ - #Gather atom names from each file + # Gather atom names from each file nameA_list, lineA_list, nameB_list, lineB_list = [], [], [], [] for l, line in enumerate(molA_file): split_line = line.split(' ') @@ -66,41 +85,48 @@ def deter_common(molA_file, molB_file, nameA : str, nameB : str): nameB_list.append(split_line[1]) lineB_list.append(l) - #Determine the atom names present in both molecules + # Determine the atom names present in both molecules common_atoms_all = list(set(nameA_list) & set(nameB_list)) - #Determine the swaps for each transformation - df_A2B = deter_R2D_D2R_miss(nameA_list, nameB_list, common_atoms_all, lineA_list, 'A2B') - df_B2A = deter_R2D_D2R_miss(nameB_list, nameA_list, common_atoms_all, lineB_list, 'B2A') + # Determine the swaps for each transformation + df_A2B = find_R2D_D2R_miss(nameA_list, nameB_list, common_atoms_all, lineA_list, 'A2B') + df_B2A = find_R2D_D2R_miss(nameB_list, nameA_list, common_atoms_all, lineB_list, 'B2A') - #Add D2R + # Add D2R df = pd.concat([df_A2B, df_B2A]) df.reset_index(inplace=True) return df -def deter_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap): +def find_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap): """ - Determine which atoms are swapped between dummy and real states and which are missing + Determines which atoms are swapped between dummy and real states and which are missing. Parameters ---------- - name_list : str - List of all the atom names for the atoms in the molecule of interest - name_other_list : str - List of all the atom names for the atoms that the molecule of interest is swapping with - common_atoms : str - List of all the atom names for atoms known to be common between the two molecules - Line_list : int - List of the line in the file which corresponds to each atom name in the molecule of interest + name_list : list + A list of all the atom names for the atoms in the molecule of interest. + name_other_list : list + A list of all the atom names for the atoms that the molecule of interest is swapping with. + common_atoms : list + A list of all the atom names for atoms known to be common between the two molecules. + line_list : list + A list of the line in the file which corresponds to each atom name in the molecule of interest. swap : str The direction of the swap based on the molecules identified as A and B Returns ------- - df : pandas DataFrame - For each atom that is not in the common list the dataframe gives the name of the atom, the atom number, the atom element, whether the atom is switchin between dummy and real or missing, the swap direction (same as input), whether the final atom type is real or dummy + df : pandas.DataFrame + A pandas DataFrame that contains the following information for each at omthat is no in the common list: + + - The name of the atom, + - The atom number + - The atom element + - Whether the atom is switching between dummy and real or missing, + - The swap direction (same as input) + - Whether the final atom type is real or dummy """ - #Determine atoms unique to either molecule + # Determine atoms unique to either molecule names, an_num, elements, directions, swaps, lines, final_type = [], [], [], [], [], [], [] for a, atom in enumerate(name_list): element = atom.strip('0123456789') @@ -131,24 +157,25 @@ def deter_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap def fix_break(mol, resname, box_dimensions, atom_connect_all): """ - Determine if there are any breaks across periodic boundary conditions in the residue of interest and shift the molecule across those boudaries to make it whole + Determines if there are any breaks across periodic boundary conditions in the residue of interest and + shifts the molecule across those boudaries to make it whole. Parameters ---------- - mol : mdtraj Trajectory object - Trajectory object for the molecule or interest + mol : :func:`mdtraj.Trajectory` object + Trajectory for the molecule or interest. resname : str - Name of the residue of interest for coordinate swapping + The name of the residue of interest for coordinate swapping. box_dimensions : list - Dimensions of the periodic box for the system of interest - atom_connect_all : pd.DataFrame - DataFrame which contains the name of all atoms which are connected to one another in the residue of interest + Dimensions of the periodic box for the system of interest. + atom_connect_all : pandas.DataFrame + A pandas DataFrame which contains the name of all atoms which are connected to one another + in the residue of interest Returns ------- - mol : mdtraj Trajecotry object - Trajectory with all breaks in the necessary portions of the molecule fixed - + mol : :func:`mdtraj.Trajectory` object + A :func:`mdtraj.Trajectory` object with all breaks in the necessary portions of the molecule fixed. """ mol_top = mol.topology @@ -160,7 +187,7 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): for atoms in atom_connect: atom_pairs.append(list(mol_top.select(f"resname {resname} and (name {atoms[0]} or name {atoms[1]})"))) - #Find any broken bonds + # Find any broken bonds broken_pairs = check_break(mol, atom_pairs) if len(broken_pairs) == 0: @@ -169,27 +196,27 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): else: print('Fixing break') - iter = 0 #Keep track of while loop iterations + iter = 0 # Keep track of while loop iterations shift_atom = [] while len(broken_pairs) > 0: - #Prevent infinite loop + # Prevent infinite loop if iter > len(atom_pairs): raise Exception('Break could not be fixed') iter += 1 - #Fix this break - mol, Fixed, shift_atom = perform_shift_1D(mol, box_dimensions, broken_pairs, atom_pairs, shift_atom) - if Fixed: + # Fix this break + mol, fixed, shift_atom = perform_shift_1D(mol, box_dimensions, broken_pairs, atom_pairs, shift_atom) + if fixed: broken_pairs = check_break(mol, atom_pairs) continue else: - mol, Fixed = perform_shift_2D(mol, box_dimensions, broken_pairs, shift_atom) - if Fixed: + mol, fixed = perform_shift_2D(mol, box_dimensions, broken_pairs, shift_atom) + if fixed: broken_pairs = check_break(mol, atom_pairs) continue else: - mol, Fixed = perform_shift_3D(mol, box_dimensions, broken_pairs, shift_atom) - if Fixed: + mol, fixed = perform_shift_3D(mol, box_dimensions, broken_pairs, shift_atom) + if fixed: broken_pairs = check_break(mol, atom_pairs) continue else: @@ -199,25 +226,25 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): """ - Shift across the periodic boundaries in 1D + Shifts the input trajectory across the periodic boundaries in 1D. Parameters ---------- - mol : mdtraj Trajectory object - Trajecotry with the original coordinates prior to the fhist - box_dimensions : list of floats - Dimensions of the periodic boundary box + mol : :func:`mdtraj.Trajectory` object + A :func:`mdtraj.Trajectory` object with the original coordinates prior to the shift. + box_dimensions : list + Dimensions of the periodic boundary box. broken_pairs_init : int - which pairs of atoms were found to be broken + Which pairs of atoms were found to be broken. prev_shift_atom : int - Which atoms have already been shifted so we don't undo what we've done + Which atoms have already been shifted so we don't undo what we've done. Returns ------- - mol : mdtraj Trajectory object - Trajectory with the new coordintes - Fixed : bool - Was the break actually fixed + mol : :func:`mdtraj.Trajectory` object + Trajectory with the new coordinates. + fixed : bool + A boolean indicating whether the break was actually fixed. prev_shift_atom : int Which atoms have already been shifted so we don't undo what we've done """ @@ -225,130 +252,130 @@ def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): broken_atom = atom_pair[1] if broken_atom in prev_shift_atom: broken_atom = atom_pair[0] - Fixed = False + fixed = False for x in range(3): #Loop through x, y, and z for shift_dir in [1, -1]: - mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) #positive shift + mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) # positive shift dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) - if dist_check > 0.2: #Didn't work so reverse and try again + if dist_check > 0.2: # Didn't work so reverse and try again mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] - (shift_dir[0] * box_dimensions[x]) - else: #Yay fixed break - Fixed = True + else: # Yay fixed break + fixed = True break - if Fixed: + if fixed: break - if Fixed: + if fixed: prev_shift_atom.append(broken_atom) - return mol, Fixed, prev_shift_atom + return mol, fixed, prev_shift_atom def perform_shift_2D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): """ - Shift across the periodic boundaries in 2D + Shifts the input trajectory across the periodic boundaries in 2D. Parameters ---------- - mol : mdtraj Trajectory object - Trajecotry with the original coordinates prior to the fhist - box_dimensions : list of floats - Dimensions of the periodic boundary box + mol : :func:`mdtraj.Trajectory` object + Trajecotry with the original coordinates prior to the shift. + box_dimensions : list + Dimensions of the periodic boundary box. broken_pairs_init : int - which pairs of atoms were found to be broken + Which pairs of atoms were found to be broken. prev_shift_atom : int - Which atoms have already been shifted so we don't undo what we've done + Which atoms have already been shifted so we don't undo what we've done. Returns ------- - mol : mdtraj Trajectory object - Trajectory with the new coordintes - Fixed : bool - Was the break actually fixed + mol : :func:`mdtraj.Trajectory` object + Trajectory with the new coordintes. + fixed : bool + A boolean indicating whether the break was actually fixed. prev_shift_atom : int - Which atoms have already been shifted so we don't undo what we've done + Which atoms have already been shifted so we don't undo what we've done. """ atom_pair = broken_pairs_init[0] broken_atom = atom_pair[1] if broken_atom in prev_shift_atom: broken_atom = atom_pair[0] - Fixed = False + fixed = False shift_combos = product([0, 1, 2], [0, 1, 2]) - for pair in shift_combos: #Loop through x, y, and z - for shift_dir in product([1, -1], [1,-1]): #Try all combos of shift direction + for pair in shift_combos: # Loop through x, y, and z + for shift_dir in product([1, -1], [1,-1]): # Try all combos of shift direction x, y = pair - mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) #positive shift + mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) # positive shift mol.xyz[0,broken_atom,y] = mol.xyz[0,broken_atom,y] + (shift_dir[1] * box_dimensions[y]) dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) - if dist_check > 0.2: #Didn't work so reverse and try again + if dist_check > 0.2: # Didn't work so reverse and try again mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] - (shift_dir[0] * box_dimensions[x]) mol.xyz[0,broken_atom,y] = mol.xyz[0,broken_atom,y] - (shift_dir[1] * box_dimensions[y]) - else: #Yay fixed break - Fixed = True + else: # Yay fixed break + fixed = True break - if Fixed: + if fixed: break - if Fixed: + if fixed: prev_shift_atom.append(broken_atom) - return mol, Fixed + return mol, fixed def perform_shift_3D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): """ - Shift across the periodic boundaries in 3D + Shifts the input trajectory across the periodic boundaries in 3D Parameters ---------- - mol : mdtraj Trajectory object - Trajecotry with the original coordinates prior to the fhist - box_dimensions : list of floats - Dimensions of the periodic boundary box + mol : :func:`mdtraj.Trajectory` object + Trajecotry with the original coordinates prior to the shift. + box_dimensions : list + Dimensions of the periodic boundary box. broken_pairs_init : int - which pairs of atoms were found to be broken + Which pairs of atoms were found to be broken. prev_shift_atom : int - Which atoms have already been shifted so we don't undo what we've done + Which atoms have already been shifted so we don't undo what we've done. Returns ------- - mol : mdtraj Trajectory object - Trajectory with the new coordintes - Fixed : bool - Was the break actually fixed + mol : :func:`mdtraj.Trajectory` object + Trajectory with the new coordintes. + fixed : bool + A boolean indicating whether the break was actually fixed. prev_shift_atom : int - Which atoms have already been shifted so we don't undo what we've done + Which atoms have already been shifted so we don't undo what we've done. """ atom_pair = broken_pairs_init[0] broken_atom = atom_pair[1] if broken_atom in prev_shift_atom: broken_atom = atom_pair[0] - Fixed = False - for shift_dir in product([1, -1], [1,-1], [1, -1]): #Try all combos of shift direction + fixed = False + for shift_dir in product([1, -1], [1,-1], [1, -1]): # Try all combos of shift direction mol.xyz[0,broken_atom,0] = mol.xyz[0,broken_atom,0] + (shift_dir[0] * box_dimensions[0]) mol.xyz[0,broken_atom,1] = mol.xyz[0,broken_atom,1] + (shift_dir[1] * box_dimensions[1]) mol.xyz[0,broken_atom,2] = mol.xyz[0,broken_atom,2] + (shift_dir[2] * box_dimensions[2]) dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) - if dist_check > 0.2: #Didn't work so reverse and try again + if dist_check > 0.2: # Didn't work so reverse and try again mol.xyz[0,broken_atom,0] = mol.xyz[0,broken_atom,0] - (shift_dir[0] * box_dimensions[0]) mol.xyz[0,broken_atom,1] = mol.xyz[0,broken_atom,1] - (shift_dir[1] * box_dimensions[1]) mol.xyz[0,broken_atom,2] = mol.xyz[0,broken_atom,2] - (shift_dir[2] * box_dimensions[2]) - else: #Yay fixed break - Fixed = True + else: # Yay fixed break + fixed = True break - if Fixed: + if fixed: prev_shift_atom.append(broken_atom) - return mol, Fixed + return mol, fixed def check_break(mol, atom_pairs): """ - Determine whether a break is present between the atom pairs of interest + Determines whether a break is present between the atom pairs of interest. Parameters ---------- - mol : mdtraj Trajectory object - Trajectory to examine for breaks + mol : :func:`mdtraj.Trajectory` object + Trajectory to examine for breaks. atom_pairs : int - The atom number pairs which should be connected in the residue of interest + The atom number pairs which should be connected in the residue of interest. Returns ------- broken_pairs : int - which pairs of atoms have breaks across the periodic boundary + Which pairs of atoms have breaks across the periodic boundary. """ dist = md.compute_distances(mol, atom_pairs=atom_pairs, periodic=False) broken_pairs = [] @@ -359,31 +386,38 @@ def check_break(mol, atom_pairs): def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, df_swap): """ - Get coordinates for the missing atoms after the conformational swap + Gets coordinates for the missing atoms after the conformational swap Parameters ---------- - mol_align : mdtraj Trajectory object - trajectory for the molecule being aligned - mol_ref : mdtraj Trajectory object - trajectory for the reference molecule + mol_align : :func:`mdtraj.Trajectory` object + Trajectory for the molecule being aligned. + mol_ref : :func:`mdtraj.Trajectory` object + Trajectory for the reference molecule. name_align : str - resname for the molecule which is being aligned + The resname for the molecule which is being aligned. name_ref : str - resname for the molecule which has the reference coordinates - df_atom_swap : pandas DataFrame - For each atom that is not in the common list the dataframe gives the name of the atom, the atom number, the atom element, whether the atom is switchin between dummy and real or missing, the swap direction (same as input), whether the final atom type is real or dummy + The resname for the molecule which has the reference coordinates. + df_atom_swap : pandas.DataFrame + A pandas DataFrame that contains the following information for each at omthat is no in the common list: + + - The name of the atom + - The atom number + - The atom element + - Whether the atom is switchin between dummy and real or missing + - The swap direction (same as input) + - Thether the final atom type is real or dummy dir : str - swapping direction - df_swap : pandas DataFrame - For each missing atoms + The swapping direction. + df_swap : pandas.DataFrame + For each missing atoms. Returns ------- - df_atom_swap : pandas DataFrame - Same dataframe as the input, but with coordinates for the missing atoms + df_atom_swap : pandas.DataFrame + Same dataframe as the input, but with coordinates for the missing atoms. """ - #Create a new column for coordinates if one does not exist + # Create a new column for coordinates if one does not exist if 'X Coordinates' not in df_atom_swap.columns: df_atom_swap['X Coordinates'] = np.NaN df_atom_swap['Y Coordinates'] = np.NaN @@ -397,7 +431,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, conn_ref = [row['Anchor Atom Name B'], row['Alignment Atom B']] miss_names_select = row['Missing Atom Name'].split(' ') geom_fix_select = [miss_names_select[0], row['Anchor Atom Name A'], row['Angle Atom A']] - #Limit to region of interest + # Limit to region of interest align_select = [] for a in conn_align + miss_names_select + geom_fix_select: atom = mol_align.topology.select(f'resname {name_align} and name {a}')[0] @@ -409,28 +443,28 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, mol_ref_select = copy.deepcopy(mol_ref.atom_slice(ref_select)) mol_align_select = copy.deepcopy(mol_align.atom_slice(align_select)) - #Select atoms in connection bond + # Select atoms in connection bond conn0_align = mol_align_select.topology.select(f'resname {name_align} and name {conn_align[0]}')[0] conn1_align = mol_align_select.topology.select(f'resname {name_align} and name {conn_align[1]}')[0] conn0_ref = mol_ref_select.topology.select(f'resname {name_ref} and name {conn_ref[0]}')[0] conn1_ref = mol_ref_select.topology.select(f'resname {name_ref} and name {conn_ref[1]}')[0] - #Step 1: Perform translation to align point 1 + # Step 1: Perform translation to align point 1 shift_vec = mol_ref_select.xyz[0,conn0_ref,:] - mol_align_select.xyz[0,conn0_align,:] for a in range(mol_align_select.n_atoms): mol_align_select.xyz[0,a,:] = mol_align_select.xyz[0,a,:] + shift_vec - #Step 2: Perform rotational motion to line up point 2 - ref_vec = mol_ref_select.xyz[0,conn1_ref,:] - mol_ref_select.xyz[0,conn0_ref,:] #defing 0-1 vector in ref - align_vec = mol_align_select.xyz[0,conn1_align,:] - mol_ref_select.xyz[0,conn0_ref,:] #defing 0-1 vector in align - axis_rot = np.cross(ref_vec/np.linalg.norm(ref_vec), (align_vec/np.linalg.norm(align_vec))) #Perpendicular vector to ref and align vectors + # Step 2: Perform rotational motion to line up point 2 + ref_vec = mol_ref_select.xyz[0,conn1_ref,:] - mol_ref_select.xyz[0,conn0_ref,:] # defing 0-1 vector in ref + align_vec = mol_align_select.xyz[0,conn1_align,:] - mol_ref_select.xyz[0,conn0_ref,:] # defing 0-1 vector in align + axis_rot = np.cross(ref_vec/np.linalg.norm(ref_vec), (align_vec/np.linalg.norm(align_vec))) # Perpendicular vector to ref and align vectors theta = find_rotation_angle(mol_align_select.xyz[0,conn1_align,:], mol_ref_select.xyz[0,conn0_ref,:], mol_ref_select.xyz[0,conn1_ref,:], axis_rot) for a in range(mol_align_select.n_atoms): if a != conn0_align: mol_align_select.xyz[0,a,:] = rotate_point_around_axis(mol_align_select.xyz[0,a,:], mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta) - #Step 3: Rotate around 0-1 bond to get the correct angle for connecting atom + # Step 3: Rotate around 0-1 bond to get the correct angle for connecting atom angle_atoms = [mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[0]}')[0], mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0], mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[2]}')[0]] @@ -439,7 +473,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, axis_rot = mol_align_select.xyz[0,conn0_align,:] - mol_align_select.xyz[0,conn1_align,:] axis_rot = axis_rot / np.linalg.norm(axis_rot) - #Determine angle of rotation to get the right internal angle + # Determine angle of rotation to get the right internal angle min_dev_angle = 3 init_coords = mol_align_select.xyz[0,change_atoms,:][0].copy() constant_coords = [mol_align_select.xyz[0,mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0],:], @@ -454,12 +488,12 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, min_dev_angle = abs(iangle - internal_angle) if min_dev_angle < 0.05: break - #Perform the rotation + # Perform the rotation for a in range(mol_align_select.n_atoms): if a != conn0_align: mol_align_select.xyz[0,a,:] = rotate_point_around_axis(mol_align_select.xyz[0,a,:], mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta_min) - #Add coordinates to df + # Add coordinates to df for r in range(len(df_atom_swap.index)): if df_atom_swap.iloc[r]['Direction'] == 'miss' and df_atom_swap.iloc[r]['Swap'] == dir: for name in miss_names_select: @@ -474,14 +508,14 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, def process_line(mol_file, i): """ - Seperate the line by spaces and correct for when the atom number merges the atom name + Seperates the line by spaces and corrects for when the atom number merges the atom name Parameters ---------- - mol_file : list of str - Reading the lines of the input gro file + mol_file : list + A list of strings containing the lines of the input GRO file. i : int - The iterator for the line in the file + The index the line in the file. Returns ------- @@ -490,15 +524,15 @@ def process_line(mol_file, i): prev_line : str Line i-1 in the file """ - #Load previous line to determine identity of previous atom + # Load previous line to determine identity of previous atom prev_line = mol_file[i-1].split(' ') while("" in prev_line): prev_line.remove("") - #Load current line in file and seperate + # Load current line in file and seperate line = mol_file[i].split(' ') while("" in line): line.remove("") - #Control for atom name and atom number merging + # Control for atom name and atom number merging if len(line[1]) > 5: line = sep_merge(line) if i > 2 and len(prev_line[1]) > 5: @@ -508,23 +542,23 @@ def process_line(mol_file, i): def print_preamble(old_file, new_file, num_add_names, num_rm_names): """ - Print the preamble of the gro file before the atom specifications begin + Prints the preamble of the gro file before the atom specifications begin. Parameters ---------- - old_file : list of str - - new_file : list of str - + old_file : list + A list of strings containing lines from the original GRO file. + new_file : file-like object + A writable file-like object where the modified content is written. num_add_names : int - Number of atoms to be added to the pre-swap molecule + The number of atoms to be added to the pre-swap molecule. num_rm_names : int - Number of atoms to be removed to the post-swap molecule + The number of atoms to be added to the post-swap molecule. Returns ------- line_start : int - The line number to start when you continue to read the file + The line number to start when you continue to read the file. """ for i in range(len(old_file)): if not re.match(r'[ \t]', old_file[i]) and not re.match('^[0-9]+$', old_file[i]): @@ -538,30 +572,26 @@ def print_preamble(old_file, new_file, num_add_names, num_rm_names): def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB=None): """ - Write a line in the file in which some parameter needs changed and maintain spacing + Writes a line in the file in which some parameter needs to be changed. Parameters ---------- - mol_new : File object - The new file that is being written to + mol_new : file-like object + A writable file-like object where the formatted molecular data is written. raw_line : str - The unseperated and unchanged line - Line : List of str - + The unseperated and unchanged line. + line : list + A list of strings representing parsed parts of the input line, such as atom names, numbers, etc. atom_num : int - The new atom number to be assigned to the atom in this line - vel : list of float - The velocities to be assigned to the atom in this line - coor : list of float - The coordinates for the atom in this line + The new atom number to be assigned to the atom in this line. + vel : list + The list of velocities in the x, y, and z directions to be assigned to the atom in this line. + coor : list + The list coordinates in the x, y, and z directions for the atom in this line. resnun : int - The new residue number if it changes else leave deafult of None + The new residue number if it changes. The default is :code:`None`:. nameB : str - The new residue name if if changes from what was in the previous file else leave deafult of None - - Returns - ------- - None + The new residue name if if changes from what was in the previous file. The default is :code:`None`:. """ coor = ["{:.7f}".format(coor[0]), "{:.7f}".format(coor[1]), "{:.7f}".format(coor[2])] if len(line) == 9: @@ -588,21 +618,21 @@ def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB= else: mol_new.write(raw_line) -def deter_res(mol_top, resname_options): +def identify_res(mol_top, resname_options): """ - Determine which of the potential residues of interest are in this molecule + Determines which of the potential residues of interest are in this molecule. Parameters ---------- mol_top : mdtraj topology - The molecule topology - resname_options : list of str - The potential residue names which may be in the moleucle + The molecule topology. + resname_options : list + The potential residue names which may be in the moleucle. Returns ------- resname : str - The name of the residue of interest which is in the molecule + The name of the residue of interest which is in the molecule. """ for name in resname_options: if len(mol_top.select(f"resname {name}")) != 0: @@ -612,30 +642,30 @@ def deter_res(mol_top, resname_options): def add_atom(mol_new, resnum, resname, df, vel, atom_num): """ - Add a new atom to the GRO file + Add a new atom to the GRO file. Parameters ---------- mol_new : file - The temporary file for the new GRO + The temporary file for the new GRO. resnum : int - The residue number of the atom being added + The residue number of the atom being added. resname : str - The name of the residue which the atom being added belongs to + The name of the residue which the atom being added belongs to. df : pandas.DataFrame - The master dataframe which contains the coordinates for the atom being added - vel : list of float - The velocity to assign to the atom being added + The master DataFrame which contains the coordinates for the atom being added. + vel : list + The list of velocities in the x, y, and z directions to be assigned to the atom in this line. atom_num : int - The atom number to assign to the atom being added + The atom number to assign to the atom being added. Returns ------- atom_num : int - The atom number for the next atom in the file + The atom number for the next atom in the file. """ name_new = df['Name'].to_list()[0] - #Reformat coordiantes + # Reformat coordiantes x_init = df['X Coordinates'].to_list() y_init = df['Y Coordinates'].to_list() z_init = df['Z Coordinates'].to_list() @@ -645,7 +675,7 @@ def add_atom(mol_new, resnum, resname, df, vel, atom_num): y = format(y_temp, '.7f') z_temp = np.round(z_init[0], decimals=7) z = format(z_temp, '.7f') - #Write line for new atom + # Write line for new atom mol_new.write(f'{resnum}{resname}'.rjust(8, ' ') + name_new.rjust(7, ' ') + str(atom_num).rjust(5, ' ') + str(x).rjust(12, ' ') + str(y).rjust(12, ' ') + str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) atom_num += 1 From 42c6a0dc0cb51f313be6e2c1898c7a33d5fd112e Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 16:02:26 +0800 Subject: [PATCH 09/68] Finished tweaking the docstrings in coordinate_swap.py --- ensemble_md/replica_exchange_EE.py | 6 +- ensemble_md/utils/coordinate_swap.py | 418 ++++++++++++++------------- 2 files changed, 226 insertions(+), 198 deletions(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index 703057dc..fb63993d 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -1550,8 +1550,8 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): molA_new = open(molA_new_file_name, 'w') # Step 3: Determine atoms for alignment and swapping - nameA = coordinate_swap.identify_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) - nameB = coordinate_swap.identify_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) + nameA = coordinate_swap.identify_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) # noqa: E501 + nameB = coordinate_swap.identify_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) # noqa: E501 df_atom_swap = coordinate_swap.find_common(molA_file, molB_file, nameA, nameB) # Step 4: Fix break if present for solvated systems only @@ -1645,7 +1645,7 @@ def process_top(self): B_only = [x for x in B_name if x not in A_name] # Seperate real to dummy switches - df = coordinate_swap.deter_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, lam[A]) # noqa: E501 + df = coordinate_swap.determine_connection(A_only, B_only, self.resname_list[A], self.resname_list[B], df_top, lam[A]) # noqa: E501 df_map = pd.concat([df_map, df]) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 76f53710..1b47dae5 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -642,7 +642,7 @@ def identify_res(mol_top, resname_options): def add_atom(mol_new, resnum, resname, df, vel, atom_num): """ - Add a new atom to the GRO file. + Adds a new atom to the GRO file. Parameters ---------- @@ -683,39 +683,40 @@ def add_atom(mol_new, resnum, resname, df, vel, atom_num): def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): """ - Add an atom to the file which is switching between dummy and real state or vice versa + Adds an atom to the file which is switching between dummy and real state or vice versa. Parameters ---------- mol_new : file - The temporary file for the new GRO + The temporary file for the new GRO. resnum : int - The residue number of the atom being added + The residue number of the atom being added. resname : str - The name of the residue which the atom being added belongs to + The name of the residue which the atom being added belongs to. df : pandas.DataFrame - The master dataframe which contains the coordinates for the atom being added + The master DataFrame which contains the coordinates for the atom being added. vel : list of float - The velocity to assign to the atom being added + The list of velocities in the x, y, and z directions to be assigned to the atom in this line. atom_num : int - The atom number to assign to the atom being added - orig_coords : list of float - The coordinates for the atom being added + The atom number to assign to the atom being added. + orig_coords : list + The XYZ coordinates for the atom being added. Returns ------- line_num : int - Since the atom may be added in a different order than it was in the previous file save the line number so that we skip it when we come to it + Since the atom may be added in a different order than it was in the previous file save the line + number so that we skip it when we come to it. """ - #Get the name for the atom we are writting + # Get the name for the atom we are writting name_orig = df['Name'].to_list()[0] - #Determine the new atom name based on whether the new atom should be real or dummy + # Determine the new atom name based on whether the new atom should be real or dummy final_state = df['Final Type'].to_list()[0] if final_state == 'dummy': element = name_orig.strip('0123456789') atom_name_num = name_orig.strip('DCVH') - #Add D or C + # Add D or C if element == 'C': name_new = f'D{element}{atom_name_num}' else: @@ -726,30 +727,30 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): else: name_new = name_orig.replace('HV', 'H') - #These may be added out of order so lets make sure we have the right coordinates + # These may be added out of order so lets make sure we have the right coordinates line_num = df['File line'].to_list()[0] c = line_num - 2 orig_coor = orig_coords[c] x, y, z = ["{:.7f}".format(orig_coor[0]), "{:.7f}".format(orig_coor[1]), "{:.7f}".format(orig_coor[2])] - #Write line + # Write line mol_new.write(f'{resnum}{resname}'.rjust(8, ' ') + name_new.rjust(7, ' ') + str(atom_num).rjust(5, ' ') + str(x).rjust(12, ' ') + str(y).rjust(12, ' ') + str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) return line_num def sep_merge(line): """ - Seperate two GRO file columns which no longer have a space sperating them + Seperates two GRO file columns which no longer have a space sperating them. Parameters ---------- line : list of str - The line contents seperated by spaces + The line contents seperated by spaces. Returns ------- - temp_line : list of str - The line contents with the merged columns + temp_line : list + The line contents with the merged columns. """ temp_line = [line[0]] merged = [*line[1]] @@ -763,31 +764,31 @@ def sep_merge(line): def rotate_point_around_axis(point, vertex, axis, angle): """ - Rotate a 3D point around an aritrary axis + Rotates a 3D point around an arbitrary axis. Parameters ---------- - point : np.array shape (1,3) - The starting point prior to rotation - start : np.array shape (1,3) - The vertex of the axis of rotation - axis : np.array shape (1,3) - The axis of rotation + point : numpy.ndarray + The XYZ coordinates of the point to rotate. The shape should be (1, 3). + start : numpy.ndarray + The XYZ coordinates of the vertex of the axis of rotation. The shape should be (1, 3). + axis : numpy.ndarray + The axis of rotation. The shape should be (1, 3). angle : float - The angle to rotate + The angle by which to rotate the point, in radians. Returns ------- - rotated point : np.array shape (1,3) - The new rotated point + rotated point : numpy.ndarray + The XYZ coordinates of the new rotated point. The shape should be (1, 3). """ - #Transformation matrix to origin + # Transformation matrix to origin T = np.eye(4) T[0:3,3] = -vertex - #Reverse the transformation to origin + # Reverse the transformation to origin T_r = np.eye(4) T_r[0:3,3] = vertex - #Normalize rotational axis + # Normalize rotational axis axis = axis / np.linalg.norm(axis) a, b, c = axis d = np.sqrt(b**2+c**2) @@ -796,37 +797,37 @@ def rotate_point_around_axis(point, vertex, axis, angle): Rx = [[1, 0, 0, 0], [0, c/d, -b/d, 0], [0, b/d, c/d, 0], [0, 0, 0, 1]] Rx_r = [[1, 0, 0, 0], [0, c/d, b/d, 0], [0, -b/d, c/d, 0], [0, 0, 0, 1]] - #Rotation about the y axis + # Rotation about the y axis Ry = [[d, 0, -a, 0], [0, 1, 0, 0], [a, 0, d, 0], [0, 0, 0, 1]] Ry_r = [[d, 0, a, 0], [0, 1, 0, 0], [-a, 0, d, 0], [0, 0, 0, 1]] - #Rotation about the z axis + # Rotation about the z axis Rz = [[np.cos(angle), np.sin(angle), 0, 0], [-np.sin(angle), np.cos(angle), 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]] - #Initial position + # Initial position x0, y0, z0 = point init_arry = [x0, y0, z0, 1] - #Perform the transofmration + # Perform the transofmration final_arry = T_r@Rx_r@Ry_r@Rz@Ry@Rx@T@init_arry - #Get the corrdinates for the rotated point + # Get the corrdinates for the rotated point rotated_point = final_arry[0:3] return rotated_point def find_rotation_angle(initial_point, vertex, rotated_point, axis): """ - Determine the angle of rotation around an arbitrary axis in 3D space. + Determines the angle of rotation around an arbitrary axis in 3D space. Parameters ---------- - initial_point: A numpy array - the initial point coordinates - rotated_point: A numpy array - the rotated point coordinates + initial_point: numpy.ndarray + The initial point coordinates. + rotated_point: numpy.ndarray + The rotated point coordinates. axis: A numpy array - the axis of rotation + The axis of rotation. Returns ------- @@ -838,32 +839,32 @@ def find_rotation_angle(initial_point, vertex, rotated_point, axis): x0, y0, z0 = initial_point a, b, c = vertex - #Determine the rotated point with the same bond length as the initial point + # Determine the rotated point with the same bond length as the initial point rotated_point_axis = rotated_point - vertex norm_rot_point_vec = rotated_point_axis / np.linalg.norm(rotated_point_axis) - final_bond_length = np.sqrt((x0-a)**2 + (y0-b)**2 + (z0-c)**2) + final_bond_length = np.sqrt((x0 - a) ** 2 + (y0 - b) ** 2 + (z0 - c) ** 2) rotated_point_standard = vertex + final_bond_length*norm_rot_point_vec - x, y, z = rotated_point_standard #Change to point with same bond length along this vector + x, y, z = rotated_point_standard # Change to point with same bond length along this vector - Q = np.sqrt(v**2+w**2) - B = ((w/Q)*(y0-b)) - ((v/Q)*(z0-c)) - A = Q*(x0-a) - u*(((v/Q)*(y0-b)) + ((w/Q)*(z0-c))) - C = u*(x0-a) + Q*(((v/Q)*(y0-b)) + ((w/Q)*(z0-c))) - L = np.arctan2(B,A) + Q = np.sqrt(v ** 2 + w ** 2) + B = ((w / Q) * (y0 - b)) - ((v / Q) * (z0 - c)) + A = Q * (x0 - a) - u * (((v / Q) * (y0 - b)) + ((w / Q) * (z0 - c))) + C = u * (x0 - a) + Q * (((v / Q) * (y0 - b)) + ((w / Q) * (z0 - c))) + L = np.arctan2(B, A) # Determine the rotational angle to line-up point - cos_arg = (x-a-u*C)/(Q*np.sqrt(A**2+B**2)) + cos_arg = (x - a - u * C) / (Q * np.sqrt(A ** 2 + B ** 2)) if cos_arg > 1 or cos_arg < -1: if abs(cos_arg - 1) < .0001: cos_arg = 1 elif abs(cos_arg + 1) < .0001: cos_arg = -1 else: - raise Exception(f'Invalid arccos argument: {(x-a-u*C)/(Q*np.sqrt(A**2+B**2))}') + raise Exception(f'Invalid arccos argument: {(x - a - u * C) / (Q * np.sqrt(A ** 2 + B ** 2))}') arc_cos = np.arccos(cos_arg) angle = L + arc_cos - #Test point + # Test point new_pt = rotate_point_around_axis(initial_point, vertex, axis / np.linalg.norm(axis), angle) if abs(new_pt[1] - y) < 0.0001: return angle @@ -877,22 +878,22 @@ def find_rotation_angle(initial_point, vertex, rotated_point, axis): def compute_angle(coords): """ - Compute the angle between two vectors + Computes the angle between two vectors. Parameters ---------- - coords : np.array - Four points which define two vectors to compute the angle between + coords : numpy.ndarray + Four points which define two vectors to compute the angle between. - Return - ------ + Returns + ------- angle : int - Angle in radians between the two points + Angle in radians between the two points. """ vec1 = coords[0] - coords[1] vec2 = coords[2] - coords[1] - angle = np.dot(vec1, vec2)/(np.linalg.norm(vec1)*np.linalg.norm(vec2)) + angle = np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2)) return angle @@ -902,99 +903,98 @@ def add_or_swap(df_select, file_new, resnum, resname, vel, atom_num, orig_coor, Parameters ---------- - df_select : pd.DataFrame - - file_new : File + df_select : pandas.DataFrame + (To be added.) + file_new : file-like object The temporary file for the new GRO resnum : int - The residue number of the atom being added + The residue number of the atom being added. resname : str - The name of the residue which the atom being added belongs to + The name of the residue which the atom being added belongs to. vel : list of float - The velocity to assign to the atom being added + The velocity in the x, y, and z directions to assign to the atom being added. atom_num : int - The atom number to assign to the atom being added + The atom number to assign to the atom being added. orig_coords : list of float - The coordinates for the atom being added - skip_line : list of str - List of line numbers that should be skipped when we come across them while reading the file + The XYZ coordinates for the atom being added. + skip_line : list + A list of line numbers that should be skipped when we come across them while reading the file. R_o_D_num : list of str - list of atoms that need added + A list of atoms that need to be added. pick : int Index in the list to add now - Return - ------ - skip_line : list of int - Updated list of line numbers that should be skipped when we come across them while reading the file - R_o_D_num_new : - Updated list of atoms that need added + Returns + ------- + skip_line : list + Updated list of line numbers that should be skipped when we come across them while reading the file. + R_o_D_num_new : list + Updated list of atoms that need added. """ c = df_select.index.values.tolist() - if df_select.loc[c[0], 'Direction'] == 'miss': #Add atom if missing + + if df_select.loc[c[0], 'Direction'] == 'miss': # Add atom if missing add_atom(file_new, resnum, resname, df_select, vel, atom_num) - else: #Swap from dummy to real + else: # Swap from dummy to real line = dummy_real_swap(file_new, resnum, resname, df_select, vel, atom_num, orig_coor) #Add the dummy atom from A as a real atom in B and save the line so it can be skipped later skip_line.append(line) - R_o_D_num_new = np.delete(R_o_D_num, pick) #Atom no longer needs added + + R_o_D_num_new = np.delete(R_o_D_num, pick) # Atom no longer needs added + return skip_line, R_o_D_num_new def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, old_res_name, new_res_name, orig_coords, miss): """ - Write a new GRO file + Writes a new GRO file. Parameters ---------- - df_atom_swap : pd.DataFrame - Master dataframe containing info on the atoms which will change before and after the swap - swap : - Swapping direction + df_atom_swap : pandas.DataFrame + Master DataFrame containing info on the atoms which will change before and after the swap. + swap : str + The swapping direction. r_swap : - Reverse of the swapping direction + Reverse of the swapping direction. line_start : int - The line number where we start reading the file - orig_file : List of str - Pre-swap file to read from - new_file : File - Temporary file to write new coordinates + The line number where we start reading the file. + orig_file : list + List of strings containing the content of the pre-swap file to read from. + new_file : file-like object + Temporary file to write new coordinates. old_res_name : str - Residue name from before the swap + Residue name from before the swap. new_res_name : str - Residue name for after the swap - orig_coords : np.array - Coordinates for all atoms in the system before the swap - miss : list of str - Residues which are needed after the swap which are not present before the swap - - Return - ------ - None + Residue name for after the swap. + orig_coords : numpy.ndarray + Coordinates for all atoms in the system before the swap. + miss : list + Residues which are needed after the swap which are not present before the swap. """ - #Add vero velocity to all atoms + # Add vero velocity to all atoms vel = ['0.000', '0.000', '0.000\n'] atom_num_A, atom_num_B = 0, 0 skip_line = [] df_interest = df_atom_swap[((df_atom_swap['Swap'] == swap) & ((df_atom_swap['Direction'] == 'R2D') | (df_atom_swap['Direction'] == 'D2R'))) | ((df_atom_swap['Swap'] == r_swap) & (df_atom_swap['Direction'] == 'miss'))] - R_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) - D_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) - R_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) - D_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) + R_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 + D_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 + R_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 + D_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 R_C_num.sort() D_C_num.sort() R_H_num.sort() D_H_num.sort() for i in range(line_start, len(orig_file)-1): - #Some atoms are added out of order from file A and thus must be skipped when they come up + # Some atoms are added out of order from file A and thus must be skipped when they come up if i in skip_line: atom_num_A += 1 continue - #Iterate atom number to keep track of file progress + # Iterate atom number to keep track of file progress atom_num_B += 1 - #Process input lines + # Process input lines line, prev_line = process_line(orig_file, i) - #Seperate resname from resnumber + # Seperate resname from resnumber res_i = [*line[0]] prev_res_i = [*prev_line[0]] @@ -1002,11 +1002,11 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, resnum = "".join(res_i[0:int(len(res_i)-3)]) prev_resname = "".join(prev_res_i[-3:]) - #Determine how to write line based on contents - if resname != old_res_name and prev_resname != old_res_name: #Change only atom number and velocities if atoms not in residue of interest + # Determine how to write line based on contents + if resname != old_res_name and prev_resname != old_res_name: # Change only atom number and velocities if atoms not in residue of interest write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A]) - elif resname == old_res_name: #Atom manipulation required for acyl chain - #determine the number for the atom being written in the current line + elif resname == old_res_name: # Atom manipulation required for acyl chain + # determine the number for the atom being written in the current line if len(line[1]) > 1: current_num = int(line[1].strip('CVHDSON')) else: @@ -1016,77 +1016,77 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, atom_num_B -= 1 atom_num_A += 1 continue - elif (current_element == 'C' and current_num in D_C_num) or (current_element == 'H' and current_num in D_H_num): #Skip this line for now as we will add it in later + elif (current_element == 'C' and current_num in D_C_num) or (current_element == 'H' and current_num in D_H_num): # Skip this line for now as we will add it in later # noqa: E501 atom_num_B -= 1 atom_num_A += 1 continue - elif (current_element == 'C' and (current_num > R_C_num).any()): #We need to add an atom or move an atom to a new line position + elif (current_element == 'C' and (current_num > R_C_num).any()): # We need to add an atom or move an atom to a new line position while (current_num > R_C_num).any(): - #Either add atom or perform swap + # Either add atom or perform swap pick = np.where(current_num > R_C_num)[0][0] df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[pick])) & (df_interest['Element'] == 'C')] skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, pick) atom_num_B += 1 if i not in skip_line: write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif (len(R_C_num) != 0 and current_element == 'H'): #Add remaining real heavy atoms if all heavy atoms have been written + elif (len(R_C_num) != 0 and current_element == 'H'): # Add remaining real heavy atoms if all heavy atoms have been written while len(R_C_num) != 0: df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[0])) & (df_interest['Element'] == 'C')] skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, 0) atom_num_B += 1 if i not in skip_line: write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif current_element == 'H' and (current_num > R_H_num).any(): #Add real Hs in proper order + elif current_element == 'H' and (current_num > R_H_num).any(): # Add real Hs in proper order while (current_num > R_H_num).any(): - #Either add atom or perform swap + # Either add atom or perform swap pick = np.where(current_num > R_H_num)[0][0] df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[pick])) & (df_interest['Element'] == 'H')] skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, pick) atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif len(R_H_num) != 0 and (current_element == 'DC' or current_element == 'HV'): #Add remaining real Hs if all H atoms have been written + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif len(R_H_num) != 0 and (current_element == 'DC' or current_element == 'HV'): # Add remaining real Hs if all H atoms have been written # noqa: E501 while len(R_H_num) != 0: df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) atom_num_B += 1 if current_element == 'DC': while (current_num > D_C_num).any(): - #Either add atom or perform swap + # Either add atom or perform swap pick = np.where(current_num > D_C_num)[0][0] df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif current_element == 'DC' and (current_num > D_C_num).any(): #Add dummy Cs in correct order + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too + elif current_element == 'DC' and (current_num > D_C_num).any(): # Add dummy Cs in correct order while (current_num > D_C_num).any(): - #Either add atom or perform swap + # Either add atom or perform swap pick = np.where(current_num > D_C_num)[0][0] df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif len(D_C_num) != 0 and current_element == 'HV': #Add remaining dummy Cs after real Hs + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too + elif len(D_C_num) != 0 and current_element == 'HV': # Add remaining dummy Cs after real Hs while len(D_C_num) != 0: df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif current_element == 'HV' and (current_num > D_H_num).any(): #Add dummy Hs in proper order + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too + elif current_element == 'HV' and (current_num > D_H_num).any(): # Add dummy Hs in proper order while (current_num > D_H_num).any(): - #Either add atom or perform swap + # Either add atom or perform swap pick = np.where(current_num > D_H_num)[0][0] df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 else: write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) - elif resname != old_res_name and prev_resname == old_res_name: #Add dummy atoms at the end of the residue + elif resname != old_res_name and prev_resname == old_res_name: # Add dummy atoms at the end of the residue while len(R_H_num) != 0: df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] skip_line, R_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) @@ -1105,48 +1105,53 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, print(f'Warning line {i+1} not written') atom_num_A += 1 - if len(R_H_num) != 0: #If we hit end of coordinates without adding Hs add them now + if len(R_H_num) != 0: # If we hit end of coordinates without adding Hs add them now while len(R_H_num) != 0: atom_num_B += 1 df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) - if len(D_C_num) != 0: #If we hit end of coordinates without adding Cs add them now + if len(D_C_num) != 0: # If we hit end of coordinates without adding Cs add them now while len(D_C_num) != 0: atom_num_B += 1 df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) - if len(D_H_num) != 0: #If we hit end of coordinates without adding Hs add them now + if len(D_H_num) != 0: # If we hit end of coordinates without adding Hs add them now while len(D_H_num) != 0: atom_num_B += 1 df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) - #Add Box dimensions to file + # Add Box dimensions to file new_file.write(orig_file[-1]) new_file.close() def swap_name(init_atom_names, new_resname, df_top): """ - Determine the corresponding atom name in new molecule + Determines the corresponding atom name in new molecule Parameters ---------- - init_atom_names : list of str - Atom name in the original molecule + init_atom_names : list + A list of atom names in the original molecule. new_resname : str - Resname for the new molecule - df_top : pd.DataFrame - Dataframe containing the connectivity between the atoms in each molecule - - Return - ------ - new_atom_names : list of str - Atom names in the new molecule + Resname for the new molecule. + df_top : pandas.DataFrame + A pandas Dataframe containing the connectivity between the atoms in each molecule. + + Returns + ------- + new_atom_names : list + A list of atom names in the new molecule. """ #Find all atom names in new moleucle - new_names = set(df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 2'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 2'].to_list()) + new_names = set( + df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + + df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + + df_top[df_top['Resname'] == new_resname]['Connect 2'].to_list() + + df_top[df_top['Resname'] == new_resname]['Connect 2'].to_list() + ) new_atom_names = [] for atom in init_atom_names: if atom in new_names: @@ -1170,21 +1175,21 @@ def swap_name(init_atom_names, new_resname, df_top): def get_names(input): """ - Determine the names of all atoms in the topology and which lambda state for which they are dummy atoms + Determines the names of all atoms in the topology and which :math:`lambda` state for which they are dummy atoms. Parameters ---------- - input : List of str - Read the lines of the input topology + input : list + A list of strings containing the lines of the input topology. - Return - ------ + Returns + ------- start_line : int - The next line to start reading from the topology - atom_name : list of str - All atom names in the topology - state : list of int - The state that the atom is a dummy atom (lambda=0, lambda=1, or -1 if nevver dummy) + The next line to start reading from the topology. + atom_name : list + All atom names in the topology. + state : list + The state that the atom is a dummy atom (:math:`lambda=0`, :math:`lambda=1`, or -1 if nevver dummy). """ atom_section = False atom_name, state = [], [] @@ -1211,28 +1216,33 @@ def get_names(input): atom_section = True return start_line, atom_name, state -def deter_connection(main_only, other_only, main_name, other_name, df_top, main_state): +def determine_connection(main_only, other_only, main_name, other_name, df_top, main_state): """ - Determine the connectivity of the missing atoms in the topology + Determines the connectivity of the missing atoms in the topology. Parameters ---------- - main_only : list of str - All atoms which can be found only in the molecule of interest - other_only : list of str - All atoms which can be found only in the other molecule + main_only : list + All atoms which can be found only in the molecule of interest. + other_only : list + All atoms which can be found only in the other molecule. main_name : str - resname for the molecule of interest + resname for the molecule of interest. other_name : str - resname for the other molecule - df_top : pd.DataFrame - Connectivity of the atoms in each molecule - main_state : list of int - Which lambda state are each atom in the molecule of interest in the dummy state - Return - ------ - df : pd.DataFrame - Dataframes contains the missing atoms, the real anchor atom that connects them, and the atom to be used to determine the angle to place the missing atoms + The resname for the other molecule. + df_top : pandas.DataFrame + Connectivity of the atoms in each molecule. + main_state : list + Which :math:`lambda` state are each atom in the molecule of interest in the dummy state. + + Returns + ------- + df : pandas.DataFrame + A pandas Dataframes containing the following information: + + - The missing atoms, + - The real anchor atom that connects them + - The atom to be used to determine the angle to place the missing atoms """ miss, D2R, R2D = [],[],[] align_atom, angle_atom = [], [] @@ -1248,32 +1258,34 @@ def deter_connection(main_only, other_only, main_name, other_name, df_top, main_ else: miss.append(atom) df_select = df_top[df_top['Resname']==main_name] - #Seperate into each seperate functional group to be added + # Seperate into each seperate functional group to be added anchor_atoms = [] for m_atom in miss: - #Find what atoms the missing atom connects to + # Find what atoms the missing atom connects to connected_atoms = [] for a in df_select[df_select['Connect 1'] == m_atom]['Connect 2'].values: connected_atoms.append(a) for a in df_select[df_select['Connect 2'] == m_atom]['Connect 1'].values: connected_atoms.append(a) - #If the atom connects to non-missing atoms than keep these as anchors + # If the atom connects to non-missing atoms than keep these as anchors for a in connected_atoms: if a not in miss: anchor_atoms.append(a) - #Seperate missing atoms connected to each anchor + # Seperate missing atoms connected to each anchor miss_sep, align_atoms, angle_atoms = [],[],[] for anchor in anchor_atoms: miss_anchor = [] - #Which missing atoms are connected to the anchor + # Which missing atoms are connected to the anchor search = True included_atoms = [anchor] while search == True: - found_atoms = list(df_select[(df_select['Connect 1'].isin(included_atoms)) & (df_select['Connect 2'].isin(miss))]['Connect 2'].values) + list(df_select[(df_select['Connect 2'].isin(included_atoms)) & (df_select['Connect 1'].isin(miss))]['Connect 1'].values) + found_1 = list(df_select[(df_select['Connect 1'].isin(included_atoms)) & (df_select['Connect 2'].isin(miss))]['Connect 2'].values) # noqa: E501 + found_2 = list(df_select[(df_select['Connect 2'].isin(included_atoms)) & (df_select['Connect 1'].isin(miss))]['Connect 1'].values) # noqa: E501 + found_atoms = list_1 + list_2 if len(found_atoms) == 0: search = False else: @@ -1284,20 +1296,35 @@ def deter_connection(main_only, other_only, main_name, other_name, df_top, main_ included_atoms.remove(anchor) miss_sep.append(included_atoms) - #Find atoms connected to the anchor which are real in main state, but dummy when the atoms we are building are real - align_atom = list(df_select[(df_select['Connect 1'] == anchor) & (df_select['State 2'] != main_state) & (df_select['State 2'] != -1)]['Connect 2'].values) + list(df_select[(df_select['Connect 2'] == anchor) & (df_select['State 1'] != main_state) & (df_select['State 1'] != -1)]['Connect 1'].values) + # Find atoms connected to the anchor which are real in main state, but dummy when the atoms we are building are real + align_1 = list(df_select[(df_select['Connect 1'] == anchor) & (df_select['State 2'] != main_state) & (df_select['State 2'] != -1)]['Connect 2'].values) # noqa: E501 + align_2 = list(df_select[(df_select['Connect 2'] == anchor) & (df_select['State 1'] != main_state) & (df_select['State 1'] != -1)]['Connect 1'].values) # noqa: E501 + align_atom = align_1 + align_2 align_atoms.append(align_atom[0]) - #Find the atom to use for matching the angle to ensure that the dummy atom is added in the correct orientation + # Find the atom to use for matching the angle to ensure that the dummy atom is added in the correct orientation ignore_atoms = anchor_atoms + included_atoms + align_atom - angle_atom = list(df_select[(df_select['Connect 1'] == anchor) & (~df_select['Connect 2'].isin(ignore_atoms))]['Connect 2'].values) + list(df_select[(df_select['Connect 2'] == anchor) & (~df_select['Connect 1'].isin(ignore_atoms))]['Connect 1'].values) + angle_atom_1 = list(df_select[(df_select['Connect 1'] == anchor) & (~df_select['Connect 2'].isin(ignore_atoms))]['Connect 2'].values) # noqa: E501 + angle_atom_2 = list(df_select[(df_select['Connect 2'] == anchor) & (~df_select['Connect 1'].isin(ignore_atoms))]['Connect 1'].values) # noqa: E501 + angle_atom = angle_atom_1 + angle_atom_2 angle_atoms.append(angle_atom[-1]) #Now let's figure out what these atoms are called in the other molecule anchor_atoms_B = swap_name(anchor_atoms, other_name, df_top) angle_atoms_B = swap_name(angle_atoms, other_name, df_top) align_atoms_B = swap_name(align_atoms, other_name, df_top) - df = pd.DataFrame({'Swap A': main_name, 'Swap B': other_name, 'Anchor Atom Name A': anchor_atoms, 'Anchor Atom Name B': anchor_atoms_B, 'Alignment Atom A': align_atoms, 'Alignment Atom B': align_atoms_B, 'Angle Atom A': angle_atoms, 'Angle Atom B': angle_atoms_B}) + df = pd.DataFrame( + { + 'Swap A': main_name, + 'Swap B': other_name, + 'Anchor Atom Name A': anchor_atoms, + 'Anchor Atom Name B': anchor_atoms_B, + 'Alignment Atom A': align_atoms, + 'Alignment Atom B': align_atoms_B, + 'Angle Atom A': angle_atoms, + 'Angle Atom B': angle_atoms_B + } + ) miss_sep_reformat = [] for missing in miss_sep: if isinstance(missing, list): @@ -1313,19 +1340,20 @@ def deter_connection(main_only, other_only, main_name, other_name, df_top, main_ def read_top(file_name, resname): """ - Read the topology to find the file containing the molecule of interest + Reads the topology to find the file containing the molecule of interest Parameters ---------- file_name : str - Name for the topology file + Name for the topology file. resname : str - Name of the residue of interest we are searching for + Name of the residue of interest we are searching for. - Return - ------ - input_file : list of str - Contents of the topology file which contains the residue of interest + Returns + ------- + input_file : list + A list of strings containing the content of the topology file which contains the + residue of interest. """ input_file = open(file_name).readlines() itp_files = [] From 9179c62e3202fbc4ca8b8b3dafcb5bd7b3992464 Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 16:12:28 +0800 Subject: [PATCH 10/68] Fixed some linting errors --- ensemble_md/utils/coordinate_swap.py | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 1b47dae5..b3411dd6 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -25,7 +25,7 @@ def get_dimensions(file): """ Determines the dimensions of the cubic box based on the input GRO file. - + Parameters ---------- file : list @@ -43,6 +43,7 @@ def get_dimensions(file): dim_vector = [float(i) for i in box_raw] return dim_vector + def find_common(molA_file, molB_file, nameA, nameB): """ Determine the atoms which are common, which are switched between dummy and real atoms, @@ -97,6 +98,7 @@ def find_common(molA_file, molB_file, nameA, nameB): df.reset_index(inplace=True) return df + def find_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap): """ Determines which atoms are swapped between dummy and real states and which are missing. @@ -155,6 +157,7 @@ def find_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap) final_type.append('real') return pd.DataFrame({'Name': names, 'Atom Name Number': an_num, 'Element': elements, 'Direction': directions, 'Swap': swaps, 'File line': lines, 'Final Type': final_type}) + def fix_break(mol, resname, box_dimensions, atom_connect_all): """ Determines if there are any breaks across periodic boundary conditions in the residue of interest and @@ -224,6 +227,7 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): return mol + def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): """ Shifts the input trajectory across the periodic boundaries in 1D. @@ -268,6 +272,7 @@ def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): prev_shift_atom.append(broken_atom) return mol, fixed, prev_shift_atom + def perform_shift_2D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): """ Shifts the input trajectory across the periodic boundaries in 2D. @@ -316,6 +321,7 @@ def perform_shift_2D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): prev_shift_atom.append(broken_atom) return mol, fixed + def perform_shift_3D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): """ Shifts the input trajectory across the periodic boundaries in 3D @@ -361,6 +367,7 @@ def perform_shift_3D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): prev_shift_atom.append(broken_atom) return mol, fixed + def check_break(mol, atom_pairs): """ Determines whether a break is present between the atom pairs of interest. @@ -384,6 +391,7 @@ def check_break(mol, atom_pairs): broken_pairs.append(atom_pairs[i]) return broken_pairs + def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, df_swap): """ Gets coordinates for the missing atoms after the conformational swap @@ -506,6 +514,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, return df_atom_swap + def process_line(mol_file, i): """ Seperates the line by spaces and corrects for when the atom number merges the atom name @@ -540,6 +549,7 @@ def process_line(mol_file, i): return line, prev_line + def print_preamble(old_file, new_file, num_add_names, num_rm_names): """ Prints the preamble of the gro file before the atom specifications begin. @@ -570,6 +580,7 @@ def print_preamble(old_file, new_file, num_add_names, num_rm_names): break return line_start + def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB=None): """ Writes a line in the file in which some parameter needs to be changed. @@ -618,6 +629,7 @@ def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB= else: mol_new.write(raw_line) + def identify_res(mol_top, resname_options): """ Determines which of the potential residues of interest are in this molecule. @@ -640,6 +652,7 @@ def identify_res(mol_top, resname_options): break return resname + def add_atom(mol_new, resnum, resname, df, vel, atom_num): """ Adds a new atom to the GRO file. @@ -681,6 +694,7 @@ def add_atom(mol_new, resnum, resname, df, vel, atom_num): atom_num += 1 return atom_num + def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): """ Adds an atom to the file which is switching between dummy and real state or vice versa. @@ -738,6 +752,7 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) return line_num + def sep_merge(line): """ Seperates two GRO file columns which no longer have a space sperating them. @@ -762,6 +777,7 @@ def sep_merge(line): temp_line.append(n) return temp_line + def rotate_point_around_axis(point, vertex, axis, angle): """ Rotates a 3D point around an arbitrary axis. @@ -816,6 +832,7 @@ def rotate_point_around_axis(point, vertex, axis, angle): return rotated_point + def find_rotation_angle(initial_point, vertex, rotated_point, axis): """ Determines the angle of rotation around an arbitrary axis in 3D space. @@ -876,6 +893,7 @@ def find_rotation_angle(initial_point, vertex, rotated_point, axis): return angle + def compute_angle(coords): """ Computes the angle between two vectors. @@ -897,6 +915,7 @@ def compute_angle(coords): return angle + def add_or_swap(df_select, file_new, resnum, resname, vel, atom_num, orig_coor, skip_line, R_o_D_num, pick): """ Determine if the atom needs added or swapped between real and dummy state and then add the atom to the new file @@ -942,6 +961,7 @@ def add_or_swap(df_select, file_new, resnum, resname, vel, atom_num, orig_coor, return skip_line, R_o_D_num_new + def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, old_res_name, new_res_name, orig_coords, miss): """ Writes a new GRO file. @@ -1127,6 +1147,7 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, new_file.write(orig_file[-1]) new_file.close() + def swap_name(init_atom_names, new_resname, df_top): """ Determines the corresponding atom name in new molecule @@ -1173,6 +1194,7 @@ def swap_name(init_atom_names, new_resname, df_top): raise Exception(f'Compatible atom could not be found for {atom}') return new_atom_names + def get_names(input): """ Determines the names of all atoms in the topology and which :math:`lambda` state for which they are dummy atoms. @@ -1216,6 +1238,7 @@ def get_names(input): atom_section = True return start_line, atom_name, state + def determine_connection(main_only, other_only, main_name, other_name, df_top, main_state): """ Determines the connectivity of the missing atoms in the topology. @@ -1338,6 +1361,7 @@ def determine_connection(main_only, other_only, main_name, other_name, df_top, m return df + def read_top(file_name, resname): """ Reads the topology to find the file containing the molecule of interest From 7f2e09be9257491533a8cc30e8ec567d6b3294d4 Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 16:54:46 +0800 Subject: [PATCH 11/68] Fixed all the linting errors! Modified lint.yaml --- .github/workflows/lint.yaml | 1 + ensemble_md/utils/coordinate_swap.py | 453 ++++++++++++++++----------- 2 files changed, 266 insertions(+), 188 deletions(-) diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index cd9726c2..1c759f92 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -2,6 +2,7 @@ name: lint on: push: + pull_request: jobs: diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index b3411dd6..e70f8416 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -59,7 +59,7 @@ def find_common(molA_file, molB_file, nameA, nameB): The name of the residue being altered in molecule A. nameB : str The name of the residue being altered in molecule B. - + Returns ------- df : pandas.DataFrame @@ -68,18 +68,20 @@ def find_common(molA_file, molB_file, nameA, nameB): """ # Gather atom names from each file nameA_list, lineA_list, nameB_list, lineB_list = [], [], [], [] - for l, line in enumerate(molA_file): + for l, line in enumerate(molA_file): # noqa: E741 split_line = line.split(' ') - while("" in split_line): split_line.remove("") + while ("" in split_line): + split_line.remove("") if len(line[1]) > 5: split_line = sep_merge(split_line) if nameA in split_line[0]: nameA_list.append(split_line[1]) lineA_list.append(l) - for l, line in enumerate(molB_file): + for l, line in enumerate(molB_file): # noqa: E741 split_line = line.split(' ') - while("" in split_line): split_line.remove("") + while ("" in split_line): + split_line.remove("") if len(line[1]) > 5: split_line = sep_merge(split_line) if nameB in split_line[0]: @@ -126,7 +128,7 @@ def find_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap) - The atom element - Whether the atom is switching between dummy and real or missing, - The swap direction (same as input) - - Whether the final atom type is real or dummy + - Whether the final atom type is real or dummy """ # Determine atoms unique to either molecule names, an_num, elements, directions, swaps, lines, final_type = [], [], [], [], [], [], [] @@ -155,7 +157,20 @@ def find_R2D_D2R_miss(name_list, name_other_list, common_atoms, line_list, swap) final_type.append('dummy') else: final_type.append('real') - return pd.DataFrame({'Name': names, 'Atom Name Number': an_num, 'Element': elements, 'Direction': directions, 'Swap': swaps, 'File line': lines, 'Final Type': final_type}) + + df = pd.DataFrame( + { + 'Name': names, + 'Atom Name Number': an_num, + 'Element': elements, + 'Direction': directions, + 'Swap': swaps, + 'File line': lines, + 'Final Type': final_type + } + ) + + return df def fix_break(mol, resname, box_dimensions, atom_connect_all): @@ -174,22 +189,22 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): atom_connect_all : pandas.DataFrame A pandas DataFrame which contains the name of all atoms which are connected to one another in the residue of interest - + Returns ------- mol : :func:`mdtraj.Trajectory` object A :func:`mdtraj.Trajectory` object with all breaks in the necessary portions of the molecule fixed. """ mol_top = mol.topology - + atom_connect = [] for i, row in atom_connect_all.iterrows(): atom_connect.append([row['Connect 1'], row['Connect 2']]) - + atom_pairs = [] for atoms in atom_connect: atom_pairs.append(list(mol_top.select(f"resname {resname} and (name {atoms[0]} or name {atoms[1]})"))) - + # Find any broken bonds broken_pairs = check_break(mol, atom_pairs) @@ -199,14 +214,14 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): else: print('Fixing break') - iter = 0 # Keep track of while loop iterations + iter = 0 # Keep track of while loop iterations shift_atom = [] while len(broken_pairs) > 0: # Prevent infinite loop if iter > len(atom_pairs): - raise Exception('Break could not be fixed') + raise Exception('Break could not be fixed') iter += 1 - + # Fix this break mol, fixed, shift_atom = perform_shift_1D(mol, box_dimensions, broken_pairs, atom_pairs, shift_atom) if fixed: @@ -223,8 +238,8 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): broken_pairs = check_break(mol, atom_pairs) continue else: - raise Exception('Break could not be fixed') - + raise Exception('Break could not be fixed') + return mol @@ -257,13 +272,13 @@ def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): if broken_atom in prev_shift_atom: broken_atom = atom_pair[0] fixed = False - for x in range(3): #Loop through x, y, and z + for x in range(3): # Loop through x, y, and z for shift_dir in [1, -1]: - mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) # positive shift + mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] + (shift_dir[0] * box_dimensions[x]) # positive shift # noqa: E501 dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) - if dist_check > 0.2: # Didn't work so reverse and try again - mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] - (shift_dir[0] * box_dimensions[x]) - else: # Yay fixed break + if dist_check > 0.2: # Didn't work so reverse and try again + mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] - (shift_dir[0] * box_dimensions[x]) + else: # Yay fixed break fixed = True break if fixed: @@ -303,16 +318,16 @@ def perform_shift_2D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): broken_atom = atom_pair[0] fixed = False shift_combos = product([0, 1, 2], [0, 1, 2]) - for pair in shift_combos: # Loop through x, y, and z - for shift_dir in product([1, -1], [1,-1]): # Try all combos of shift direction + for pair in shift_combos: # Loop through x, y, and z + for shift_dir in product([1, -1], [1, -1]): # Try all combos of shift direction x, y = pair - mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] + (shift_dir[0] * box_dimensions[x]) # positive shift - mol.xyz[0,broken_atom,y] = mol.xyz[0,broken_atom,y] + (shift_dir[1] * box_dimensions[y]) + mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] + (shift_dir[0] * box_dimensions[x]) # positive shift # noqa: E501 + mol.xyz[0, broken_atom, y] = mol.xyz[0, broken_atom, y] + (shift_dir[1] * box_dimensions[y]) dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) - if dist_check > 0.2: # Didn't work so reverse and try again - mol.xyz[0,broken_atom,x] = mol.xyz[0,broken_atom,x] - (shift_dir[0] * box_dimensions[x]) - mol.xyz[0,broken_atom,y] = mol.xyz[0,broken_atom,y] - (shift_dir[1] * box_dimensions[y]) - else: # Yay fixed break + if dist_check > 0.2: # Didn't work so reverse and try again + mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] - (shift_dir[0] * box_dimensions[x]) + mol.xyz[0, broken_atom, y] = mol.xyz[0, broken_atom, y] - (shift_dir[1] * box_dimensions[y]) + else: # Yay fixed break fixed = True break if fixed: @@ -351,16 +366,16 @@ def perform_shift_3D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): if broken_atom in prev_shift_atom: broken_atom = atom_pair[0] fixed = False - for shift_dir in product([1, -1], [1,-1], [1, -1]): # Try all combos of shift direction - mol.xyz[0,broken_atom,0] = mol.xyz[0,broken_atom,0] + (shift_dir[0] * box_dimensions[0]) - mol.xyz[0,broken_atom,1] = mol.xyz[0,broken_atom,1] + (shift_dir[1] * box_dimensions[1]) - mol.xyz[0,broken_atom,2] = mol.xyz[0,broken_atom,2] + (shift_dir[2] * box_dimensions[2]) + for shift_dir in product([1, -1], [1, -1], [1, -1]): # Try all combos of shift direction + mol.xyz[0, broken_atom, 0] = mol.xyz[0, broken_atom, 0] + (shift_dir[0] * box_dimensions[0]) + mol.xyz[0, broken_atom, 1] = mol.xyz[0, broken_atom, 1] + (shift_dir[1] * box_dimensions[1]) + mol.xyz[0, broken_atom, 2] = mol.xyz[0, broken_atom, 2] + (shift_dir[2] * box_dimensions[2]) dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) - if dist_check > 0.2: # Didn't work so reverse and try again - mol.xyz[0,broken_atom,0] = mol.xyz[0,broken_atom,0] - (shift_dir[0] * box_dimensions[0]) - mol.xyz[0,broken_atom,1] = mol.xyz[0,broken_atom,1] - (shift_dir[1] * box_dimensions[1]) - mol.xyz[0,broken_atom,2] = mol.xyz[0,broken_atom,2] - (shift_dir[2] * box_dimensions[2]) - else: # Yay fixed break + if dist_check > 0.2: # Didn't work so reverse and try again + mol.xyz[0, broken_atom, 0] = mol.xyz[0, broken_atom, 0] - (shift_dir[0] * box_dimensions[0]) + mol.xyz[0, broken_atom, 1] = mol.xyz[0, broken_atom, 1] - (shift_dir[1] * box_dimensions[1]) + mol.xyz[0, broken_atom, 2] = mol.xyz[0, broken_atom, 2] - (shift_dir[2] * box_dimensions[2]) + else: # Yay fixed break fixed = True break if fixed: @@ -378,7 +393,7 @@ def check_break(mol, atom_pairs): Trajectory to examine for breaks. atom_pairs : int The atom number pairs which should be connected in the residue of interest. - + Returns ------- broken_pairs : int @@ -419,7 +434,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, The swapping direction. df_swap : pandas.DataFrame For each missing atoms. - + Returns ------- df_atom_swap : pandas.DataFrame @@ -430,10 +445,10 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, df_atom_swap['X Coordinates'] = np.NaN df_atom_swap['Y Coordinates'] = np.NaN df_atom_swap['Z Coordinates'] = np.NaN - + if len(df_swap.index) == 0: return df_atom_swap - + for i, row in df_swap.iterrows(): conn_align = [row['Anchor Atom Name A'], row['Alignment Atom A']] conn_ref = [row['Anchor Atom Name B'], row['Alignment Atom B']] @@ -446,8 +461,8 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, if atom not in align_select: align_select.append(atom) align_select.sort() - ref_select = mol_ref.topology.select(f"resname {name_ref} and (name {conn_ref[0]} or name {conn_ref[1]} or name {row['Angle Atom B']})") - + ref_select = mol_ref.topology.select(f"resname {name_ref} and (name {conn_ref[0]} or name {conn_ref[1]} or name {row['Angle Atom B']})") # noqa: E501 + mol_ref_select = copy.deepcopy(mol_ref.atom_slice(ref_select)) mol_align_select = copy.deepcopy(mol_align.atom_slice(align_select)) @@ -458,38 +473,42 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, conn1_ref = mol_ref_select.topology.select(f'resname {name_ref} and name {conn_ref[1]}')[0] # Step 1: Perform translation to align point 1 - shift_vec = mol_ref_select.xyz[0,conn0_ref,:] - mol_align_select.xyz[0,conn0_align,:] + shift_vec = mol_ref_select.xyz[0, conn0_ref, :] - mol_align_select.xyz[0, conn0_align, :] for a in range(mol_align_select.n_atoms): - mol_align_select.xyz[0,a,:] = mol_align_select.xyz[0,a,:] + shift_vec + mol_align_select.xyz[0, a, :] = mol_align_select.xyz[0, a, :] + shift_vec # Step 2: Perform rotational motion to line up point 2 - ref_vec = mol_ref_select.xyz[0,conn1_ref,:] - mol_ref_select.xyz[0,conn0_ref,:] # defing 0-1 vector in ref - align_vec = mol_align_select.xyz[0,conn1_align,:] - mol_ref_select.xyz[0,conn0_ref,:] # defing 0-1 vector in align - axis_rot = np.cross(ref_vec/np.linalg.norm(ref_vec), (align_vec/np.linalg.norm(align_vec))) # Perpendicular vector to ref and align vectors - theta = find_rotation_angle(mol_align_select.xyz[0,conn1_align,:], mol_ref_select.xyz[0,conn0_ref,:], mol_ref_select.xyz[0,conn1_ref,:], axis_rot) + ref_vec = mol_ref_select.xyz[0, conn1_ref, :] - mol_ref_select.xyz[0, conn0_ref, :] # defing 0-1 vector in ref # noqa: E501 + align_vec = mol_align_select.xyz[0, conn1_align, :] - mol_ref_select.xyz[0, conn0_ref, :] # defing 0-1 vector in align # noqa: E501 + axis_rot = np.cross(ref_vec/np.linalg.norm(ref_vec), (align_vec/np.linalg.norm(align_vec))) # Perpendicular vector to ref and align vectors # noqa: E501 + theta = find_rotation_angle(mol_align_select.xyz[0, conn1_align, :], mol_ref_select.xyz[0, conn0_ref, :], mol_ref_select.xyz[0, conn1_ref, :], axis_rot) # noqa: E501 for a in range(mol_align_select.n_atoms): if a != conn0_align: - mol_align_select.xyz[0,a,:] = rotate_point_around_axis(mol_align_select.xyz[0,a,:], mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta) + mol_align_select.xyz[0, a, :] = rotate_point_around_axis(mol_align_select.xyz[0, a, :], mol_ref_select.xyz[0, conn0_ref, :], axis_rot, theta) # noqa: E501 # Step 3: Rotate around 0-1 bond to get the correct angle for connecting atom - angle_atoms = [mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[0]}')[0], - mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0], - mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[2]}')[0]] - internal_angle = compute_angle([mol_align.xyz[0,angle_atoms[0],:], mol_align.xyz[0,angle_atoms[1],:], mol_align.xyz[0,angle_atoms[2],:]]) + angle_atoms = [ + mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[0]}')[0], + mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0], + mol_align.topology.select(f'resname {name_align} and name {geom_fix_select[2]}')[0] + ] + internal_angle = compute_angle([mol_align.xyz[0, angle_atoms[0], :], mol_align.xyz[0, angle_atoms[1], :], mol_align.xyz[0, angle_atoms[2], :]]) # noqa: E501 change_atoms = mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[0]}') - axis_rot = mol_align_select.xyz[0,conn0_align,:] - mol_align_select.xyz[0,conn1_align,:] + axis_rot = mol_align_select.xyz[0, conn0_align, :] - mol_align_select.xyz[0, conn1_align, :] # noqa: E501 axis_rot = axis_rot / np.linalg.norm(axis_rot) # Determine angle of rotation to get the right internal angle min_dev_angle = 3 - init_coords = mol_align_select.xyz[0,change_atoms,:][0].copy() - constant_coords = [mol_align_select.xyz[0,mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0],:], - mol_ref_select.xyz[0,mol_ref_select.topology.select(f"resname {name_ref} and name {row['Angle Atom B']}")[0],:]] - for theta in np.linspace(0, 2*np.pi, num=10): - new_coors = np.zeros((3,3)) - new_coors[0,:] = rotate_point_around_axis(init_coords, mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta) - new_coors[1:,:] = constant_coords + init_coords = mol_align_select.xyz[0, change_atoms, :][0].copy() + constant_coords = [ + mol_align_select.xyz[0, mol_align_select.topology.select(f'resname {name_align} and name {geom_fix_select[1]}')[0], :], # noqa: E501 + mol_ref_select.xyz[0, mol_ref_select.topology.select(f"resname {name_ref} and name {row['Angle Atom B']}")[0], :] # noqa: E501 + ] + for theta in np.linspace(0, 2 * np.pi, num=10): + new_coors = np.zeros((3, 3)) + new_coors[0, :] = rotate_point_around_axis(init_coords, mol_ref_select.xyz[0, conn0_ref, :], axis_rot, theta) # noqa: E501 + new_coors[1:, :] = constant_coords iangle = compute_angle(new_coors) if abs(iangle - internal_angle) < min_dev_angle: theta_min = theta @@ -499,7 +518,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, # Perform the rotation for a in range(mol_align_select.n_atoms): if a != conn0_align: - mol_align_select.xyz[0,a,:] = rotate_point_around_axis(mol_align_select.xyz[0,a,:], mol_ref_select.xyz[0,conn0_ref,:], axis_rot, theta_min) + mol_align_select.xyz[0, a, :] = rotate_point_around_axis(mol_align_select.xyz[0, a, :], mol_ref_select.xyz[0, conn0_ref, :], axis_rot, theta_min) # noqa: E501 # Add coordinates to df for r in range(len(df_atom_swap.index)): @@ -507,11 +526,11 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, for name in miss_names_select: if df_atom_swap.iloc[r]['Name'] == name: a = mol_align_select.topology.select(f'name {name}') - df_atom_swap.at[r, 'X Coordinates'] = mol_align_select.xyz[0,a,0] - df_atom_swap.at[r, 'Y Coordinates'] = mol_align_select.xyz[0,a,1] - df_atom_swap.at[r, 'Z Coordinates'] = mol_align_select.xyz[0,a,2] + df_atom_swap.at[r, 'X Coordinates'] = mol_align_select.xyz[0, a, 0] + df_atom_swap.at[r, 'Y Coordinates'] = mol_align_select.xyz[0, a, 1] + df_atom_swap.at[r, 'Z Coordinates'] = mol_align_select.xyz[0, a, 2] continue - + return df_atom_swap @@ -525,7 +544,7 @@ def process_line(mol_file, i): A list of strings containing the lines of the input GRO file. i : int The index the line in the file. - + Returns ------- line : str @@ -535,12 +554,14 @@ def process_line(mol_file, i): """ # Load previous line to determine identity of previous atom prev_line = mol_file[i-1].split(' ') - while("" in prev_line): prev_line.remove("") - + while ("" in prev_line): + prev_line.remove("") + # Load current line in file and seperate line = mol_file[i].split(' ') - while("" in line): line.remove("") - + while ("" in line): + line.remove("") + # Control for atom name and atom number merging if len(line[1]) > 5: line = sep_merge(line) @@ -606,13 +627,31 @@ def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB= """ coor = ["{:.7f}".format(coor[0]), "{:.7f}".format(coor[1]), "{:.7f}".format(coor[2])] if len(line) == 9: - if nameB == None: - mol_new.write(line[0].rjust(8, ' ') + line[1].rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + - vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + if nameB is None: + mol_new.write( + line[0].rjust(8, ' ') + + line[1].rjust(7, ' ') + + str(atom_num).rjust(5, ' ') + + str(coor[0]).rjust(12, ' ') + + str(coor[1]).rjust(12, ' ') + + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + + vel[1].rjust(8, ' ') + + vel[2].rjust(9, ' ') + ) else: - mol_new.write(f'{resnum}{nameB}'.rjust(8, ' ') + line[1].rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + - vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) - elif len(line) == 8: #Atom name and number blend together because of number size so they need seperated + mol_new.write( + f'{resnum}{nameB}'.rjust(8, ' ') + + line[1].rjust(7, ' ') + + str(atom_num).rjust(5, ' ') + + str(coor[0]).rjust(12, ' ') + + str(coor[1]).rjust(12, ' ') + + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + + vel[1].rjust(8, ' ') + + vel[2].rjust(9, ' ') + ) + elif len(line) == 8: # Atom name and number blend together because of number size so they need seperated if 'HW1' in line[1]: atom_name = 'HW1' elif 'HW2' in line[1]: @@ -620,12 +659,30 @@ def write_line(mol_new, raw_line, line, atom_num, vel, coor, resnum=None, nameB= else: atom_name = re.sub(r'[0-9]', '', line[1]) - if nameB == None: - mol_new.write(line[0].rjust(8, ' ') + atom_name.rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + - vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + if nameB is None: + mol_new.write( + line[0].rjust(8, ' ') + + atom_name.rjust(7, ' ') + + str(atom_num).rjust(5, ' ') + + str(coor[0]).rjust(12, ' ') + + str(coor[1]).rjust(12, ' ') + + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + + vel[1].rjust(8, ' ') + + vel[2].rjust(9, ' ') + ) else: - mol_new.write(f'{resnum}{nameB}'.rjust(8, ' ') + atom_name.rjust(7,' ') + str(atom_num).rjust(5, ' ') + str(coor[0]).rjust(12, ' ') + str(coor[1]).rjust(12, ' ') + str(coor[2]).rjust(12, ' ') + - vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + mol_new.write( + f'{resnum}{nameB}'.rjust(8, ' ') + + atom_name.rjust(7, ' ') + + str(atom_num).rjust(5, ' ') + + str(coor[0]).rjust(12, ' ') + + str(coor[1]).rjust(12, ' ') + + str(coor[2]).rjust(12, ' ') + + vel[0].rjust(8, ' ') + + vel[1].rjust(8, ' ') + + vel[2].rjust(9, ' ') + ) else: mol_new.write(raw_line) @@ -650,6 +707,7 @@ def identify_res(mol_top, resname_options): if len(mol_top.select(f"resname {name}")) != 0: resname = name break + return resname @@ -689,9 +747,19 @@ def add_atom(mol_new, resnum, resname, df, vel, atom_num): z_temp = np.round(z_init[0], decimals=7) z = format(z_temp, '.7f') # Write line for new atom - mol_new.write(f'{resnum}{resname}'.rjust(8, ' ') + name_new.rjust(7, ' ') + str(atom_num).rjust(5, ' ') + str(x).rjust(12, ' ') + str(y).rjust(12, ' ') + - str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) - atom_num += 1 + mol_new.write( + f'{resnum}{resname}'.rjust(8, ' ') + + name_new.rjust(7, ' ') + + str(atom_num).rjust(5, ' ') + + str(x).rjust(12, ' ') + + str(y).rjust(12, ' ') + + str(z).rjust(12, ' ') + + vel[0].rjust(8, ' ') + + vel[1].rjust(8, ' ') + + vel[2].rjust(9, ' ') + ) + atom_num += 1 + return atom_num @@ -715,7 +783,7 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): The atom number to assign to the atom being added. orig_coords : list The XYZ coordinates for the atom being added. - + Returns ------- line_num : int @@ -724,7 +792,7 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): """ # Get the name for the atom we are writting name_orig = df['Name'].to_list()[0] - + # Determine the new atom name based on whether the new atom should be real or dummy final_state = df['Final Type'].to_list()[0] if final_state == 'dummy': @@ -748,8 +816,17 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords): x, y, z = ["{:.7f}".format(orig_coor[0]), "{:.7f}".format(orig_coor[1]), "{:.7f}".format(orig_coor[2])] # Write line - mol_new.write(f'{resnum}{resname}'.rjust(8, ' ') + name_new.rjust(7, ' ') + str(atom_num).rjust(5, ' ') + str(x).rjust(12, ' ') + str(y).rjust(12, ' ') + - str(z).rjust(12, ' ') + vel[0].rjust(8, ' ') + vel[1].rjust(8, ' ') + vel[2].rjust(9, ' ')) + mol_new.write( + f'{resnum}{resname}'.rjust(8, ' ') + + name_new.rjust(7, ' ') + + str(atom_num).rjust(5, ' ') + + str(x).rjust(12, ' ') + + str(y).rjust(12, ' ') + + str(z).rjust(12, ' ') + + vel[0].rjust(8, ' ') + + vel[1].rjust(8, ' ') + + vel[2].rjust(9, ' ') + ) return line_num @@ -761,7 +838,7 @@ def sep_merge(line): ---------- line : list of str The line contents seperated by spaces. - + Returns ------- temp_line : list @@ -781,7 +858,7 @@ def sep_merge(line): def rotate_point_around_axis(point, vertex, axis, angle): """ Rotates a 3D point around an arbitrary axis. - + Parameters ---------- point : numpy.ndarray @@ -800,18 +877,18 @@ def rotate_point_around_axis(point, vertex, axis, angle): """ # Transformation matrix to origin T = np.eye(4) - T[0:3,3] = -vertex + T[0:3, 3] = -vertex # Reverse the transformation to origin T_r = np.eye(4) - T_r[0:3,3] = vertex + T_r[0:3, 3] = vertex # Normalize rotational axis axis = axis / np.linalg.norm(axis) a, b, c = axis - d = np.sqrt(b**2+c**2) + d = np.sqrt(b ** 2 + c ** 2) # Rotation about the x axis - Rx = [[1, 0, 0, 0], [0, c/d, -b/d, 0], [0, b/d, c/d, 0], [0, 0, 0, 1]] - Rx_r = [[1, 0, 0, 0], [0, c/d, b/d, 0], [0, -b/d, c/d, 0], [0, 0, 0, 1]] + Rx = [[1, 0, 0, 0], [0, c / d, -b / d, 0], [0, b / d, c / d, 0], [0, 0, 0, 1]] + Rx_r = [[1, 0, 0, 0], [0, c / d, b / d, 0], [0, -b / d, c / d, 0], [0, 0, 0, 1]] # Rotation about the y axis Ry = [[d, 0, -a, 0], [0, 1, 0, 0], [a, 0, d, 0], [0, 0, 0, 1]] @@ -820,13 +897,13 @@ def rotate_point_around_axis(point, vertex, axis, angle): # Rotation about the z axis Rz = [[np.cos(angle), np.sin(angle), 0, 0], [-np.sin(angle), np.cos(angle), 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]] - # Initial position + # Initial position x0, y0, z0 = point init_arry = [x0, y0, z0, 1] # Perform the transofmration final_arry = T_r@Rx_r@Ry_r@Rz@Ry@Rx@T@init_arry - + # Get the corrdinates for the rotated point rotated_point = final_arry[0:3] @@ -836,7 +913,7 @@ def rotate_point_around_axis(point, vertex, axis, angle): def find_rotation_angle(initial_point, vertex, rotated_point, axis): """ Determines the angle of rotation around an arbitrary axis in 3D space. - + Parameters ---------- initial_point: numpy.ndarray @@ -845,7 +922,7 @@ def find_rotation_angle(initial_point, vertex, rotated_point, axis): The rotated point coordinates. axis: A numpy array The axis of rotation. - + Returns ------- angle: int @@ -855,7 +932,7 @@ def find_rotation_angle(initial_point, vertex, rotated_point, axis): u, v, w = axis / np.linalg.norm(axis) x0, y0, z0 = initial_point a, b, c = vertex - + # Determine the rotated point with the same bond length as the initial point rotated_point_axis = rotated_point - vertex norm_rot_point_vec = rotated_point_axis / np.linalg.norm(rotated_point_axis) @@ -950,19 +1027,19 @@ def add_or_swap(df_select, file_new, resnum, resname, vel, atom_num, orig_coor, Updated list of atoms that need added. """ c = df_select.index.values.tolist() - - if df_select.loc[c[0], 'Direction'] == 'miss': # Add atom if missing + + if df_select.loc[c[0], 'Direction'] == 'miss': # Add atom if missing add_atom(file_new, resnum, resname, df_select, vel, atom_num) - else: # Swap from dummy to real - line = dummy_real_swap(file_new, resnum, resname, df_select, vel, atom_num, orig_coor) #Add the dummy atom from A as a real atom in B and save the line so it can be skipped later + else: # Swap from dummy to real + line = dummy_real_swap(file_new, resnum, resname, df_select, vel, atom_num, orig_coor) # Add the dummy atom from A as a real atom in B and save the line so it can be skipped later # noqa: E501 skip_line.append(line) - - R_o_D_num_new = np.delete(R_o_D_num, pick) # Atom no longer needs added - + + R_o_D_num_new = np.delete(R_o_D_num, pick) # Atom no longer needs added + return skip_line, R_o_D_num_new -def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, old_res_name, new_res_name, orig_coords, miss): +def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, old_res_name, new_res_name, orig_coords, miss): # noqa: E501 """ Writes a new GRO file. @@ -972,7 +1049,7 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, Master DataFrame containing info on the atoms which will change before and after the swap. swap : str The swapping direction. - r_swap : + r_swap : str Reverse of the swapping direction. line_start : int The line number where we start reading the file. @@ -994,7 +1071,7 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, atom_num_A, atom_num_B = 0, 0 skip_line = [] - df_interest = df_atom_swap[((df_atom_swap['Swap'] == swap) & ((df_atom_swap['Direction'] == 'R2D') | (df_atom_swap['Direction'] == 'D2R'))) | ((df_atom_swap['Swap'] == r_swap) & (df_atom_swap['Direction'] == 'miss'))] + df_interest = df_atom_swap[((df_atom_swap['Swap'] == swap) & ((df_atom_swap['Direction'] == 'R2D') | (df_atom_swap['Direction'] == 'D2R'))) | ((df_atom_swap['Swap'] == r_swap) & (df_atom_swap['Direction'] == 'miss'))] # noqa: E501 R_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 D_C_num = df_interest[(df_interest['Element'] == 'C') & ((df_interest['Direction'] == 'R2D') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'dummy')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 R_H_num = df_interest[(df_interest['Element'] == 'H') & ((df_interest['Direction'] == 'D2R') | ((df_interest['Direction'] == 'miss') & (df_interest['Final Type'] == 'real')))]['Atom Name Number'].to_numpy(dtype=int) # noqa: E501 @@ -1010,7 +1087,7 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, continue # Iterate atom number to keep track of file progress atom_num_B += 1 - + # Process input lines line, prev_line = process_line(orig_file, i) @@ -1021,128 +1098,128 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, resname = "".join(res_i[-3:]) resnum = "".join(res_i[0:int(len(res_i)-3)]) prev_resname = "".join(prev_res_i[-3:]) - + # Determine how to write line based on contents - if resname != old_res_name and prev_resname != old_res_name: # Change only atom number and velocities if atoms not in residue of interest + if resname != old_res_name and prev_resname != old_res_name: # Change only atom number and velocities if atoms not in residue of interest # noqa: E501 write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A]) - elif resname == old_res_name: # Atom manipulation required for acyl chain + elif resname == old_res_name: # Atom manipulation required for acyl chain # determine the number for the atom being written in the current line if len(line[1]) > 1: current_num = int(line[1].strip('CVHDSON')) else: current_num = np.NaN current_element = line[1].strip('0123456789') - if line[1] in miss: #Do not write coordinates if atoms are not present in B + if line[1] in miss: # Do not write coordinates if atoms are not present in B atom_num_B -= 1 atom_num_A += 1 continue - elif (current_element == 'C' and current_num in D_C_num) or (current_element == 'H' and current_num in D_H_num): # Skip this line for now as we will add it in later # noqa: E501 + elif (current_element == 'C' and current_num in D_C_num) or (current_element == 'H' and current_num in D_H_num): # Skip this line for now as we will add it in later # noqa: E501 atom_num_B -= 1 atom_num_A += 1 continue - elif (current_element == 'C' and (current_num > R_C_num).any()): # We need to add an atom or move an atom to a new line position + elif (current_element == 'C' and (current_num > R_C_num).any()): # We need to add an atom or move an atom to a new line position # noqa: E501 while (current_num > R_C_num).any(): # Either add atom or perform swap pick = np.where(current_num > R_C_num)[0][0] - df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[pick])) & (df_interest['Element'] == 'C')] - skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, pick) + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[pick])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, pick) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif (len(R_C_num) != 0 and current_element == 'H'): # Add remaining real heavy atoms if all heavy atoms have been written + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif (len(R_C_num) != 0 and current_element == 'H'): # Add remaining real heavy atoms if all heavy atoms have been written # noqa: E501 while len(R_C_num) != 0: - df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[0])) & (df_interest['Element'] == 'C')] - skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_C_num[0])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, R_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_C_num, 0) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) #Add this current line too - elif current_element == 'H' and (current_num > R_H_num).any(): # Add real Hs in proper order + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif current_element == 'H' and (current_num > R_H_num).any(): # Add real Hs in proper order while (current_num > R_H_num).any(): # Either add atom or perform swap pick = np.where(current_num > R_H_num)[0][0] - df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[pick])) & (df_interest['Element'] == 'H')] - skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, pick) + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[pick])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, pick) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 - elif len(R_H_num) != 0 and (current_element == 'DC' or current_element == 'HV'): # Add remaining real Hs if all H atoms have been written # noqa: E501 + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif len(R_H_num) != 0 and (current_element == 'DC' or current_element == 'HV'): # Add remaining real Hs if all H atoms have been written # noqa: E501 while len(R_H_num) != 0: - df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] - skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) # noqa: E501 atom_num_B += 1 if current_element == 'DC': while (current_num > D_C_num).any(): # Either add atom or perform swap pick = np.where(current_num > D_C_num)[0][0] - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] - skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too - elif current_element == 'DC' and (current_num > D_C_num).any(): # Add dummy Cs in correct order + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif current_element == 'DC' and (current_num > D_C_num).any(): # Add dummy Cs in correct order # noqa: E501 while (current_num > D_C_num).any(): # Either add atom or perform swap pick = np.where(current_num > D_C_num)[0][0] - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] - skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[pick])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, pick) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too - elif len(D_C_num) != 0 and current_element == 'HV': # Add remaining dummy Cs after real Hs + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif len(D_C_num) != 0 and current_element == 'HV': # Add remaining dummy Cs after real Hs while len(D_C_num) != 0: - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] - skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too - elif current_element == 'HV' and (current_num > D_H_num).any(): # Add dummy Hs in proper order + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + elif current_element == 'HV' and (current_num > D_H_num).any(): # Add dummy Hs in proper order # noqa: E501 while (current_num > D_H_num).any(): # Either add atom or perform swap pick = np.where(current_num > D_H_num)[0][0] - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] - skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) # noqa: E501 atom_num_B += 1 if i not in skip_line: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # Add this current line too # noqa: E501 else: - write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) - elif resname != old_res_name and prev_resname == old_res_name: # Add dummy atoms at the end of the residue + write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name) # noqa: E501 + elif resname != old_res_name and prev_resname == old_res_name: # Add dummy atoms at the end of the residue while len(R_H_num) != 0: - df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] - skip_line, R_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, R_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) # noqa: E501 atom_num_B += 1 while len(D_C_num) != 0: - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] - skip_line, D_C_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, D_C_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) # noqa: E501 atom_num_B += 1 while len(D_H_num) != 0: - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] - skip_line, D_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, D_H_num = add_or_swap(df_select, new_file, int(resnum)-1, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) # noqa: E501 atom_num_B += 1 line, prev_line = process_line(orig_file, i) write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A]) else: print(f'Warning line {i+1} not written') atom_num_A += 1 - - if len(R_H_num) != 0: # If we hit end of coordinates without adding Hs add them now + + if len(R_H_num) != 0: # If we hit end of coordinates without adding Hs add them now while len(R_H_num) != 0: atom_num_B += 1 - df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] - skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(R_H_num[0])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, R_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, R_H_num, 0) # noqa: E501 - if len(D_C_num) != 0: # If we hit end of coordinates without adding Cs add them now + if len(D_C_num) != 0: # If we hit end of coordinates without adding Cs add them now while len(D_C_num) != 0: atom_num_B += 1 - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] - skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_C_num[0])) & (df_interest['Element'] == 'C')] # noqa: E501 + skip_line, D_C_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_C_num, 0) # noqa: E501 - if len(D_H_num) != 0: # If we hit end of coordinates without adding Hs add them now + if len(D_H_num) != 0: # If we hit end of coordinates without adding Hs add them now while len(D_H_num) != 0: atom_num_B += 1 - df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] - skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) - + df_select = df_interest[(df_interest['Atom Name Number'] == str(D_H_num[0])) & (df_interest['Element'] == 'H')] # noqa: E501 + skip_line, D_H_num = add_or_swap(df_select, new_file, resnum, new_res_name, vel, atom_num_B, orig_coords, skip_line, D_H_num, 0) # noqa: E501 + # Add Box dimensions to file new_file.write(orig_file[-1]) new_file.close() @@ -1166,7 +1243,7 @@ def swap_name(init_atom_names, new_resname, df_top): new_atom_names : list A list of atom names in the new molecule. """ - #Find all atom names in new moleucle + # Find all atom names in new moleucle new_names = set( df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + df_top[df_top['Resname'] == new_resname]['Connect 1'].to_list() + @@ -1215,7 +1292,7 @@ def get_names(input): """ atom_section = False atom_name, state = [], [] - for l, line in enumerate(input): + for l, line in enumerate(input): # noqa: E741 if atom_section: line_sep = line.split(' ') if line_sep[0] == ';': @@ -1257,33 +1334,33 @@ def determine_connection(main_only, other_only, main_name, other_name, df_top, m Connectivity of the atoms in each molecule. main_state : list Which :math:`lambda` state are each atom in the molecule of interest in the dummy state. - + Returns ------- df : pandas.DataFrame A pandas Dataframes containing the following information: - - The missing atoms, + - The missing atoms - The real anchor atom that connects them - The atom to be used to determine the angle to place the missing atoms """ - miss, D2R, R2D = [],[],[] + miss, D2R, R2D = [], [], [] align_atom, angle_atom = [], [] for atom in main_only: element = atom.strip('0123456789') real_element = element.strip('DV') num = atom.strip('ABCDEFGHIJKLMNOPQRSTUVWXYZ') - + if f'D{atom}' in other_only or f'{element}V{num}' in other_only: D2R.append(atom) elif f'{real_element}{num}' in other_only: R2D.append(atom) else: miss.append(atom) - df_select = df_top[df_top['Resname']==main_name] + df_select = df_top[df_top['Resname'] == main_name] # Seperate into each seperate functional group to be added - anchor_atoms = [] - + anchor_atoms = [] + for m_atom in miss: # Find what atoms the missing atom connects to connected_atoms = [] @@ -1291,24 +1368,24 @@ def determine_connection(main_only, other_only, main_name, other_name, df_top, m connected_atoms.append(a) for a in df_select[df_select['Connect 2'] == m_atom]['Connect 1'].values: connected_atoms.append(a) - + # If the atom connects to non-missing atoms than keep these as anchors for a in connected_atoms: if a not in miss: anchor_atoms.append(a) # Seperate missing atoms connected to each anchor - miss_sep, align_atoms, angle_atoms = [],[],[] + miss_sep, align_atoms, angle_atoms = [], [], [] for anchor in anchor_atoms: miss_anchor = [] # Which missing atoms are connected to the anchor search = True included_atoms = [anchor] - while search == True: + while search is True: found_1 = list(df_select[(df_select['Connect 1'].isin(included_atoms)) & (df_select['Connect 2'].isin(miss))]['Connect 2'].values) # noqa: E501 found_2 = list(df_select[(df_select['Connect 2'].isin(included_atoms)) & (df_select['Connect 1'].isin(miss))]['Connect 1'].values) # noqa: E501 - found_atoms = list_1 + list_2 + found_atoms = found_1 + found_2 if len(found_atoms) == 0: search = False else: @@ -1318,8 +1395,8 @@ def determine_connection(main_only, other_only, main_name, other_name, df_top, m miss.remove(atom) included_atoms.remove(anchor) miss_sep.append(included_atoms) - - # Find atoms connected to the anchor which are real in main state, but dummy when the atoms we are building are real + + # Find atoms connected to the anchor which are real in main state, but dummy when the atoms we are building are real # noqa: E501 align_1 = list(df_select[(df_select['Connect 1'] == anchor) & (df_select['State 2'] != main_state) & (df_select['State 2'] != -1)]['Connect 2'].values) # noqa: E501 align_2 = list(df_select[(df_select['Connect 2'] == anchor) & (df_select['State 1'] != main_state) & (df_select['State 1'] != -1)]['Connect 1'].values) # noqa: E501 align_atom = align_1 + align_2 @@ -1331,8 +1408,8 @@ def determine_connection(main_only, other_only, main_name, other_name, df_top, m angle_atom_2 = list(df_select[(df_select['Connect 2'] == anchor) & (~df_select['Connect 1'].isin(ignore_atoms))]['Connect 1'].values) # noqa: E501 angle_atom = angle_atom_1 + angle_atom_2 angle_atoms.append(angle_atom[-1]) - - #Now let's figure out what these atoms are called in the other molecule + + # Now let's figure out what these atoms are called in the other molecule anchor_atoms_B = swap_name(anchor_atoms, other_name, df_top) angle_atoms_B = swap_name(angle_atoms, other_name, df_top) align_atoms_B = swap_name(align_atoms, other_name, df_top) @@ -1390,13 +1467,13 @@ def read_top(file_name, resname): atom_sect = False line_sep = line.split(' ') while '' in line_sep: - line_sep.remove('') + line_sep.remove('') if len(line_sep) > 4 and line_sep[3] == resname: return input_file if '#include' in line: line_sep = line.split(' ') while '' in line_sep: - line_sep.remove('') + line_sep.remove('') itp_files.append(line_sep[-1].strip('\n""')) for file in itp_files: if os.path.exists(file): @@ -1410,7 +1487,7 @@ def read_top(file_name, resname): break line_sep = line.split(' ') while '' in line_sep: - line_sep.remove('') + line_sep.remove('') if len(line_sep) > 4 and line_sep[3] == resname: return input_file raise Exception(f'Residue {resname} can not be found in {file_name}') From e70770cf53d5bf8d289b44b51074b7150c4748cb Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 18:16:11 +0800 Subject: [PATCH 12/68] Added simple unit tests for get_dimensions and compute_angle in coordinate_swap --- ensemble_md/tests/test_coordinate_swap.py | 55 +++++++++++++++++++++++ ensemble_md/utils/coordinate_swap.py | 4 +- 2 files changed, 57 insertions(+), 2 deletions(-) create mode 100644 ensemble_md/tests/test_coordinate_swap.py diff --git a/ensemble_md/tests/test_coordinate_swap.py b/ensemble_md/tests/test_coordinate_swap.py new file mode 100644 index 00000000..2bd7540e --- /dev/null +++ b/ensemble_md/tests/test_coordinate_swap.py @@ -0,0 +1,55 @@ +#################################################################### +# # +# ensemble_md, # +# a python package for running GROMACS simulation ensembles # +# # +# Written by Wei-Tse Hsu # +# Copyright (c) 2022 University of Colorado Boulder # +# # +#################################################################### +""" +Unit tests for the module test_coordainte_swap.py. +""" +import os +import numpy as np +from ensemble_md.utils import coordinate_swap + +current_path = os.path.dirname(os.path.abspath(__file__)) +input_path = os.path.join(current_path, "data") + + +def test_get_dimensions(): + gro = os.path.join(input_path, 'sys.gro') + f = open(gro, 'r') + lines = f.readlines() + f.close() + vec = coordinate_swap.get_dimensions(lines) + assert vec == [3.32017, 3.32017, 2.34772, 0.00000, 0.00000, 0.00000, 0.00000, 1.66009, 1.66009] + + # Write a flat file with cubic box dimensions + f = open('test.gro', 'w') + f.write('test\n') + f.write(' 1.00000 2.00000 3.00000\n') + f.close() + + f = open('test.gro', 'r') + lines = f.readlines() + f.close() + vec = coordinate_swap.get_dimensions(lines) + assert vec == [1.0, 2.0, 3.0] + + os.remove('test.gro') + + +def test_compute_angle(): + coords_1 = [ + np.array([0.0, 0.0, 0.0]), + np.array([1.0, 0.0, 0.0]), + np.array([0.0, 1.0, 0.0]) + ] + coords_2 = coords_1[-1::-1] + coords_3 = [coords_1[1], coords_1[0], coords_1[2]] + + assert np.isclose(coordinate_swap.compute_angle(coords_1), np.sqrt(2) / 2) + assert np.isclose(coordinate_swap.compute_angle(coords_2), np.sqrt(2) / 2) + assert np.isclose(coordinate_swap.compute_angle(coords_3), 0) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index e70f8416..a6b0a116 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -977,8 +977,8 @@ def compute_angle(coords): Parameters ---------- - coords : numpy.ndarray - Four points which define two vectors to compute the angle between. + coords : list + A list of numpy arrays containing the XYZ coordinates of 3 points, for which the angle 1-2-3 is to be computed. Returns ------- From c5cbd33fc21c4766c7194d46e27f688ca142bf65 Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 11 Sep 2024 18:36:15 +0800 Subject: [PATCH 13/68] Tweaked the docstrings of the new functions in replica_exchange_EE.py --- ensemble_md/replica_exchange_EE.py | 36 +++++++++--------------------- 1 file changed, 11 insertions(+), 25 deletions(-) diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py index fb63993d..91ee7765 100644 --- a/ensemble_md/replica_exchange_EE.py +++ b/ensemble_md/replica_exchange_EE.py @@ -19,6 +19,8 @@ import warnings import importlib import subprocess +import mdtraj as md +import pandas as pd import numpy as np from mpi4py import MPI from itertools import combinations @@ -1511,24 +1513,17 @@ def run_REXEE(self, n, swap_pattern=None): # rank 3 that has not been generated, which will lead to an I/O error. comm.barrier() - def default_coords_fn(self, molA_file_name: str, molB_file_name: str): + def default_coords_fn(self, molA_file_name, molB_file_name): """ - Swap coordinates between two GRO files + Swaps coordinates between two GRO files. Parameters ---------- molA_file_name : str - GRO file name for the moleucle to be swapped + GRO file name for the moleucle to be swapped. molB_file_name : str - GRO file name for the other moleucle to be swapped - Return - ------ - None + GRO file name for the other moleucle to be swapped. """ - # Step 1: Load necessary files - import mdtraj as md - import pandas as pd - # Determine name for transformed residue molA_dir = molA_file_name.rsplit('/', 1)[0] + '/' molB_dir = molB_file_name.rsplit('/', 1)[0] + '/' @@ -1541,7 +1536,7 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): connection_map = pd.read_csv('residue_connect.csv') swap_map = pd.read_csv('residue_swap_map.csv') - # Step 2: Read the GRO input coordinate files and open temporary Output files + # Step 1: Read the GRO input coordinate files and open temporary Output files molA_file = open(molA_file_name, 'r').readlines() # open input file molB_new_file_name = 'B_hybrid_swap.gro' molB_new = open(molB_new_file_name, 'w') @@ -1549,19 +1544,19 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): molA_new_file_name = 'A_hybrid_swap.gro' molA_new = open(molA_new_file_name, 'w') - # Step 3: Determine atoms for alignment and swapping + # Step 2: Determine atoms for alignment and swapping nameA = coordinate_swap.identify_res(molA.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) # noqa: E501 nameB = coordinate_swap.identify_res(molB.topology, swap_map['Swap A'].to_list() + swap_map['Swap B'].to_list()) # noqa: E501 df_atom_swap = coordinate_swap.find_common(molA_file, molB_file, nameA, nameB) - # Step 4: Fix break if present for solvated systems only + # Step 3: Fix break if present for solvated systems only if len(molA.topology.select('water')) != 0: A_dimensions = coordinate_swap.get_dimensions(molA_file) B_dimensions = coordinate_swap.get_dimensions(molB_file) molA = coordinate_swap.fix_break(molA, nameA, A_dimensions, connection_map[connection_map['Resname'] == nameA]) # noqa: E501 molB = coordinate_swap.fix_break(molB, nameB, B_dimensions, connection_map[connection_map['Resname'] == nameB]) # noqa: E501 - # Step 5: Determine coordinates of atoms which need to be reconstructed as we swap coordinates between molecules # noqa: E501 + # Step 4: Determine coordinates of atoms which need to be reconstructed as we swap coordinates between molecules # noqa: E501 miss_B = df_atom_swap[(df_atom_swap['Swap'] == 'B2A') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() # noqa: E501 miss_A = df_atom_swap[(df_atom_swap['Swap'] == 'A2B') & (df_atom_swap['Direction'] == 'miss')]['Name'].to_list() # noqa: E501 if len(miss_B) != 0: @@ -1588,18 +1583,9 @@ def default_coords_fn(self, molA_file_name: str, molB_file_name: str): def process_top(self): """ - Process the input topologies in order to determine the atoms for alignment in the default GRO swapping + Processes the input topologies in order to determine the atoms for alignment in the default GRO swapping function. Output as csv files to prevent needing to re-run this step. - - Parameters - ---------- - None - Return - ------ - None """ - import pandas as pd - if not os.path.exists('residue_connect.csv'): df_top = pd.DataFrame() for f, file_name in enumerate(self.top): From 2ea895b9a3a3c3fc283c70fc44acda8b537eac33 Mon Sep 17 00:00:00 2001 From: Anika Friedman <74794503+ajfriedman22@users.noreply.github.com> Date: Wed, 11 Sep 2024 10:21:02 -0600 Subject: [PATCH 14/68] Fill in missing docstring for add_or_swap function --- ensemble_md/utils/coordinate_swap.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index e70f8416..e2fa6690 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -1000,7 +1000,7 @@ def add_or_swap(df_select, file_new, resnum, resname, vel, atom_num, orig_coor, Parameters ---------- df_select : pandas.DataFrame - (To be added.) + This dataframe should include only the atom which is currently being added or having it's name swapped. file_new : file-like object The temporary file for the new GRO resnum : int From f3fdbfab9cc46877cc3043f78d83302cad4e6a3a Mon Sep 17 00:00:00 2001 From: Anika Friedman <74794503+ajfriedman22@users.noreply.github.com> Date: Wed, 11 Sep 2024 10:30:03 -0600 Subject: [PATCH 15/68] Fix error in compute_angle function --- ensemble_md/utils/coordinate_swap.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index e2fa6690..8aaa5a95 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -988,7 +988,7 @@ def compute_angle(coords): vec1 = coords[0] - coords[1] vec2 = coords[2] - coords[1] - angle = np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2)) + angle = np.arccos(np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2))) return angle From 878121b4ed6dc05eb3c3186063fd3cd068b247ab Mon Sep 17 00:00:00 2001 From: Anika Friedman <74794503+ajfriedman22@users.noreply.github.com> Date: Wed, 11 Sep 2024 10:41:45 -0600 Subject: [PATCH 16/68] Fill in docstring for get_miss_coord --- ensemble_md/utils/coordinate_swap.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 8aaa5a95..93526bf2 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -433,7 +433,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, dir : str The swapping direction. df_swap : pandas.DataFrame - For each missing atoms. + Swapping map for the given conformational swap direction to determine which atoms to use for anchor, alignment, and angle determination. Returns ------- From 710db92d17b4623c10421cbd00ea20434f3f921f Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Thu, 12 Sep 2024 00:45:01 +0800 Subject: [PATCH 17/68] Fixed linting errors --- ensemble_md/utils/coordinate_swap.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 93526bf2..ac0a903c 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -433,7 +433,8 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir, dir : str The swapping direction. df_swap : pandas.DataFrame - Swapping map for the given conformational swap direction to determine which atoms to use for anchor, alignment, and angle determination. + Swapping map for the given conformational swap direction to determine which atoms + to use for anchor, alignment, and angle determination. Returns ------- From b6d5fe146fe97a10763bccbbdbe21736d2640db0 Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Thu, 12 Sep 2024 00:54:50 +0800 Subject: [PATCH 18/68] Fixed the unit test for compute_angle --- ensemble_md/tests/test_coordinate_swap.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ensemble_md/tests/test_coordinate_swap.py b/ensemble_md/tests/test_coordinate_swap.py index 2bd7540e..aa6d6771 100644 --- a/ensemble_md/tests/test_coordinate_swap.py +++ b/ensemble_md/tests/test_coordinate_swap.py @@ -50,6 +50,6 @@ def test_compute_angle(): coords_2 = coords_1[-1::-1] coords_3 = [coords_1[1], coords_1[0], coords_1[2]] - assert np.isclose(coordinate_swap.compute_angle(coords_1), np.sqrt(2) / 2) - assert np.isclose(coordinate_swap.compute_angle(coords_2), np.sqrt(2) / 2) - assert np.isclose(coordinate_swap.compute_angle(coords_3), 0) + assert np.isclose(coordinate_swap.compute_angle(coords_1), np.pi / 4) + assert np.isclose(coordinate_swap.compute_angle(coords_2), np.pi / 4) + assert np.isclose(coordinate_swap.compute_angle(coords_3), np.pi / 2) From d36642229bfd2d47768189b1f5912230c3406705 Mon Sep 17 00:00:00 2001 From: ajfriedman22 Date: Wed, 18 Sep 2024 16:06:43 -0600 Subject: [PATCH 19/68] Fix minor error for large systems(>10,000 atoms) --- ensemble_md/utils/coordinate_swap.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index ac0a903c..9f31b34e 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -72,7 +72,7 @@ def find_common(molA_file, molB_file, nameA, nameB): split_line = line.split(' ') while ("" in split_line): split_line.remove("") - if len(line[1]) > 5: + if len(split_line[1]) > 5: split_line = sep_merge(split_line) if nameA in split_line[0]: nameA_list.append(split_line[1]) @@ -82,7 +82,7 @@ def find_common(molA_file, molB_file, nameA, nameB): split_line = line.split(' ') while ("" in split_line): split_line.remove("") - if len(line[1]) > 5: + if len(split_line[1]) > 5: split_line = sep_merge(split_line) if nameB in split_line[0]: nameB_list.append(split_line[1]) @@ -223,7 +223,7 @@ def fix_break(mol, resname, box_dimensions, atom_connect_all): iter += 1 # Fix this break - mol, fixed, shift_atom = perform_shift_1D(mol, box_dimensions, broken_pairs, atom_pairs, shift_atom) + mol, fixed, shift_atom = perform_shift_1D(mol, box_dimensions, broken_pairs, shift_atom) if fixed: broken_pairs = check_break(mol, atom_pairs) continue @@ -1089,6 +1089,10 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file, # Iterate atom number to keep track of file progress atom_num_B += 1 + #Account for the fact that the max atom number is 99999 + if atom_num_B == 100000: + atom_num_B = 0 + # Process input lines line, prev_line = process_line(orig_file, i) From 59f477d28ae3fa9896b3da2dec2a468cb2e3afbb Mon Sep 17 00:00:00 2001 From: ajfriedman22 Date: Wed, 18 Sep 2024 16:07:16 -0600 Subject: [PATCH 20/68] add test --- ensemble_md/tests/data/coord_swap/A-B.gro | 2055 ++++++++++++++++ ensemble_md/tests/data/coord_swap/A-B.itp | 158 ++ ensemble_md/tests/data/coord_swap/A-B.top | 32 + ensemble_md/tests/data/coord_swap/B-C.gro | 2058 ++++++++++++++++ ensemble_md/tests/data/coord_swap/B-C.itp | 192 ++ ensemble_md/tests/data/coord_swap/B-C.top | 32 + ensemble_md/tests/data/coord_swap/C-D.gro | 2062 ++++++++++++++++ ensemble_md/tests/data/coord_swap/C-D.itp | 235 ++ ensemble_md/tests/data/coord_swap/C-D.top | 32 + ensemble_md/tests/data/coord_swap/D-E.gro | 2061 ++++++++++++++++ ensemble_md/tests/data/coord_swap/D-E.itp | 229 ++ ensemble_md/tests/data/coord_swap/D-E.top | 32 + ensemble_md/tests/data/coord_swap/E-F.gro | 2065 +++++++++++++++++ ensemble_md/tests/data/coord_swap/E-F.itp | 293 +++ ensemble_md/tests/data/coord_swap/E-F.top | 32 + ensemble_md/tests/data/coord_swap/params.yaml | 27 + ensemble_md/tests/test_coordinate_swap.py | 20 + 17 files changed, 11615 insertions(+) create mode 100644 ensemble_md/tests/data/coord_swap/A-B.gro create mode 100644 ensemble_md/tests/data/coord_swap/A-B.itp create mode 100644 ensemble_md/tests/data/coord_swap/A-B.top create mode 100644 ensemble_md/tests/data/coord_swap/B-C.gro create mode 100644 ensemble_md/tests/data/coord_swap/B-C.itp create mode 100644 ensemble_md/tests/data/coord_swap/B-C.top create mode 100644 ensemble_md/tests/data/coord_swap/C-D.gro create mode 100644 ensemble_md/tests/data/coord_swap/C-D.itp create mode 100644 ensemble_md/tests/data/coord_swap/C-D.top create mode 100644 ensemble_md/tests/data/coord_swap/D-E.gro create mode 100644 ensemble_md/tests/data/coord_swap/D-E.itp create mode 100644 ensemble_md/tests/data/coord_swap/D-E.top create mode 100644 ensemble_md/tests/data/coord_swap/E-F.gro create mode 100644 ensemble_md/tests/data/coord_swap/E-F.itp create mode 100644 ensemble_md/tests/data/coord_swap/E-F.top create mode 100644 ensemble_md/tests/data/coord_swap/params.yaml create mode 100644 ensemble_md/tests/test_coordinate_swap.py diff --git a/ensemble_md/tests/data/coord_swap/A-B.gro b/ensemble_md/tests/data/coord_swap/A-B.gro new file mode 100644 index 00000000..afa79c79 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/A-B.gro @@ -0,0 +1,2055 @@ +Generic title in water + 2052 + 1A2B S1 1 1.391 1.260 1.100 -0.1138 0.5179 -0.0827 + 1A2B C2 2 1.330 1.353 1.231 0.1345 1.0335 0.3925 + 1A2B N3 3 1.420 1.418 1.301 0.2878 0.0365 -0.0981 + 1A2B C4 4 1.547 1.387 1.253 0.0362 0.1422 -0.4540 + 1A2B C5 5 1.546 1.303 1.148 0.0030 0.0727 0.5168 + 1A2B C6 6 1.180 1.348 1.271 -0.7783 0.0883 -0.3195 + 1A2B H1 7 1.627 1.420 1.318 0.4651 -0.5532 -0.6199 + 1A2B H2 8 1.632 1.268 1.092 -0.0639 -0.5563 0.8055 + 1A2B H3 9 1.121 1.313 1.185 -2.7017 0.6777 0.7602 + 1A2B H4 10 1.160 1.276 1.351 -0.0128 -2.5298 -2.4969 + 1A2B H17 11 1.135 1.446 1.295 0.4500 0.6558 -0.3329 + 1A2B DC7 12 1.126 1.491 1.303 -0.3127 0.0937 0.7875 + 1A2B HV5 13 1.212 1.556 1.321 0.1827 -0.4530 0.3997 + 1A2B HV6 14 1.068 1.479 1.395 0.0428 1.0305 1.1350 + 1A2B HV7 15 1.067 1.539 1.225 0.4331 0.4336 0.4368 + 2SOL OW 16 1.845 1.045 1.151 0.5750 -0.4849 -0.8545 + 2SOL HW1 17 1.880 1.087 1.073 0.1633 -1.3032 -1.4885 + 2SOL HW2 18 1.866 1.104 1.223 0.6363 0.4390 -1.6412 + 3SOL OW 19 0.901 0.344 0.795 0.6316 0.6279 -0.6367 + 3SOL HW1 20 0.902 0.255 0.832 -0.7053 1.4309 1.2963 + 3SOL HW2 21 0.993 0.365 0.783 0.9838 -0.7342 -0.3781 + 4SOL OW 22 0.422 0.695 2.081 -0.0550 -0.0797 0.4219 + 4SOL HW1 23 0.427 0.752 2.158 2.6160 -0.3725 0.4662 + 4SOL HW2 24 0.338 0.650 2.090 -1.6451 3.0105 0.9767 + 5SOL OW 25 1.645 0.630 1.876 0.0338 0.4519 0.2557 + 5SOL HW1 26 1.613 0.720 1.869 -0.0700 0.2433 -1.9835 + 5SOL HW2 27 1.584 0.588 1.936 -1.5726 1.1286 -0.8957 + 6SOL OW 28 2.119 0.919 2.470 -0.1274 0.1404 0.1075 + 6SOL HW1 29 2.117 0.932 2.376 -1.3954 -1.5834 -0.1154 + 6SOL HW2 30 2.027 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-2.1241 + 637SOL HW2 1923 1.675 0.046 1.860 -0.6039 0.9558 1.2942 + 638SOL OW 1924 1.903 0.423 1.983 -0.3716 -0.4543 -0.2442 + 638SOL HW1 1925 1.846 0.496 2.007 0.3443 0.3102 -0.8966 + 638SOL HW2 1926 1.891 0.414 1.888 2.0069 0.8781 -0.6606 + 639SOL OW 1927 2.201 1.705 1.060 0.1054 -0.1095 -0.0003 + 639SOL HW1 1928 2.279 1.699 1.005 -0.0519 -1.4398 -0.0877 + 639SOL HW2 1929 2.216 1.643 1.131 0.3477 1.6811 1.5097 + 640SOL OW 1930 2.107 2.507 2.440 0.6198 -0.2848 0.0317 + 640SOL HW1 1931 2.139 2.432 2.389 -0.8584 -0.4149 -0.6943 + 640SOL HW2 1932 2.152 2.582 2.401 -0.3412 -0.4102 -1.3251 + 641SOL OW 1933 2.733 1.817 0.853 0.4018 -0.1845 0.3251 + 641SOL HW1 1934 2.646 1.847 0.879 1.0419 1.9280 -0.0020 + 641SOL HW2 1935 2.782 1.813 0.936 0.4598 0.0742 0.3004 + 642SOL OW 1936 0.330 2.527 0.859 -0.2684 0.7125 0.1795 + 642SOL HW1 1937 0.282 2.497 0.936 -1.0307 1.0678 -0.1594 + 642SOL HW2 1938 0.397 2.459 0.844 -0.9928 -0.0359 0.3389 + 643SOL OW 1939 1.459 0.021 2.152 1.2176 -0.3319 -0.0770 + 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OW 1957 2.383 2.640 2.317 -0.1781 0.1953 0.2280 + 649SOL HW1 1958 2.332 2.702 2.265 0.2444 -0.8423 -1.4360 + 649SOL HW2 1959 2.409 2.689 2.395 -0.7845 1.7551 -0.5583 + 650SOL OW 1960 2.066 0.677 2.348 -0.6737 0.2402 0.5691 + 650SOL HW1 1961 2.030 0.592 2.373 1.6383 -0.2753 2.1734 + 650SOL HW2 1962 2.039 0.736 2.418 1.4622 -0.1268 1.7298 + 651SOL OW 1963 1.663 1.425 2.657 -0.9413 -0.0682 -0.6671 + 651SOL HW1 1964 1.659 1.483 2.582 -2.5189 0.2874 -0.3010 + 651SOL HW2 1965 1.581 1.441 2.705 0.9652 1.1623 2.1959 + 652SOL OW 1966 0.809 1.132 1.183 0.7107 -0.5354 0.1738 + 652SOL HW1 1967 0.789 1.200 1.119 0.9436 1.5198 2.2975 + 652SOL HW2 1968 0.880 1.082 1.142 -0.4633 -0.4230 -2.0254 + 653SOL OW 1969 1.874 1.213 1.408 -0.6208 -0.1755 -0.5576 + 653SOL HW1 1970 1.961 1.200 1.446 -0.4206 0.6595 -0.7151 + 653SOL HW2 1971 1.813 1.186 1.477 -0.2437 -0.0639 -0.1772 + 654SOL OW 1972 1.809 0.131 0.355 0.4033 -0.4873 -0.0105 + 654SOL HW1 1973 1.766 0.106 0.437 3.0710 0.4235 1.6794 + 654SOL HW2 1974 1.823 0.225 0.363 0.2381 -0.3302 -1.7006 + 655SOL OW 1975 2.441 0.443 1.353 -0.2254 -0.2164 -0.1843 + 655SOL HW1 1976 2.463 0.518 1.298 -0.3659 0.8041 1.1404 + 655SOL HW2 1977 2.366 0.473 1.405 1.6756 -0.2106 2.5405 + 656SOL OW 1978 2.458 1.666 0.545 0.5770 -0.0048 0.2732 + 656SOL HW1 1979 2.375 1.688 0.502 -0.1382 -0.9294 1.1916 + 656SOL HW2 1980 2.485 1.584 0.503 0.2199 -0.5507 1.1134 + 657SOL OW 1981 1.721 1.167 0.174 0.1473 -0.3044 0.2647 + 657SOL HW1 1982 1.809 1.195 0.198 -0.0705 1.3253 -0.8948 + 657SOL HW2 1983 1.666 1.191 0.249 0.3486 0.4178 0.1806 + 658SOL OW 1984 0.160 1.321 1.420 0.4666 -0.0311 0.8757 + 658SOL HW1 1985 0.173 1.258 1.490 0.0490 -0.2891 0.7226 + 658SOL HW2 1986 0.135 1.268 1.344 0.4455 0.2874 0.6585 + 659SOL OW 1987 0.448 1.071 2.472 0.0336 -0.1584 -0.6087 + 659SOL HW1 1988 0.399 1.107 2.546 0.9921 -2.0423 0.9570 + 659SOL HW2 1989 0.538 1.099 2.487 0.8407 -3.4827 0.7896 + 660SOL OW 1990 1.224 0.930 2.311 -0.4946 0.1384 -0.0157 + 660SOL HW1 1991 1.306 0.980 2.304 0.4135 -1.1716 1.2096 + 660SOL HW2 1992 1.158 0.995 2.337 0.1427 1.2170 -1.1373 + 661SOL OW 1993 2.516 2.009 2.102 -0.0384 0.4503 0.4367 + 661SOL HW1 1994 2.469 2.013 2.018 -0.7473 2.7685 0.9322 + 661SOL HW2 1995 2.600 1.969 2.080 -1.4891 -1.9767 -0.8032 + 662SOL OW 1996 0.676 2.064 1.082 0.0852 0.3301 0.2486 + 662SOL HW1 1997 0.622 2.132 1.041 -1.3021 -0.4425 0.7867 + 662SOL HW2 1998 0.648 1.983 1.039 0.8840 -0.0609 0.4762 + 663SOL OW 1999 2.423 1.137 0.196 -0.1459 0.0706 0.3422 + 663SOL HW1 2000 2.348 1.079 0.204 0.0832 -0.1947 0.5914 + 663SOL HW2 2001 2.407 1.186 0.115 -1.2213 0.9557 1.0952 + 664SOL OW 2002 0.965 0.431 1.502 0.4159 -0.4068 -0.3650 + 664SOL HW1 2003 1.055 0.455 1.526 0.3571 0.3326 -0.9099 + 664SOL HW2 2004 0.975 0.365 1.434 0.5199 0.6779 -1.3887 + 665SOL OW 2005 0.229 0.194 1.232 0.0664 0.0073 -0.1921 + 665SOL HW1 2006 0.165 0.232 1.172 -0.2600 -1.1201 -0.5707 + 665SOL HW2 2007 0.303 0.170 1.175 0.6938 1.0413 0.1999 + 666SOL OW 2008 2.317 1.434 0.259 -0.1038 -0.2375 -0.1767 + 666SOL HW1 2009 2.260 1.405 0.330 -0.5950 -0.1071 -0.5199 + 666SOL HW2 2010 2.403 1.398 0.282 -0.1949 0.0505 0.6376 + 667SOL OW 2011 2.512 0.974 1.675 -0.1708 -0.1937 -0.7061 + 667SOL HW1 2012 2.541 1.007 1.760 -1.5096 1.0807 -0.7391 + 667SOL HW2 2013 2.469 0.891 1.696 -1.3084 0.5567 -0.0166 + 668SOL OW 2014 1.949 0.738 1.467 0.2606 -0.7083 -0.0873 + 668SOL HW1 2015 1.981 0.757 1.555 0.8962 -0.8951 -0.2787 + 668SOL HW2 2016 1.864 0.696 1.480 -0.7873 1.5593 0.3649 + 669SOL OW 2017 2.473 0.110 2.031 0.4626 0.5975 -0.0317 + 669SOL HW1 2018 2.386 0.087 1.999 1.0327 -1.0555 -0.4261 + 669SOL HW2 2019 2.516 0.150 1.956 0.9223 -0.9535 -0.6108 + 670SOL OW 2020 2.052 2.300 2.607 0.7010 -0.0564 0.1098 + 670SOL HW1 2021 2.082 2.364 2.543 -0.1506 -0.4510 -0.6873 + 670SOL HW2 2022 2.113 2.308 2.680 1.6902 0.3740 -0.7678 + 671SOL OW 2023 1.992 0.744 0.193 -0.3290 0.3597 0.3979 + 671SOL HW1 2024 1.964 0.684 0.124 -0.0333 1.0863 -0.3544 + 671SOL HW2 2025 2.059 0.696 0.241 -0.1456 0.0611 -0.1577 + 672SOL OW 2026 2.547 0.807 1.434 -0.4124 0.3953 -0.1422 + 672SOL HW1 2027 2.471 0.813 1.492 -1.3530 -0.6015 -1.2808 + 672SOL HW2 2028 2.595 0.889 1.449 -1.7752 1.0825 0.4558 + 673SOL OW 2029 2.089 0.033 2.216 -0.3692 0.1985 -0.4377 + 673SOL HW1 2030 2.069 -0.045 2.165 2.0826 0.0384 -1.1600 + 673SOL HW2 2031 2.103 0.102 2.151 -0.2815 0.7164 0.1283 + 674SOL OW 2032 0.427 0.132 1.025 -0.2597 0.4841 -0.1567 + 674SOL HW1 2033 0.470 0.207 0.983 0.5879 -0.1778 -0.4634 + 674SOL HW2 2034 0.353 0.112 0.968 0.1571 0.3814 -0.6589 + 675SOL OW 2035 1.102 1.906 0.596 -0.3172 0.7840 -0.4976 + 675SOL HW1 2036 1.089 1.892 0.690 -0.8400 0.1624 -0.6623 + 675SOL HW2 2037 1.134 1.996 0.589 -0.8056 1.0151 0.2389 + 676SOL OW 2038 0.770 0.964 2.006 -0.5969 0.2892 1.3086 + 676SOL HW1 2039 0.839 1.013 1.961 1.0105 -1.5914 1.7368 + 676SOL HW2 2040 0.698 0.962 1.943 0.0494 1.5051 0.5194 + 677SOL OW 2041 2.660 1.441 2.664 -0.2255 0.3714 -0.3718 + 677SOL HW1 2042 2.682 1.401 2.748 1.3360 0.3467 -0.7943 + 677SOL HW2 2043 2.674 1.535 2.678 1.2263 0.2342 -0.9986 + 678SOL OW 2044 2.554 2.623 1.855 -0.1556 -0.0105 0.8887 + 678SOL HW1 2045 2.582 2.703 1.900 -0.0963 0.1025 0.6461 + 678SOL HW2 2046 2.565 2.554 1.921 0.9998 -0.0150 0.6812 + 679SOL OW 2047 2.132 0.957 0.762 0.5496 -0.2959 -0.5930 + 679SOL HW1 2048 2.094 0.909 0.836 -0.7533 1.5342 -0.0665 + 679SOL HW2 2049 2.226 0.960 0.781 0.1425 0.6495 1.2492 + 680SOL OW 2050 0.973 2.301 0.791 -0.0695 -0.2422 0.6727 + 680SOL HW1 2051 0.917 2.326 0.717 0.3575 1.5055 0.9512 + 680SOL HW2 2052 1.015 2.220 0.762 -2.1064 -1.1109 0.1265 + 2.76488 2.76488 2.76488 diff --git a/ensemble_md/tests/data/coord_swap/A-B.itp b/ensemble_md/tests/data/coord_swap/A-B.itp new file mode 100644 index 00000000..dd3e43f9 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/A-B.itp @@ -0,0 +1,158 @@ + + + +[ moleculetype ] +; Name nrexcl +A2B 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB + 1 ss 1 A2B S1 1 -0.116300 32.0600 + 2 cc 1 A2B C2 2 0.402700 12.0100 + 3 nd 1 A2B N3 3 -0.636000 14.0100 nd -0.634000 14.0100 + 4 cd 1 A2B C4 4 0.333200 12.0100 cd 0.332200 12.0100 + 5 cc 1 A2B C5 5 -0.252400 12.0100 cc -0.251400 12.0100 + 6 c3 1 A2B C6 6 -0.131400 12.0100 c3 -0.110700 12.0100 + 7 h4 1 A2B H1 7 0.044100 1.0080 h4 0.043100 1.0080 + 8 h4 1 A2B H2 8 0.180000 1.0080 + 9 hc 1 A2B H3 9 0.058700 1.0080 hc 0.057250 1.0080 + 10 hc 1 A2B H4 10 0.058700 1.0080 hc 0.057250 1.0080 + 11 hc 1 A2B H17 11 0.058700 1.0080 DUM_hc 0.000000 1.0080 + 12 DUM_c3 1 A2B DC7 12 0.000000 12.0100 c3 -0.089100 12.0100 + 13 DUM_hc 1 A2B HV5 13 0.000000 1.0080 hc 0.043000 1.0080 + 14 DUM_hc 1 A2B HV6 14 0.000000 1.0080 hc 0.043000 1.0080 + 15 DUM_hc 1 A2B HV7 15 0.000000 1.0080 hc 0.043000 1.0080 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 0.175380 193853.088000 0.175380 193853.088000 + 1 5 1 0.175380 193853.088000 0.175380 193853.088000 + 2 3 1 0.131580 351221.696000 0.131580 351221.696000 + 2 6 1 0.150020 213501.152000 0.150020 213501.152000 + 3 4 1 0.137130 289474.224000 0.137130 289474.224000 + 4 5 1 0.137300 323205.632000 0.137300 323205.632000 + 4 7 1 0.108180 307348.272000 0.108180 307348.272000 + 5 8 1 0.108090 308544.896000 0.108090 308544.896000 + 6 9 1 0.109620 288905.200000 0.109620 288905.200000 + 6 10 1 0.109620 288905.200000 0.109620 288905.200000 + 6 11 1 0.109620 288905.200000 0.109620 288905.200000 + 6 12 1 0.153540 191535.152000 0.153540 191535.152000 + 12 13 1 0.109620 288905.200000 0.109620 288905.200000 + 12 14 1 0.109620 288905.200000 0.109620 288905.200000 + 12 15 1 0.109620 288905.200000 0.109620 288905.200000 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 4 6 1 + 5 6 1 + 1 9 1 + 1 10 1 + 1 11 1 + 1 7 1 + 2 8 1 + 2 7 1 + 3 9 1 + 3 10 1 + 3 11 1 + 3 8 1 + 7 8 1 + 1 12 1 + 3 12 1 + 2 13 1 + 2 14 1 + 2 15 1 + 9 13 1 + 9 14 1 + 9 15 1 + 10 13 1 + 10 14 1 + 10 15 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3 + 1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6 + 1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4 + 2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5 + 2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4 + 3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6 + 3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5 + 1 5 8 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2 + 2 6 9 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3 + 2 6 10 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H4 + 2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H17 + 3 4 7 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1 + 4 5 8 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2 + 5 4 7 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1 + 9 6 10 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H4 + 9 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H17 + 10 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H4 C6 H17 + 2 6 12 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 DC7 + 6 12 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV5 + 6 12 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV6 + 6 12 15 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV7 + 12 6 9 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H3 + 12 6 10 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H4 + 13 12 14 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV6 + 13 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV7 + 14 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV6 DC7 HV7 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD) + 1 5 4 7 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 8 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 7 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD) + 3 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 7 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA) + 1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA) + 1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA) + 3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA) + 4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA) + 1 5 4 7 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 8 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 7 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 12 13 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV5 (AADD->AAAA) + 2 6 12 14 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV6 (AADD->AAAA) + 2 6 12 15 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV7 (AADD->AAAA) + 3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA) + 3 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 7 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 9 6 12 13 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV5 (AADD->AAAA) + 9 6 12 14 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV6 (AADD->AAAA) + 9 6 12 15 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV7 (AADD->AAAA) + 10 6 12 13 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV5 (AADD->AAAA) + 10 6 12 14 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV6 (AADD->AAAA) + 10 6 12 15 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV7 (AADD->AAAA) + 5 7 4 3 4 180.0000771 0 2 180.0000771 4.6024 2 ; C5 H1 C4 N3 (AAAA->AAAA) + 1 5 8 4 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C5 H2 C4 (AAAA->AAAA) + +#ifdef POSRES +#include "posre.itp" +#endif \ No newline at end of file diff --git a/ensemble_md/tests/data/coord_swap/A-B.top b/ensemble_md/tests/data/coord_swap/A-B.top new file mode 100644 index 00000000..19395fd1 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/A-B.top @@ -0,0 +1,32 @@ +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.83333333 + +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +ss 16 32.060000 0.00000000 A 0.35324134 1.1815616 +cc 6 12.010000 0.00000000 A 0.33152123 0.4133792 +nd 7 14.010000 0.00000000 A 0.33841679 0.3937144 +cd 6 12.010000 0.00000000 A 0.33152123 0.4133792 +c3 6 12.010000 0.00000000 A 0.33977095 0.4510352 +h4 1 1.008000 0.00000000 A 0.25363887 0.0673624 +hc 1 1.008000 0.00000000 A 0.2600177 0.0870272 +DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000 +DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000 +Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02 +Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 + +#include "A-B.itp" + +#include "water_and_ions.itp" + +[ system ] +; Name +Generic title in water + +[ molecules ] +; Compound #mols +A2B 1 +SOL 679 diff --git a/ensemble_md/tests/data/coord_swap/B-C.gro b/ensemble_md/tests/data/coord_swap/B-C.gro new file mode 100644 index 00000000..49de406c --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/B-C.gro @@ -0,0 +1,2058 @@ +Generic title in water + 2055 + 1B2C S1 1 0.789 1.574 0.420 0.0071 -0.0708 -0.0310 + 1B2C C2 2 0.736 1.588 0.588 -0.1420 -0.1562 0.0279 + 1B2C N3 3 0.608 1.557 0.611 -0.4381 -0.4817 -0.6783 + 1B2C C4 4 0.542 1.518 0.497 0.1039 0.9450 -0.3496 + 1B2C C5 5 0.627 1.516 0.385 0.2905 -0.2050 0.6227 + 1B2C C6 6 0.844 1.623 0.698 -0.3346 0.8643 -0.1499 + 1B2C C7 7 0.922 1.753 0.675 0.3444 -0.3585 0.3316 + 1B2C H1 8 0.442 1.477 0.502 1.2332 -2.2463 -3.0055 + 1B2C H2 9 0.602 1.459 0.296 0.8855 -0.5786 0.6992 + 1B2C H3 10 0.796 1.641 0.795 -3.5370 1.8671 -1.9210 + 1B2C H4 11 0.903 1.530 0.698 -1.0445 0.3855 3.2997 + 1B2C H5 12 0.993 1.736 0.594 -0.2444 2.7978 -0.8513 + 1B2C H6 13 0.978 1.784 0.764 0.8850 0.0352 -0.1462 + 1B2C H7 14 0.853 1.830 0.637 0.3856 -0.5188 -0.0566 + 1B2C DC8 15 1.017 1.747 0.559 0.7179 -0.3652 -0.1557 + 1B2C HV8 16 0.990 1.674 0.482 0.3085 -0.6297 0.2383 + 1B2C HV9 17 1.030 1.847 0.515 0.1047 -0.0283 0.4330 + 1B2C HV10 18 1.118 1.720 0.591 -0.1254 -1.9710 1.1269 + 2SOL OW 19 0.699 1.126 1.560 0.2243 -0.0980 -0.1696 + 2SOL HW1 20 0.778 1.106 1.510 1.6546 0.3340 1.8975 + 2SOL HW2 21 0.683 1.219 1.544 0.1496 -0.1763 -0.5556 + 3SOL OW 22 1.273 1.566 2.229 -0.4856 0.6436 0.3006 + 3SOL HW1 23 1.347 1.552 2.289 0.3669 0.5284 -0.7914 + 3SOL HW2 24 1.296 1.516 2.151 -1.2761 1.4036 -0.4082 + 4SOL OW 25 1.848 2.103 0.567 -0.4242 0.0063 0.1775 + 4SOL HW1 26 1.858 2.106 0.472 0.5595 -0.9128 0.2480 + 4SOL HW2 27 1.876 2.190 0.597 0.8072 -0.2535 -0.2274 + 5SOL OW 28 0.462 1.810 1.542 -0.2189 -0.5238 0.4927 + 5SOL HW1 29 0.400 1.883 1.539 -1.4456 -1.5993 -0.6759 + 5SOL HW2 30 0.415 1.740 1.588 1.3411 -0.2187 2.5664 + 6SOL OW 31 0.965 1.620 1.079 -0.2038 -0.3497 0.5850 + 6SOL HW1 32 1.053 1.581 1.076 -0.8520 -1.6411 -1.4159 + 6SOL HW2 33 0.949 1.636 1.172 1.4690 -1.6742 1.0927 + 7SOL OW 34 2.197 2.342 1.252 0.3213 -0.0036 0.4549 + 7SOL HW1 35 2.195 2.269 1.314 -1.9061 0.0173 0.3907 + 7SOL HW2 36 2.249 2.410 1.296 -0.9313 -0.1429 2.1114 + 8SOL OW 37 2.244 2.699 0.670 -0.2398 -0.2241 0.0073 + 8SOL HW1 38 2.235 2.670 0.760 -0.1445 -2.5351 -0.7347 + 8SOL HW2 39 2.155 2.694 0.634 -0.1290 -0.1445 -0.2810 + 9SOL OW 40 1.851 0.024 2.083 -0.4791 -0.1076 -0.1200 + 9SOL HW1 41 1.793 0.094 2.111 0.0328 0.0737 0.4848 + 9SOL HW2 42 1.918 0.019 2.152 -0.5374 -1.2001 -0.1430 + 10SOL OW 43 2.392 2.194 1.643 0.1652 0.0396 0.3859 + 10SOL HW1 44 2.427 2.133 1.709 -1.5395 0.0322 1.2975 + 10SOL HW2 45 2.323 2.144 1.599 -0.5912 0.9937 0.4877 + 11SOL OW 46 1.055 0.688 1.602 0.2146 0.4858 -0.0757 + 11SOL HW1 47 0.962 0.693 1.579 -0.3133 0.0901 1.9766 + 11SOL HW2 48 1.064 0.748 1.676 1.0226 -1.7156 1.6072 + 12SOL OW 49 0.151 1.133 0.890 0.3687 0.1284 0.8608 + 12SOL HW1 50 0.122 1.113 0.802 0.6497 1.1209 0.5450 + 12SOL HW2 51 0.197 1.217 0.882 -0.5696 0.7565 2.1484 + 13SOL OW 52 1.352 2.303 1.380 -0.0918 -0.6300 -0.0377 + 13SOL HW1 53 1.373 2.274 1.468 1.4612 -0.7013 -0.4297 + 13SOL HW2 54 1.279 2.363 1.391 -0.5835 -1.4687 1.1880 + 14SOL OW 55 0.705 0.414 2.632 0.5001 -0.5228 -0.2710 + 14SOL HW1 56 0.665 0.455 2.708 0.1449 -1.3247 -0.0225 + 14SOL HW2 57 0.788 0.461 2.619 -0.6330 1.2999 -0.9262 + 15SOL OW 58 0.829 1.986 0.302 0.2567 -0.2081 -0.0626 + 15SOL HW1 59 0.763 1.965 0.368 -0.5168 1.3602 -0.3221 + 15SOL HW2 60 0.913 1.980 0.348 -0.0677 -2.1192 0.2939 + 16SOL OW 61 0.109 2.679 1.346 0.2411 0.4318 0.2322 + 16SOL HW1 62 0.060 2.600 1.371 -0.2440 -0.0741 -2.3026 + 16SOL HW2 63 0.200 2.650 1.344 0.3392 0.6277 2.0479 + 17SOL OW 64 0.447 2.187 0.065 -0.1260 -0.3299 0.0793 + 17SOL HW1 65 0.436 2.219 0.155 -0.6376 -1.1826 0.3254 + 17SOL HW2 66 0.524 2.131 0.068 -0.3700 -0.6712 0.0798 + 18SOL OW 67 2.095 2.292 1.983 0.1254 -0.0968 0.4347 + 18SOL HW1 68 2.180 2.252 2.000 0.8560 0.7031 -1.3610 + 18SOL HW2 69 2.037 2.217 1.966 1.1219 -0.4984 -1.2494 + 19SOL OW 70 0.850 0.586 0.598 -0.1264 0.0552 0.6062 + 19SOL HW1 71 0.895 0.621 0.522 0.2234 0.8568 1.1766 + 19SOL HW2 72 0.884 0.638 0.672 -1.7282 0.4501 1.0741 + 20SOL OW 73 1.137 0.265 1.654 0.0584 0.0223 0.1353 + 20SOL HW1 74 1.079 0.318 1.710 -0.4546 0.0051 -0.3723 + 20SOL HW2 75 1.214 0.320 1.640 -0.8644 0.9855 -1.1209 + 21SOL OW 76 2.723 1.385 2.639 0.3728 0.2095 -0.3546 + 21SOL HW1 77 2.719 1.335 2.558 1.4373 1.2158 -1.0246 + 21SOL HW2 78 2.817 1.388 2.660 0.3409 2.4556 -0.6264 + 22SOL OW 79 1.536 2.237 2.285 -1.0194 0.0052 0.2771 + 22SOL HW1 80 1.466 2.172 2.294 -1.2270 0.5297 2.3759 + 22SOL HW2 81 1.517 2.303 2.351 0.0403 1.4609 -0.8615 + 23SOL OW 82 2.638 0.516 0.989 0.3464 0.8789 -0.8390 + 23SOL HW1 83 2.721 0.499 0.945 1.3707 0.2827 1.3334 + 23SOL HW2 84 2.662 0.542 1.077 -1.8116 -0.1161 0.0505 + 24SOL OW 85 0.429 0.844 2.420 -0.0592 -0.1921 -0.2239 + 24SOL HW1 86 0.363 0.904 2.455 1.1027 1.5275 -0.9851 + 24SOL HW2 87 0.465 0.801 2.498 -1.6277 -0.6590 0.2422 + 25SOL OW 88 0.581 1.265 0.824 0.3872 -1.2111 0.0306 + 25SOL HW1 89 0.543 1.189 0.867 0.3825 -1.0565 0.2968 + 25SOL HW2 90 0.639 1.304 0.889 -1.3307 0.3030 0.6579 + 26SOL OW 91 0.149 2.087 2.587 -0.4300 0.9187 -0.4826 + 26SOL HW1 92 0.124 2.010 2.639 -1.1794 1.0212 -0.7007 + 26SOL HW2 93 0.243 2.075 2.571 0.2080 1.8804 2.5679 + 27SOL OW 94 2.071 0.050 2.233 0.7687 -0.2558 -0.0375 + 27SOL HW1 95 2.118 0.082 2.311 0.6555 1.2619 -0.5995 + 27SOL HW2 96 2.134 0.060 2.162 0.7746 -1.3932 -0.1956 + 28SOL OW 97 2.090 0.260 2.702 -0.4086 -0.0270 -0.6837 + 28SOL HW1 98 2.133 0.336 2.663 -0.4962 0.3218 -0.1045 + 28SOL HW2 99 2.050 0.294 2.782 1.5489 -1.1813 0.7870 + 29SOL OW 100 1.631 0.437 2.269 -0.3669 0.0164 -0.4479 + 29SOL HW1 101 1.601 0.450 2.179 -0.4355 0.7238 -0.3254 + 29SOL HW2 102 1.563 0.477 2.323 -0.6318 -0.9713 -0.0572 + 30SOL OW 103 2.097 2.411 1.005 -1.1595 -0.2640 0.1890 + 30SOL HW1 104 2.123 2.412 1.097 -0.4649 0.8990 -0.0230 + 30SOL HW2 105 2.075 2.319 0.987 1.9860 -1.0782 0.5741 + 31SOL OW 106 0.258 0.397 1.901 -0.1814 0.4380 -0.2839 + 31SOL HW1 107 0.211 0.467 1.947 -1.6447 0.4989 -1.9223 + 31SOL HW2 108 0.193 0.328 1.888 0.3297 0.2991 -2.0267 + 32SOL OW 109 0.257 2.051 1.251 0.7027 0.1602 -0.3491 + 32SOL HW1 110 0.328 1.991 1.228 0.1042 -0.8824 0.4860 + 32SOL HW2 111 0.202 2.054 1.172 -0.7753 -2.5773 0.5810 + 33SOL OW 112 1.915 1.721 1.895 -0.5822 -0.1798 -0.3293 + 33SOL HW1 113 1.930 1.802 1.847 3.1055 -1.0713 -0.6362 + 33SOL HW2 114 1.945 1.740 1.984 -0.0777 -1.0567 -0.3039 + 34SOL OW 115 1.323 0.809 0.827 0.6720 -0.3990 -0.8020 + 34SOL HW1 116 1.334 0.815 0.922 -1.6197 -0.4505 -0.5318 + 34SOL HW2 117 1.326 0.899 0.797 0.5063 -0.3231 -0.5884 + 35SOL OW 118 2.608 2.161 0.605 0.1636 -0.2105 -0.0009 + 35SOL HW1 119 2.605 2.134 0.514 0.7932 -1.1604 0.2556 + 35SOL HW2 120 2.567 2.248 0.606 -0.5228 -0.5262 -1.0546 + 36SOL OW 121 2.194 0.281 1.557 0.0369 -0.4983 -0.3436 + 36SOL HW1 122 2.137 0.348 1.519 0.0675 1.4921 3.1188 + 36SOL HW2 123 2.135 0.222 1.604 0.5941 0.1126 1.1075 + 37SOL OW 124 0.777 2.269 1.775 0.1348 -0.0302 0.9778 + 37SOL HW1 125 0.694 2.279 1.822 -0.0066 1.0768 0.5147 + 37SOL HW2 126 0.759 2.307 1.688 1.0259 -0.0980 0.7700 + 38SOL OW 127 1.043 2.272 2.677 -0.2695 0.3966 -0.2090 + 38SOL HW1 128 0.968 2.297 2.624 0.9431 1.4817 -1.4148 + 38SOL HW2 129 1.033 2.178 2.690 -2.0566 0.6125 -0.0294 + 39SOL OW 130 0.616 1.027 2.158 0.0090 0.1910 -0.6958 + 39SOL HW1 131 0.583 1.109 2.121 -1.2073 0.0439 0.0775 + 39SOL HW2 132 0.603 1.036 2.252 1.2620 -0.2743 -0.4819 + 40SOL OW 133 0.677 1.410 1.550 -0.3802 -0.3054 0.2565 + 40SOL HW1 134 0.581 1.413 1.553 -0.4423 0.2009 -2.1911 + 40SOL HW2 135 0.705 1.489 1.595 -1.1284 0.1590 -0.0957 + 41SOL OW 136 1.121 0.812 2.610 0.1064 -0.5023 -0.0555 + 41SOL HW1 137 1.187 0.881 2.617 0.1044 -0.5330 0.2763 + 41SOL HW2 138 1.047 0.845 2.662 -0.7503 0.2534 -1.7621 + 42SOL OW 139 0.001 1.575 2.291 0.3773 -0.2907 0.6859 + 42SOL HW1 140 -0.010 1.482 2.308 0.0919 -0.7905 -2.1912 + 42SOL HW2 141 0.066 1.579 2.220 0.0715 1.6775 0.5138 + 43SOL OW 142 1.807 1.206 1.137 -0.7559 -0.3433 -0.3638 + 43SOL HW1 143 1.765 1.278 1.088 0.5200 0.2070 -0.6501 + 43SOL HW2 144 1.832 1.143 1.069 -0.8884 -0.5534 -0.2167 + 44SOL OW 145 0.321 2.591 0.199 0.2019 -0.5734 -0.4725 + 44SOL HW1 146 0.343 2.621 0.287 0.4920 1.4184 -1.2165 + 44SOL HW2 147 0.403 2.555 0.165 0.0740 -1.3924 0.1050 + 45SOL OW 148 2.483 0.084 1.303 0.5206 0.1403 0.4123 + 45SOL HW1 149 2.419 0.032 1.253 0.8478 0.5216 -0.4018 + 45SOL HW2 150 2.553 0.102 1.240 1.5299 -0.4744 1.3791 + 46SOL OW 151 0.518 1.732 2.035 -0.0205 0.3126 0.0140 + 46SOL HW1 152 0.438 1.713 1.985 0.9083 -1.3843 -0.8394 + 46SOL HW2 153 0.541 1.648 2.076 2.0436 0.5044 -0.7569 + 47SOL OW 154 1.666 2.579 2.565 0.4199 -0.4247 0.3098 + 47SOL HW1 155 1.639 2.504 2.619 0.7916 -0.3082 0.6581 + 47SOL HW2 156 1.656 2.548 2.475 0.1761 -0.7550 0.4452 + 48SOL OW 157 1.068 0.996 1.334 -0.7489 -0.2519 -0.2142 + 48SOL HW1 158 1.104 1.030 1.252 -0.5227 -0.0315 -0.0289 + 48SOL HW2 159 1.050 1.075 1.386 0.6200 -0.4426 0.5684 + 49SOL OW 160 0.451 0.721 1.903 0.3448 -0.4918 0.3403 + 49SOL HW1 161 0.526 0.743 1.959 0.6902 -0.0601 -0.2940 + 49SOL HW2 162 0.381 0.779 1.934 0.8133 0.4186 -0.3165 + 50SOL OW 163 0.231 0.029 1.861 0.6214 0.2681 -0.3238 + 50SOL HW1 164 0.176 -0.001 1.789 1.5655 -3.1770 0.4326 + 50SOL HW2 165 0.314 0.052 1.819 0.2281 0.9504 -0.7430 + 51SOL OW 166 2.102 2.025 0.796 -1.1713 0.0678 -0.0483 + 51SOL HW1 167 2.158 2.061 0.727 -1.3550 0.2364 -0.1080 + 51SOL HW2 168 2.047 2.098 0.823 0.0326 0.4512 1.4172 + 52SOL OW 169 0.459 1.932 0.260 0.2220 0.6133 0.2140 + 52SOL HW1 170 0.520 1.926 0.334 -0.8108 -1.1643 0.9208 + 52SOL HW2 171 0.434 2.025 0.257 0.3645 0.7155 2.0175 + 53SOL OW 172 1.855 2.534 0.900 0.3390 0.4565 0.5634 + 53SOL HW1 173 1.887 2.622 0.879 -0.4646 0.5995 -0.0587 + 53SOL HW2 174 1.934 2.482 0.911 0.8032 1.0188 -0.0958 + 54SOL OW 175 0.598 0.773 0.368 -0.0264 -0.3660 -0.0761 + 54SOL HW1 176 0.641 0.696 0.331 0.4425 0.5166 -1.3817 + 54SOL HW2 177 0.661 0.844 0.355 -0.4744 0.2576 1.0825 + 55SOL OW 178 0.736 2.466 0.148 -0.0273 0.5391 -0.5600 + 55SOL HW1 179 0.754 2.560 0.141 -1.3962 0.8130 -0.4274 + 55SOL HW2 180 0.802 2.434 0.209 0.8266 1.3101 -1.0668 + 56SOL OW 181 1.509 0.935 2.254 0.1999 -0.1693 -0.7037 + 56SOL HW1 182 1.503 0.924 2.349 2.5062 -0.3645 -0.5650 + 56SOL HW2 183 1.508 1.030 2.241 0.2546 -0.1345 -0.4613 + 57SOL OW 184 2.448 0.462 1.235 0.0726 -0.1896 -0.4061 + 57SOL HW1 185 2.432 0.426 1.147 -0.3750 -0.7223 -0.1006 + 57SOL HW2 186 2.502 0.540 1.219 0.2056 -0.4320 -1.1374 + 58SOL OW 187 0.456 1.903 1.168 -0.5626 0.0957 0.5677 + 58SOL HW1 188 0.522 1.960 1.207 -1.2821 -0.3702 2.4861 + 58SOL HW2 189 0.487 1.814 1.185 -0.3859 -0.0987 -0.7737 + 59SOL OW 190 2.370 1.044 2.119 0.0234 -0.2827 -0.3456 + 59SOL HW1 191 2.299 1.005 2.069 -0.9604 -0.0514 0.8670 + 59SOL HW2 192 2.348 1.025 2.211 0.4364 1.6565 0.1442 + 60SOL OW 193 0.409 1.687 0.130 0.9001 -0.0711 0.3532 + 60SOL HW1 194 0.371 1.620 0.188 4.6935 -2.2672 0.3317 + 60SOL HW2 195 0.416 1.765 0.185 0.8396 -1.0249 1.7279 + 61SOL OW 196 2.461 0.233 1.938 -0.7688 0.2684 -0.4418 + 61SOL HW1 197 2.519 0.167 1.899 0.7801 0.8321 0.9468 + 61SOL HW2 198 2.407 0.184 2.000 0.8882 0.4343 1.1336 + 62SOL OW 199 2.268 2.042 2.006 -0.7151 -0.0326 0.1354 + 62SOL HW1 200 2.297 1.988 2.079 -0.7321 1.3955 1.1893 + 62SOL HW2 201 2.336 2.109 1.996 -1.6809 0.9555 0.1083 + 63SOL OW 202 1.284 2.535 2.055 -0.6584 0.5583 -0.0691 + 63SOL HW1 203 1.276 2.443 2.031 0.7581 0.3673 0.1937 + 63SOL HW2 204 1.195 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0.265 2.594 0.1087 0.3328 -0.1468 + 635SOL HW1 1919 0.556 0.286 2.598 0.1085 -0.2031 2.4548 + 635SOL HW2 1920 0.452 0.191 2.653 -2.5187 2.3972 1.9792 + 636SOL OW 1921 1.707 1.242 0.589 -0.4519 0.2162 0.2778 + 636SOL HW1 1922 1.695 1.239 0.684 -0.0429 -0.2555 0.3127 + 636SOL HW2 1923 1.640 1.303 0.559 1.2224 2.5198 1.1684 + 637SOL OW 1924 1.431 1.410 0.742 -0.3875 0.2731 -0.1822 + 637SOL HW1 1925 1.492 1.446 0.806 -1.7041 2.8456 -0.3963 + 637SOL HW2 1926 1.345 1.422 0.781 -0.6967 -4.2406 0.5537 + 638SOL OW 1927 1.891 1.847 0.668 0.6121 0.2142 -0.1455 + 638SOL HW1 1928 1.849 1.919 0.622 2.2424 1.0863 -0.2557 + 638SOL HW2 1929 1.946 1.889 0.734 -0.3535 -0.9795 1.4286 + 639SOL OW 1930 1.493 1.530 2.364 -0.5750 0.4402 0.4708 + 639SOL HW1 1931 1.557 1.560 2.429 0.8451 -1.3546 -0.1106 + 639SOL HW2 1932 1.436 1.470 2.413 -1.7778 1.9980 0.9759 + 640SOL OW 1933 1.383 2.702 2.297 -0.3449 0.0457 -0.3488 + 640SOL HW1 1934 1.365 2.640 2.225 1.2108 -1.6411 0.7031 + 640SOL HW2 1935 1.398 2.646 2.373 -2.0973 1.8481 1.3284 + 641SOL OW 1936 0.923 2.084 2.113 -0.4725 -0.1256 0.1503 + 641SOL HW1 1937 0.935 2.041 2.028 -0.0338 -0.6001 0.4496 + 641SOL HW2 1938 0.929 2.178 2.093 1.9071 -0.3051 -0.0042 + 642SOL OW 1939 2.743 1.279 2.388 0.5270 -0.0877 -0.8404 + 642SOL HW1 1940 2.669 1.304 2.333 -0.2829 -1.5816 -0.4344 + 642SOL HW2 1941 2.820 1.294 2.332 -0.2757 -1.3702 -2.3173 + 643SOL OW 1942 2.088 1.680 0.520 0.0616 -0.6132 0.1857 + 643SOL HW1 1943 2.054 1.592 0.503 -2.0184 -0.0060 1.3017 + 643SOL HW2 1944 2.014 1.728 0.557 1.7454 1.0541 1.3749 + 644SOL OW 1945 2.568 2.456 0.489 0.3549 -0.0420 0.2014 + 644SOL HW1 1946 2.475 2.472 0.508 0.0710 -2.0172 0.5750 + 644SOL HW2 1947 2.585 2.502 0.407 -1.3251 -0.8219 -0.5899 + 645SOL OW 1948 1.765 0.465 2.675 0.2852 -0.5857 -0.0373 + 645SOL HW1 1949 1.787 0.374 2.655 1.8677 -0.3260 0.5171 + 645SOL HW2 1950 1.845 0.514 2.655 -0.6759 0.7320 -0.6754 + 646SOL OW 1951 0.781 0.722 1.426 0.0942 0.0866 -0.3950 + 646SOL HW1 1952 0.796 0.745 1.335 -1.8741 -0.4370 -0.8455 + 646SOL HW2 1953 0.700 0.767 1.450 -0.0359 -0.7409 0.7452 + 647SOL OW 1954 1.568 2.444 1.593 0.1763 -0.0713 0.5210 + 647SOL HW1 1955 1.664 2.443 1.591 0.1277 -0.3274 -1.5280 + 647SOL HW2 1956 1.544 2.355 1.616 0.4247 -0.0687 0.7928 + 648SOL OW 1957 1.606 0.151 2.095 0.2479 0.2598 -0.1989 + 648SOL HW1 1958 1.521 0.186 2.121 0.6531 0.4651 0.8495 + 648SOL HW2 1959 1.633 0.206 2.021 -0.2293 0.6121 -0.1086 + 649SOL OW 1960 0.403 1.372 1.479 -0.0774 0.3293 0.4984 + 649SOL HW1 1961 0.372 1.461 1.465 1.4632 0.6184 -1.0361 + 649SOL HW2 1962 0.333 1.316 1.443 -1.1253 0.9150 1.6400 + 650SOL OW 1963 2.657 1.644 1.507 0.0317 0.4079 0.3517 + 650SOL HW1 1964 2.587 1.652 1.572 -1.3902 0.8247 -1.2536 + 650SOL HW2 1965 2.621 1.589 1.438 1.4148 0.2857 -0.2744 + 651SOL OW 1966 2.100 0.549 1.511 0.0493 -0.0962 -0.1314 + 651SOL HW1 1967 2.115 0.548 1.416 2.1221 -0.4321 0.1923 + 651SOL HW2 1968 2.187 0.566 1.548 -0.5357 -1.2414 1.7480 + 652SOL OW 1969 1.376 1.833 0.736 -0.0633 0.1528 0.5469 + 652SOL HW1 1970 1.327 1.780 0.673 0.4046 0.6198 -0.2170 + 652SOL HW2 1971 1.460 1.848 0.692 0.4945 -0.0668 1.5564 + 653SOL OW 1972 0.014 0.788 2.332 -0.1766 -0.3103 -0.3931 + 653SOL HW1 1973 -0.029 0.740 2.261 0.6918 0.2641 -1.3111 + 653SOL HW2 1974 0.008 0.880 2.306 -2.4263 0.1219 1.6840 + 654SOL OW 1975 0.434 2.098 2.537 0.2668 0.0819 0.1329 + 654SOL HW1 1976 0.524 2.071 2.519 -0.1837 -0.7710 -0.8541 + 654SOL HW2 1977 0.440 2.149 2.618 1.5340 -0.5454 0.4410 + 655SOL OW 1978 2.699 0.844 1.030 0.4957 -0.2857 0.0160 + 655SOL HW1 1979 2.669 0.778 1.092 0.8025 1.0338 1.5908 + 655SOL HW2 1980 2.631 0.848 0.963 -1.0653 0.0605 1.6149 + 656SOL OW 1981 1.504 1.426 1.417 -0.2854 0.0802 -0.3695 + 656SOL HW1 1982 1.537 1.491 1.479 2.6587 -1.1154 -0.6843 + 656SOL HW2 1983 1.470 1.355 1.471 -1.4130 0.8543 -0.0632 + 657SOL OW 1984 0.161 0.593 1.135 0.6199 -0.0444 -0.6181 + 657SOL HW1 1985 0.192 0.616 1.223 -0.2707 -0.5140 -0.1890 + 657SOL HW2 1986 0.233 0.542 1.098 0.8248 -0.1971 -0.0115 + 658SOL OW 1987 0.103 0.685 0.808 0.5167 -0.0174 0.2686 + 658SOL HW1 1988 0.183 0.732 0.830 1.3237 -1.6834 0.8879 + 658SOL HW2 1989 0.046 0.699 0.884 1.0636 -0.7566 0.8077 + 659SOL OW 1990 0.759 1.448 1.006 -0.3741 -0.2210 0.2449 + 659SOL HW1 1991 0.776 1.385 1.076 -0.9503 0.0887 0.6730 + 659SOL HW2 1992 0.821 1.519 1.022 -0.4428 -0.1932 0.3924 + 660SOL OW 1993 1.005 0.710 0.397 -0.0645 -0.0597 -0.3827 + 660SOL HW1 1994 1.062 0.702 0.320 -0.4461 0.9072 -0.7655 + 660SOL HW2 1995 1.066 0.724 0.470 0.1874 1.1464 -0.8176 + 661SOL OW 1996 0.349 1.148 2.423 0.4415 -0.0668 0.0872 + 661SOL HW1 1997 0.290 1.204 2.372 0.9129 0.9977 0.7039 + 661SOL HW2 1998 0.423 1.205 2.445 1.2153 -1.1106 0.1887 + 662SOL OW 1999 2.381 1.485 1.900 -0.5421 -0.3903 0.6089 + 662SOL HW1 2000 2.377 1.480 1.995 -1.6564 -2.7613 0.4475 + 662SOL HW2 2001 2.290 1.471 1.872 -0.1436 -0.1288 -0.8121 + 663SOL OW 2002 2.198 0.481 2.557 -0.5547 0.2364 -0.0028 + 663SOL HW1 2003 2.237 0.478 2.470 -2.6833 0.5336 -0.9675 + 663SOL HW2 2004 2.126 0.544 2.549 0.5076 1.7575 2.4680 + 664SOL OW 2005 0.691 1.694 0.061 -0.1091 0.4072 -0.2967 + 664SOL HW1 2006 0.670 1.645 -0.019 -1.0358 0.5557 -0.1528 + 664SOL HW2 2007 0.614 1.681 0.117 -0.0551 1.4532 0.0140 + 665SOL OW 2008 2.358 2.557 1.887 -0.3927 0.0003 -0.5449 + 665SOL HW1 2009 2.403 2.589 1.965 -0.1191 0.7341 -1.0053 + 665SOL HW2 2010 2.273 2.601 1.888 0.3653 1.4919 -1.7054 + 666SOL OW 2011 2.160 0.312 0.686 -0.4695 -0.3591 -0.0482 + 666SOL HW1 2012 2.246 0.346 0.664 -1.5836 2.5863 0.0956 + 666SOL HW2 2013 2.142 0.246 0.619 1.2477 0.0709 -0.9203 + 667SOL OW 2014 0.083 2.191 0.158 0.7137 0.3561 -0.2947 + 667SOL HW1 2015 0.020 2.130 0.119 -0.1620 -0.2758 2.1455 + 667SOL HW2 2016 0.168 2.150 0.142 0.2347 -0.7453 -0.0069 + 668SOL OW 2017 2.021 0.831 1.354 0.7416 -0.5588 -0.5376 + 668SOL HW1 2018 1.946 0.874 1.393 0.2846 -0.1343 -1.8838 + 668SOL HW2 2019 1.998 0.738 1.353 -0.2902 -0.2832 -2.1218 + 669SOL OW 2020 0.922 1.825 0.126 0.0016 0.0916 0.3885 + 669SOL HW1 2021 0.877 1.890 0.179 0.9055 -0.4473 1.8198 + 669SOL HW2 2022 0.852 1.769 0.091 -0.6427 0.8770 0.4200 + 670SOL OW 2023 1.093 1.448 0.155 0.3406 0.0412 0.3213 + 670SOL HW1 2024 1.018 1.396 0.128 -0.4294 -0.1328 2.8346 + 670SOL HW2 2025 1.155 1.440 0.083 -0.3549 -3.1787 0.0996 + 671SOL OW 2026 2.533 1.739 0.963 0.8306 0.4031 0.0296 + 671SOL HW1 2027 2.508 1.673 0.899 -0.0507 -0.2605 1.0722 + 671SOL HW2 2028 2.473 1.812 0.947 0.1163 -0.0645 0.6316 + 672SOL OW 2029 0.339 1.364 0.756 -0.0836 0.0628 0.0272 + 672SOL HW1 2030 0.428 1.338 0.778 0.7321 1.9559 -1.0201 + 672SOL HW2 2031 0.335 1.358 0.660 -1.5561 -1.5635 0.1818 + 673SOL OW 2032 2.489 1.363 1.555 -0.0314 0.1905 -0.2258 + 673SOL HW1 2033 2.426 1.302 1.594 0.9917 -2.5890 -2.9222 + 673SOL HW2 2034 2.452 1.450 1.572 -1.3238 -1.1640 3.9207 + 674SOL OW 2035 1.277 0.792 1.117 0.6240 0.4402 0.4712 + 674SOL HW1 2036 1.243 0.734 1.185 1.6634 -0.6545 0.0674 + 674SOL HW2 2037 1.206 0.853 1.098 -0.2818 -0.3872 1.2739 + 675SOL OW 2038 2.096 2.435 1.578 0.3599 0.1524 0.0504 + 675SOL HW1 2039 2.082 2.521 1.538 -0.3263 0.4105 0.8403 + 675SOL HW2 2040 2.187 2.437 1.609 0.8879 -0.0462 -1.4884 + 676SOL OW 2041 1.082 0.433 1.275 -0.2254 0.2026 -0.4785 + 676SOL HW1 2042 0.999 0.444 1.229 -0.1512 1.3119 -0.3443 + 676SOL HW2 2043 1.059 0.391 1.358 -0.6065 0.1806 -0.5973 + 677SOL OW 2044 2.002 2.016 2.307 0.2612 -0.0095 0.3725 + 677SOL HW1 2045 1.938 2.078 2.270 -0.2255 -1.4111 -1.1569 + 677SOL HW2 2046 2.064 2.071 2.355 0.1320 1.7136 -1.4212 + 678SOL OW 2047 0.653 1.959 2.489 -0.2630 0.0352 -0.0432 + 678SOL HW1 2048 0.739 2.000 2.477 -0.4320 -0.0608 -1.5935 + 678SOL HW2 2049 0.657 1.878 2.439 -0.5886 -0.9418 1.4927 + 679SOL OW 2050 0.266 1.760 2.333 0.3583 -0.1572 0.2423 + 679SOL HW1 2051 0.259 1.669 2.305 0.2558 -0.0843 0.0285 + 679SOL HW2 2052 0.329 1.759 2.404 0.4320 -0.3816 0.1722 + 680SOL OW 2053 2.108 1.566 0.980 -0.3633 0.3381 -0.0810 + 680SOL HW1 2054 2.180 1.503 0.978 -0.3715 0.3409 -0.4094 + 680SOL HW2 2055 2.143 1.641 1.028 -1.1841 -0.9435 2.5463 + 2.75671 2.75671 2.75671 diff --git a/ensemble_md/tests/data/coord_swap/B-C.itp b/ensemble_md/tests/data/coord_swap/B-C.itp new file mode 100644 index 00000000..1e789156 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/B-C.itp @@ -0,0 +1,192 @@ + + + +[ moleculetype ] +; Name nrexcl +B2C 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB + 1 ss 1 B2C S1 1 -0.116300 32.0600 + 2 cc 1 B2C C2 2 0.402700 12.0100 cc 0.403700 12.0100 + 3 nd 1 B2C N3 3 -0.634000 14.0100 nd -0.635000 14.0100 + 4 cd 1 B2C C4 4 0.332200 12.0100 + 5 cc 1 B2C C5 5 -0.251400 12.0100 cc -0.252400 12.0100 + 6 c3 1 B2C C6 6 -0.110700 12.0100 + 7 c3 1 B2C C7 7 -0.089100 12.0100 c3 -0.076400 12.0100 + 8 h4 1 B2C H1 8 0.043100 1.0080 + 9 h4 1 B2C H2 9 0.180000 1.0080 + 10 hc 1 B2C H3 10 0.057250 1.0080 hc 0.058200 1.0080 + 11 hc 1 B2C H4 11 0.057250 1.0080 hc 0.058200 1.0080 + 12 hc 1 B2C H5 12 0.043000 1.0080 DUM_hc 0.000000 1.0080 + 13 hc 1 B2C H6 13 0.043000 1.0080 hc 0.052700 1.0080 + 14 hc 1 B2C H7 14 0.043000 1.0080 hc 0.052700 1.0080 + 15 DUM_c3 1 B2C DC8 15 0.000000 12.0100 c3 -0.095100 12.0100 + 16 DUM_hc 1 B2C HV8 16 0.000000 1.0080 hc 0.035033 1.0080 + 17 DUM_hc 1 B2C HV9 17 0.000000 1.0080 hc 0.035033 1.0080 + 18 DUM_hc 1 B2C HV10 18 0.000000 1.0080 hc 0.035033 1.0080 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 0.175380 193853.088000 0.175380 193853.088000 + 1 5 1 0.175380 193853.088000 0.175380 193853.088000 + 2 3 1 0.131580 351221.696000 0.131580 351221.696000 + 2 6 1 0.150020 213501.152000 0.150020 213501.152000 + 3 4 1 0.137130 289474.224000 0.137130 289474.224000 + 4 5 1 0.137300 323205.632000 0.137300 323205.632000 + 6 7 1 0.153540 191535.152000 0.153540 191535.152000 + 4 8 1 0.108180 307348.272000 0.108180 307348.272000 + 5 9 1 0.108090 308544.896000 0.108090 308544.896000 + 6 10 1 0.109620 288905.200000 0.109620 288905.200000 + 6 11 1 0.109620 288905.200000 0.109620 288905.200000 + 7 12 1 0.109620 288905.200000 0.109620 288905.200000 + 7 13 1 0.109620 288905.200000 0.109620 288905.200000 + 7 14 1 0.109620 288905.200000 0.109620 288905.200000 + 7 15 1 0.153540 191535.152000 0.153540 191535.152000 + 15 16 1 0.109620 288905.200000 0.109620 288905.200000 + 15 17 1 0.109620 288905.200000 0.109620 288905.200000 + 15 18 1 0.109620 288905.200000 0.109620 288905.200000 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 7 1 + 3 7 1 + 4 6 1 + 5 6 1 + 1 10 1 + 1 11 1 + 1 8 1 + 2 9 1 + 2 8 1 + 2 12 1 + 2 13 1 + 2 14 1 + 3 10 1 + 3 11 1 + 3 9 1 + 8 9 1 + 10 12 1 + 10 13 1 + 10 14 1 + 11 12 1 + 11 13 1 + 11 14 1 + 2 15 1 + 6 16 1 + 6 17 1 + 6 18 1 + 15 10 1 + 15 11 1 + 13 16 1 + 13 17 1 + 13 18 1 + 14 16 1 + 14 17 1 + 14 18 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3 + 1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6 + 1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4 + 2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5 + 2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4 + 2 6 7 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 C7 + 3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6 + 3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5 + 1 5 9 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2 + 2 6 10 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3 + 2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H4 + 3 4 8 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1 + 4 5 9 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2 + 5 4 8 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1 + 6 7 12 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H5 + 6 7 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H6 + 6 7 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H7 + 7 6 10 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 H3 + 7 6 11 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 H4 + 10 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H4 + 12 7 13 1 107.730046 299.574400 107.730046 299.574400 ; H5 C7 H6 + 12 7 14 1 107.730046 299.574400 107.730046 299.574400 ; H5 C7 H7 + 13 7 14 1 107.730046 299.574400 107.730046 299.574400 ; H6 C7 H7 + 6 7 15 1 112.630048 500.992160 112.630048 500.992160 ; C6 C7 DC8 + 7 15 16 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC8 HV8 + 7 15 17 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC8 HV9 + 7 15 18 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC8 HV10 + 15 7 13 1 109.680047 362.083360 109.680047 362.083360 ; DC8 C7 H6 + 15 7 14 1 109.680047 362.083360 109.680047 362.083360 ; DC8 C7 H7 + 16 15 17 1 107.730046 299.574400 107.730046 299.574400 ; HV8 DC8 HV9 + 16 15 18 1 107.730046 299.574400 107.730046 299.574400 ; HV8 DC8 HV10 + 17 15 18 1 107.730046 299.574400 107.730046 299.574400 ; HV9 DC8 HV10 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA) + 1 5 4 8 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 9 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 8 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 12 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H5 (AAAA->AAAD) + 2 6 7 13 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H6 (AAAA->AAAA) + 2 6 7 14 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA) + 3 4 5 9 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 8 4 5 9 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 10 6 7 12 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H5 (AAAA->AAAD) + 10 6 7 13 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H6 (AAAA->AAAA) + 10 6 7 14 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 11 6 7 12 1 0 0.50208 3 0 0 3 ; H4 C6 C7 H5 (AAAA->AAAD) + 11 6 7 13 1 0 0.50208 3 0 0 3 ; H4 C6 C7 H6 (AAAA->AAAA) + 11 6 7 14 1 0 0.50208 3 0 0 3 ; H4 C6 C7 H7 (AAAA->AAAA) + 5 8 4 3 4 180.0000771 4.6024 2 180.0000771 0 2 ; C5 H1 C4 N3 (AAAA->AAAA) + 1 5 9 4 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C5 H2 C4 (AAAA->AAAA) + 1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 2 6 7 15 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 DC8 (AAAD->AAAA) + 5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA) + 1 5 4 8 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 9 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 8 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 13 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H6 (AAAA->AAAA) + 2 6 7 14 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA) + 3 4 5 9 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 6 7 15 16 1 0 0 3 0 0.54392 3 ; C6 C7 DC8 HV8 (AADD->AAAA) + 6 7 15 17 1 0 0 3 0 0.54392 3 ; C6 C7 DC8 HV9 (AADD->AAAA) + 6 7 15 18 1 0 0 3 0 0.54392 3 ; C6 C7 DC8 HV10 (AADD->AAAA) + 15 7 6 10 1 0 0 3 0 0.54392 3 ; DC8 C7 C6 H3 (DAAA->AAAA) + 15 7 6 11 1 0 0 3 0 0.54392 3 ; DC8 C7 C6 H4 (DAAA->AAAA) + 8 4 5 9 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 10 6 7 13 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H6 (AAAA->AAAA) + 10 6 7 14 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 11 6 7 13 1 0 0 3 0 0.50208 3 ; H4 C6 C7 H6 (AAAA->AAAA) + 11 6 7 14 1 0 0 3 0 0.50208 3 ; H4 C6 C7 H7 (AAAA->AAAA) + 13 7 15 16 1 0 0 3 0 0.50208 3 ; H6 C7 DC8 HV8 (AADD->AAAA) + 13 7 15 17 1 0 0 3 0 0.50208 3 ; H6 C7 DC8 HV9 (AADD->AAAA) + 13 7 15 18 1 0 0 3 0 0.50208 3 ; H6 C7 DC8 HV10 (AADD->AAAA) + 14 7 15 16 1 0 0 3 0 0.50208 3 ; H7 C7 DC8 HV8 (AADD->AAAA) + 14 7 15 17 1 0 0 3 0 0.50208 3 ; H7 C7 DC8 HV9 (AADD->AAAA) + 14 7 15 18 1 0 0 3 0 0.50208 3 ; H7 C7 DC8 HV10 (AADD->AAAA) + + diff --git a/ensemble_md/tests/data/coord_swap/B-C.top b/ensemble_md/tests/data/coord_swap/B-C.top new file mode 100644 index 00000000..7850b194 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/B-C.top @@ -0,0 +1,32 @@ +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.83333333 + +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +ss 16 32.060000 0.00000000 A 0.35324134 1.1815616 +cc 6 12.010000 0.00000000 A 0.33152123 0.4133792 +nd 7 14.010000 0.00000000 A 0.33841679 0.3937144 +cd 6 12.010000 0.00000000 A 0.33152123 0.4133792 +c3 6 12.010000 0.00000000 A 0.33977095 0.4510352 +h4 1 1.008000 0.00000000 A 0.25363887 0.0673624 +hc 1 1.008000 0.00000000 A 0.2600177 0.0870272 +DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000 +DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000 +Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02 +Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 + +#include "B-C.itp" + +#include "water_and_ions.itp" + +[ system ] +; Name +Generic title in water + +[ molecules ] +; Compound #mols +B2C 1 +SOL 679 diff --git a/ensemble_md/tests/data/coord_swap/C-D.gro b/ensemble_md/tests/data/coord_swap/C-D.gro new file mode 100644 index 00000000..c0520045 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/C-D.gro @@ -0,0 +1,2062 @@ +Generic title in water + 2059 + 1C2D S1 1 1.877 2.610 2.252 -0.4051 0.0356 0.4633 + 1C2D C2 2 2.005 2.511 2.185 0.2228 -0.2524 0.2354 + 1C2D N3 3 2.051 2.405 2.258 -0.0154 -0.6269 -0.3307 + 1C2D C4 4 1.979 2.396 2.376 -0.5186 0.1612 -0.3217 + 1C2D C5 5 1.894 2.500 2.390 0.1033 -0.0150 0.2187 + 1C2D C6 6 2.078 2.568 2.077 0.2465 0.4146 0.0415 + 1C2D C7 7 2.023 2.506 1.945 0.0938 0.1640 -0.0050 + 1C2D C8 8 2.106 2.551 1.826 -0.0494 1.2855 -0.2842 + 1C2D H1 9 1.987 2.316 2.449 0.6878 -0.5710 -1.2489 + 1C2D H2 10 1.815 2.515 2.462 1.1325 -1.3555 1.6176 + 1C2D H3 11 2.074 2.678 2.079 -1.9944 0.3092 2.1186 + 1C2D H4 12 2.184 2.546 2.098 0.0208 -0.4765 0.2409 + 1C2D H6 13 1.918 2.535 1.934 0.4469 0.9739 -1.2483 + 1C2D H7 14 2.019 2.397 1.952 -0.8770 0.1640 -0.5263 + 1C2D H8 15 2.209 2.515 1.841 -1.1683 -2.3604 -1.3316 + 1C2D H9 16 2.067 2.511 1.732 -0.0578 -2.6054 1.3513 + 1C2D H10 17 2.110 2.661 1.827 1.8657 1.2102 0.4343 + 1C2D DC9 18 2.222 2.531 2.086 -0.7856 -0.3972 -0.0263 + 1C2D HV5 19 2.084 2.541 1.861 0.3456 0.4618 0.3004 + 1C2D HV11 20 2.260 2.576 2.179 2.7839 -0.0740 -1.6623 + 1C2D HV12 21 2.280 2.572 2.003 1.4614 -0.4531 1.5101 + 1C2D HV13 22 2.228 2.421 2.090 1.4577 -0.3007 -0.8839 + 2SOL OW 23 0.275 1.873 0.391 0.5566 0.2768 -0.6974 + 2SOL HW1 24 0.338 1.803 0.406 0.7363 0.1688 -1.9380 + 2SOL HW2 25 0.306 1.916 0.311 -0.4923 0.7185 -0.8667 + 3SOL OW 26 0.873 1.174 2.340 0.3121 -0.0660 0.3243 + 3SOL HW1 27 0.921 1.256 2.356 -0.3143 0.5798 -1.0595 + 3SOL HW2 28 0.782 1.195 2.359 0.3326 -0.7973 1.2163 + 4SOL OW 29 1.925 1.877 2.429 -0.3819 0.0526 -0.0077 + 4SOL HW1 30 1.998 1.895 2.370 -1.1077 -2.6086 -1.7084 + 4SOL HW2 31 1.863 1.949 2.413 0.5063 0.6587 -0.7297 + 5SOL OW 32 0.870 1.583 0.069 0.0569 -0.2438 0.5884 + 5SOL HW1 33 0.864 1.631 0.152 -1.3583 -1.0049 0.9310 + 5SOL HW2 34 0.828 1.499 0.088 -0.9948 -0.0929 -1.1610 + 6SOL OW 35 1.097 2.257 0.858 -0.4282 0.1043 -0.6437 + 6SOL HW1 36 1.070 2.178 0.812 1.4072 0.8009 -2.9207 + 6SOL HW2 37 1.096 2.234 0.950 1.4584 -2.9526 -1.4062 + 7SOL OW 38 0.671 1.173 1.840 0.1104 0.0087 0.0857 + 7SOL HW1 39 0.583 1.142 1.859 0.2806 1.0557 2.6352 + 7SOL HW2 40 0.662 1.223 1.759 -1.4397 -0.8711 -0.2715 + 8SOL OW 41 0.691 2.189 1.747 0.1171 1.0587 0.1291 + 8SOL HW1 42 0.742 2.118 1.788 -1.2214 0.3215 0.5090 + 8SOL HW2 43 0.711 2.181 1.654 0.4594 0.5697 0.2384 + 9SOL OW 44 1.155 1.830 2.080 0.5313 0.4611 -0.0732 + 9SOL HW1 45 1.209 1.773 2.025 -1.6833 -1.4658 -0.2636 + 9SOL HW2 46 1.173 1.800 2.169 0.0875 0.0402 -0.1175 + 10SOL OW 47 0.822 1.343 1.069 0.0713 0.1056 0.0183 + 10SOL HW1 48 0.735 1.320 1.103 -0.4080 -0.8478 -1.8280 + 10SOL HW2 49 0.805 1.415 1.008 0.5773 -0.0629 -0.3213 + 11SOL OW 50 0.936 1.158 0.898 0.1719 -0.1173 0.0404 + 11SOL HW1 51 0.884 1.219 0.951 1.7114 -0.4043 1.8885 + 11SOL HW2 52 1.025 1.165 0.934 0.7489 -1.9680 -1.0495 + 12SOL OW 53 0.671 2.276 1.108 -0.0639 -0.0928 -0.4182 + 12SOL HW1 54 0.734 2.307 1.044 0.9740 1.9872 1.6403 + 12SOL HW2 55 0.628 2.355 1.140 0.1161 -1.0664 2.1983 + 13SOL OW 56 1.816 1.547 0.518 -0.0253 0.2366 -0.0123 + 13SOL HW1 57 1.884 1.614 0.513 -0.1346 0.3469 -0.0108 + 13SOL HW2 58 1.755 1.579 0.584 0.3303 -0.2325 0.5471 + 14SOL OW 59 2.171 2.648 0.430 0.0940 -0.0086 0.3025 + 14SOL HW1 60 2.176 2.574 0.491 -0.4338 -0.9931 -0.8407 + 14SOL HW2 61 2.078 2.656 0.409 0.1724 0.8914 0.3081 + 15SOL OW 62 0.807 0.175 0.286 -0.1648 -0.7139 -0.6854 + 15SOL HW1 63 0.834 0.262 0.315 -1.9007 -0.2833 -0.3557 + 15SOL HW2 64 0.813 0.120 0.364 0.5210 -0.7963 -0.7958 + 16SOL OW 65 0.132 2.082 0.868 0.4789 0.1305 -0.0840 + 16SOL HW1 66 0.170 2.040 0.790 0.4137 0.4646 -0.3001 + 16SOL HW2 67 0.095 2.011 0.919 1.3075 -0.1861 0.0689 + 17SOL OW 68 0.746 1.408 0.630 -0.6923 -0.0051 0.1391 + 17SOL HW1 69 0.671 1.442 0.581 -1.5659 -0.8059 0.9414 + 17SOL HW2 70 0.749 1.315 0.608 0.5833 0.2034 -0.5784 + 18SOL OW 71 1.739 2.398 0.711 0.3776 -0.0295 -0.2789 + 18SOL HW1 72 1.744 2.486 0.747 0.4019 0.5163 -1.5958 + 18SOL HW2 73 1.767 2.341 0.782 -0.3022 0.9764 0.7870 + 19SOL OW 74 1.925 2.052 0.852 0.1206 -0.3104 0.3495 + 19SOL HW1 75 1.926 1.974 0.796 0.0105 -0.7050 0.8993 + 19SOL HW2 76 1.970 2.119 0.801 -2.4001 0.0945 -1.3677 + 20SOL OW 77 0.331 1.333 1.183 0.1249 0.0990 0.2463 + 20SOL HW1 78 0.363 1.318 1.095 1.5067 1.2905 0.5401 + 20SOL HW2 79 0.300 1.247 1.213 1.3645 -0.6825 -0.7089 + 21SOL OW 80 0.579 0.703 1.994 0.2966 -0.4068 -0.3757 + 21SOL HW1 81 0.588 0.617 1.954 -0.1696 -0.3401 -0.6271 + 21SOL HW2 82 0.491 0.704 2.031 0.3295 -0.0716 -0.3035 + 22SOL OW 83 1.229 0.020 1.634 -0.3670 -0.3701 0.3499 + 22SOL HW1 84 1.151 -0.033 1.617 -0.7684 0.4820 -0.4787 + 22SOL HW2 85 1.246 0.009 1.727 -1.4754 -0.5653 0.5286 + 23SOL OW 86 1.836 0.265 0.042 1.1331 0.2792 -0.2785 + 23SOL HW1 87 1.870 0.295 -0.042 -1.3607 0.3566 -1.2698 + 23SOL HW2 88 1.853 0.337 0.102 2.4365 0.4383 -0.8338 + 24SOL OW 89 1.272 0.331 2.289 -0.4528 0.0684 0.1896 + 24SOL HW1 90 1.339 0.295 2.347 -0.8664 0.3067 0.8280 + 24SOL HW2 91 1.292 0.425 2.284 -0.9282 0.1978 0.6502 + 25SOL OW 92 1.959 2.656 1.402 -0.0029 0.2851 -0.0791 + 25SOL HW1 93 2.033 2.597 1.416 -1.4052 -1.5622 -0.3853 + 25SOL HW2 94 1.974 2.692 1.315 1.2651 0.9618 0.4214 + 26SOL OW 95 1.053 1.563 0.860 0.1194 -0.0307 -0.3598 + 26SOL HW1 96 1.130 1.507 0.858 0.9799 1.1248 0.5441 + 26SOL HW2 97 1.053 1.601 0.948 -0.1482 1.8410 -1.1749 + 27SOL OW 98 2.607 0.741 0.329 -0.3882 0.3738 -0.1755 + 27SOL HW1 99 2.540 0.778 0.271 -0.0038 0.1583 -0.7528 + 27SOL HW2 100 2.562 0.671 0.375 -1.1875 1.7226 1.0971 + 28SOL OW 101 1.678 1.689 2.537 -0.2863 0.6369 -0.2665 + 28SOL HW1 102 1.712 1.653 2.619 -0.1245 -0.0603 -0.6370 + 28SOL HW2 103 1.753 1.733 2.497 -0.3816 1.0305 -0.0034 + 29SOL OW 104 1.260 1.701 0.183 0.0151 0.1241 0.2655 + 29SOL HW1 105 1.288 1.792 0.193 2.4842 -0.6907 0.6904 + 29SOL HW2 106 1.298 1.656 0.259 0.0330 -1.5671 -0.7563 + 30SOL OW 107 0.293 0.771 1.775 -0.5422 -0.3870 0.4693 + 30SOL HW1 108 0.234 0.843 1.755 -0.2763 -0.2892 0.0388 + 30SOL HW2 109 0.242 0.692 1.757 -0.6976 -0.3056 0.5544 + 31SOL OW 110 1.758 0.695 0.199 0.3543 -0.2490 -0.4790 + 31SOL HW1 111 1.711 0.679 0.280 -0.9806 1.5109 -0.9304 + 31SOL HW2 112 1.691 0.716 0.135 1.7411 2.0413 -1.1730 + 32SOL OW 113 2.328 1.916 1.736 0.2088 0.3165 0.2654 + 32SOL HW1 114 2.356 1.852 1.801 2.4786 -0.0780 -1.0699 + 32SOL HW2 115 2.353 2.001 1.773 -2.4478 0.3870 1.8625 + 33SOL OW 116 1.933 2.126 1.291 -0.7391 -0.1114 0.0509 + 33SOL HW1 117 1.845 2.156 1.313 -0.8052 -1.0468 1.0477 + 33SOL HW2 118 1.963 2.187 1.224 -2.2893 -0.0162 -0.5535 + 34SOL OW 119 2.562 1.851 0.847 0.2332 0.5215 0.7575 + 34SOL HW1 120 2.624 1.878 0.914 0.7643 -2.3069 1.3740 + 34SOL HW2 121 2.615 1.843 0.767 0.6198 -1.7478 1.2513 + 35SOL OW 122 2.159 1.326 2.456 -0.1462 0.5792 -1.1347 + 35SOL HW1 123 2.116 1.389 2.399 0.1050 -0.1909 -2.1796 + 35SOL HW2 124 2.167 1.247 2.402 0.2183 -0.0964 -0.0840 + 36SOL OW 125 1.896 0.475 0.727 -0.1075 0.0187 0.5706 + 36SOL HW1 126 1.865 0.565 0.722 -1.5501 -0.4248 1.5446 + 36SOL HW2 127 1.885 0.441 0.638 1.6290 1.1974 -0.0992 + 37SOL OW 128 1.629 2.306 1.241 0.5608 0.8778 0.0333 + 37SOL HW1 129 1.678 2.316 1.159 -0.1273 0.6388 -0.4101 + 37SOL HW2 130 1.581 2.387 1.250 0.6494 0.9106 0.2126 + 38SOL OW 131 2.085 0.165 1.223 0.6235 -0.3879 0.1815 + 38SOL HW1 132 2.096 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2055 2.703 0.081 2.457 0.1308 -0.8946 0.3506 + 679SOL HW2 2056 2.619 0.112 2.579 -0.2103 1.1445 -0.3878 + 680SOL OW 2057 0.348 2.536 2.340 -0.3106 0.5240 0.3472 + 680SOL HW1 2058 0.425 2.494 2.377 0.0117 -0.1401 -1.0890 + 680SOL HW2 2059 0.278 2.518 2.404 0.9638 2.0288 2.1497 + 2.74964 2.74964 2.74964 diff --git a/ensemble_md/tests/data/coord_swap/C-D.itp b/ensemble_md/tests/data/coord_swap/C-D.itp new file mode 100644 index 00000000..a18a6d54 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/C-D.itp @@ -0,0 +1,235 @@ + + + +[ moleculetype ] +; Name nrexcl +C2D 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB + 1 ss 1 C2D S1 1 -0.116300 32.0600 ss -0.117300 32.0600 + 2 cc 1 C2D C2 2 0.403700 12.0100 cc 0.405700 12.0100 + 3 nd 1 C2D N3 3 -0.635000 14.0100 nd -0.633000 14.0100 + 4 cd 1 C2D C4 4 0.332200 12.0100 cd 0.331200 12.0100 + 5 cc 1 C2D C5 5 -0.252400 12.0100 cc -0.251400 12.0100 + 6 c3 1 C2D C6 6 -0.110700 12.0100 c3 -0.092000 12.0100 + 7 c3 1 C2D C7 7 -0.076400 12.0100 c3 -0.087100 12.0100 + 8 c3 1 C2D C8 8 -0.095100 12.0100 DUM_c3 0.000000 12.0100 + 9 h4 1 C2D H1 9 0.043100 1.0080 + 10 h4 1 C2D H2 10 0.180000 1.0080 + 11 hc 1 C2D H3 11 0.058200 1.0080 hc 0.049700 1.0080 + 12 hc 1 C2D H4 12 0.058200 1.0080 DUM_hc 0.000000 1.0080 + 13 hc 1 C2D H6 13 0.052700 1.0080 hc 0.043033 1.0080 + 14 hc 1 C2D H7 14 0.052700 1.0080 hc 0.043033 1.0080 + 15 hc 1 C2D H8 15 0.035033 1.0080 DUM_hc 0.000000 1.0080 + 16 hc 1 C2D H9 16 0.035033 1.0080 DUM_hc 0.000000 1.0080 + 17 hc 1 C2D H10 17 0.035033 1.0080 DUM_hc 0.000000 1.0080 + 18 DUM_c3 1 C2D DC9 18 0.000000 12.0100 c3 -0.087100 12.0100 + 19 DUM_hc 1 C2D HV5 19 0.000000 1.0080 hc 0.043033 1.0080 + 20 DUM_hc 1 C2D HV11 20 0.000000 1.0080 hc 0.043033 1.0080 + 21 DUM_hc 1 C2D HV12 21 0.000000 1.0080 hc 0.043033 1.0080 + 22 DUM_hc 1 C2D HV13 22 0.000000 1.0080 hc 0.043033 1.0080 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 0.175380 193853.088000 0.175380 193853.088000 + 1 5 1 0.175380 193853.088000 0.175380 193853.088000 + 2 3 1 0.131580 351221.696000 0.131580 351221.696000 + 2 6 1 0.150020 213501.152000 0.150020 213501.152000 + 3 4 1 0.137130 289474.224000 0.137130 289474.224000 + 4 5 1 0.137300 323205.632000 0.137300 323205.632000 + 6 7 1 0.153540 191535.152000 0.153540 191535.152000 + 7 8 1 0.153540 191535.152000 0.153540 191535.152000 + 4 9 1 0.108180 307348.272000 0.108180 307348.272000 + 5 10 1 0.108090 308544.896000 0.108090 308544.896000 + 6 11 1 0.109620 288905.200000 0.109620 288905.200000 + 6 12 1 0.109620 288905.200000 0.109620 288905.200000 + 7 13 1 0.109620 288905.200000 0.109620 288905.200000 + 7 14 1 0.109620 288905.200000 0.109620 288905.200000 + 8 15 1 0.109620 288905.200000 0.109620 288905.200000 + 8 16 1 0.109620 288905.200000 0.109620 288905.200000 + 8 17 1 0.109620 288905.200000 0.109620 288905.200000 + 6 18 1 0.153540 191535.152000 0.153540 191535.152000 + 7 19 1 0.109620 288905.200000 0.109620 288905.200000 + 18 20 1 0.109620 288905.200000 0.109620 288905.200000 + 18 21 1 0.109620 288905.200000 0.109620 288905.200000 + 18 22 1 0.109620 288905.200000 0.109620 288905.200000 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 7 1 + 2 8 1 + 3 7 1 + 4 6 1 + 5 6 1 + 1 11 1 + 1 12 1 + 1 9 1 + 2 10 1 + 2 9 1 + 2 13 1 + 2 14 1 + 3 11 1 + 3 12 1 + 3 10 1 + 6 15 1 + 6 16 1 + 6 17 1 + 8 11 1 + 8 12 1 + 9 10 1 + 11 13 1 + 11 14 1 + 12 13 1 + 12 14 1 + 13 15 1 + 13 16 1 + 13 17 1 + 14 15 1 + 14 16 1 + 14 17 1 + 1 18 1 + 3 18 1 + 2 19 1 + 2 20 1 + 2 21 1 + 2 22 1 + 7 20 1 + 7 21 1 + 7 22 1 + 18 19 1 + 18 13 1 + 18 14 1 + 11 19 1 + 11 20 1 + 11 21 1 + 11 22 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3 + 1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6 + 1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4 + 2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5 + 2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4 + 2 6 7 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 C7 + 3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6 + 3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5 + 6 7 8 1 112.630048 500.992160 112.630048 500.992160 ; C6 C7 C8 + 1 5 10 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2 + 2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3 + 2 6 12 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H4 + 3 4 9 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1 + 4 5 10 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2 + 5 4 9 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1 + 6 7 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H6 + 6 7 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H7 + 7 6 11 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 H3 + 7 6 12 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 H4 + 7 8 15 1 109.680047 362.083360 109.680047 362.083360 ; C7 C8 H8 + 7 8 16 1 109.680047 362.083360 109.680047 362.083360 ; C7 C8 H9 + 7 8 17 1 109.680047 362.083360 109.680047 362.083360 ; C7 C8 H10 + 8 7 13 1 109.680047 362.083360 109.680047 362.083360 ; C8 C7 H6 + 8 7 14 1 109.680047 362.083360 109.680047 362.083360 ; C8 C7 H7 + 11 6 12 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H4 + 13 7 14 1 107.730046 299.574400 107.730046 299.574400 ; H6 C7 H7 + 15 8 16 1 107.730046 299.574400 107.730046 299.574400 ; H8 C8 H9 + 15 8 17 1 107.730046 299.574400 107.730046 299.574400 ; H8 C8 H10 + 16 8 17 1 107.730046 299.574400 107.730046 299.574400 ; H9 C8 H10 + 2 6 18 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 DC9 + 7 6 18 1 112.630048 500.992160 112.630048 500.992160 ; C7 C6 DC9 + 6 7 19 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 HV5 + 6 18 20 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC9 HV11 + 6 18 21 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC9 HV12 + 6 18 22 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC9 HV13 + 18 6 11 1 109.680047 362.083360 109.680047 362.083360 ; DC9 C6 H3 + 19 7 13 1 107.730046 299.574400 107.730046 299.574400 ; HV5 C7 H6 + 19 7 14 1 107.730046 299.574400 107.730046 299.574400 ; HV5 C7 H7 + 20 18 21 1 107.730046 299.574400 107.730046 299.574400 ; HV11 DC9 HV12 + 20 18 22 1 107.730046 299.574400 107.730046 299.574400 ; HV11 DC9 HV13 + 21 18 22 1 107.730046 299.574400 107.730046 299.574400 ; HV12 DC9 HV13 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 2 6 7 8 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 C8 (AAAA->AAAD) + 5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAD) + 1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAD) + 1 5 4 9 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 10 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 9 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 13 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H6 (AAAA->AAAA) + 2 6 7 14 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAD) + 3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAD) + 3 4 5 10 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 6 7 8 15 1 0 0.54392 3 0 0 3 ; C6 C7 C8 H8 (AAAA->AADD) + 6 7 8 16 1 0 0.54392 3 0 0 3 ; C6 C7 C8 H9 (AAAA->AADD) + 6 7 8 17 1 0 0.54392 3 0 0 3 ; C6 C7 C8 H10 (AAAA->AADD) + 8 7 6 11 1 0 0.54392 3 0 0 3 ; C8 C7 C6 H3 (AAAA->DAAA) + 8 7 6 12 1 0 0.54392 3 0 0 3 ; C8 C7 C6 H4 (AAAA->DAAD) + 9 4 5 10 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 11 6 7 13 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H6 (AAAA->AAAA) + 11 6 7 14 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 12 6 7 13 1 0 0.50208 3 0 0 3 ; H4 C6 C7 H6 (AAAA->DAAA) + 12 6 7 14 1 0 0.50208 3 0 0 3 ; H4 C6 C7 H7 (AAAA->DAAA) + 13 7 8 15 1 0 0.50208 3 0 0 3 ; H6 C7 C8 H8 (AAAA->AADD) + 13 7 8 16 1 0 0.50208 3 0 0 3 ; H6 C7 C8 H9 (AAAA->AADD) + 13 7 8 17 1 0 0.50208 3 0 0 3 ; H6 C7 C8 H10 (AAAA->AADD) + 14 7 8 15 1 0 0.50208 3 0 0 3 ; H7 C7 C8 H8 (AAAA->AADD) + 14 7 8 16 1 0 0.50208 3 0 0 3 ; H7 C7 C8 H9 (AAAA->AADD) + 14 7 8 17 1 0 0.50208 3 0 0 3 ; H7 C7 C8 H10 (AAAA->AADD) + 1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 2 6 18 1 0 0 3 0 0 3 ; S1 C2 C6 DC9 (AAAD->AAAA) + 1 2 6 18 1 0 0 3 0 0 3 ; S1 C2 C6 DC9 (AAAD->AAAA) + 1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 3 2 6 18 1 0 0 3 0 0 3 ; N3 C2 C6 DC9 (AAAD->AAAA) + 3 2 6 18 1 0 0 3 0 0 3 ; N3 C2 C6 DC9 (AAAD->AAAA) + 4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 5 4 9 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 10 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 9 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 19 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 HV5 (AAAD->AAAA) + 2 6 7 19 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 HV5 (AAAD->AAAA) + 2 6 7 13 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H6 (AAAA->AAAA) + 2 6 7 14 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 2 6 18 20 1 0 0 3 0 0.6508444 3 ; C2 C6 DC9 HV11 (AADD->AAAA) + 2 6 18 21 1 0 0 3 0 0.6508444 3 ; C2 C6 DC9 HV12 (AADD->AAAA) + 2 6 18 22 1 0 0 3 0 0.6508444 3 ; C2 C6 DC9 HV13 (AADD->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 4 5 10 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 7 6 18 20 1 0 0 3 0 0.54392 3 ; C7 C6 DC9 HV11 (AADD->AAAA) + 7 6 18 21 1 0 0 3 0 0.54392 3 ; C7 C6 DC9 HV12 (AADD->AAAA) + 7 6 18 22 1 0 0 3 0 0.54392 3 ; C7 C6 DC9 HV13 (AADD->AAAA) + 18 6 7 19 1 0 0 3 0 0.54392 3 ; DC9 C6 C7 HV5 (DAAD->AAAA) + 18 6 7 13 1 0 0 3 0 0.54392 3 ; DC9 C6 C7 H6 (DAAA->AAAA) + 18 6 7 14 1 0 0 3 0 0.54392 3 ; DC9 C6 C7 H7 (DAAA->AAAA) + 9 4 5 10 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 11 6 7 19 1 0 0 3 0 0.50208 3 ; H3 C6 C7 HV5 (AAAD->AAAA) + 11 6 7 19 1 0 0.50208 3 0 0 3 ; H3 C6 C7 HV5 (AAAD->AAAA) + 11 6 7 13 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H6 (AAAA->AAAA) + 11 6 7 14 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 11 6 18 20 1 0 0 3 0 0.50208 3 ; H3 C6 DC9 HV11 (AADD->AAAA) + 11 6 18 21 1 0 0 3 0 0.50208 3 ; H3 C6 DC9 HV12 (AADD->AAAA) + 11 6 18 22 1 0 0 3 0 0.50208 3 ; H3 C6 DC9 HV13 (AADD->AAAA) + + diff --git a/ensemble_md/tests/data/coord_swap/C-D.top b/ensemble_md/tests/data/coord_swap/C-D.top new file mode 100644 index 00000000..385b5a9b --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/C-D.top @@ -0,0 +1,32 @@ +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.83333333 + +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +ss 16 32.060000 0.00000000 A 0.35324134 1.1815616 +cc 6 12.010000 0.00000000 A 0.33152123 0.4133792 +nd 7 14.010000 0.00000000 A 0.33841679 0.3937144 +cd 6 12.010000 0.00000000 A 0.33152123 0.4133792 +c3 6 12.010000 0.00000000 A 0.33977095 0.4510352 +h4 1 1.008000 0.00000000 A 0.25363887 0.0673624 +hc 1 1.008000 0.00000000 A 0.2600177 0.0870272 +DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000 +DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000 +Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02 +Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 + +#include "C-D.itp" + +#include "water_and_ions.itp" + +[ system ] +; Name +Generic title in water + +[ molecules ] +; Compound #mols +C2D 1 +SOL 679 diff --git a/ensemble_md/tests/data/coord_swap/D-E.gro b/ensemble_md/tests/data/coord_swap/D-E.gro new file mode 100644 index 00000000..73e8ef42 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/D-E.gro @@ -0,0 +1,2061 @@ +Generic title in water + 2058 + 1D2E S1 1 2.387 1.634 2.218 -0.0164 0.3202 0.1180 + 1D2E C2 2 2.382 1.793 2.287 0.0869 -0.1968 -0.1835 + 1D2E N3 3 2.423 1.894 2.208 0.1566 -0.2049 -0.3624 + 1D2E C4 4 2.466 1.845 2.083 0.3743 0.0005 0.4184 + 1D2E C5 5 2.451 1.710 2.073 -0.1611 -0.0190 -0.5394 + 1D2E C6 6 2.350 1.828 2.431 0.1785 0.3492 0.8874 + 1D2E C7 7 2.382 1.709 2.525 -0.4758 0.1671 -0.2554 + 1D2E C9 8 2.196 1.863 2.446 -0.7263 0.2653 0.2269 + 1D2E H1 9 2.505 1.910 2.006 1.5300 0.5042 1.4388 + 1D2E H2 10 2.487 1.644 1.995 -0.5606 -1.6460 0.6670 + 1D2E H3 11 2.418 1.905 2.469 0.1139 1.0344 -0.3542 + 1D2E H5 12 2.459 1.643 2.484 1.3568 1.4546 1.0984 + 1D2E H6 13 2.299 1.638 2.539 2.8397 -3.6454 -0.1536 + 1D2E H7 14 2.414 1.746 2.624 0.9368 0.2166 -0.7363 + 1D2E H11 15 2.126 1.789 2.404 0.6554 -1.0220 0.1893 + 1D2E H12 16 2.179 1.960 2.398 0.2770 -0.6621 -2.0014 + 1D2E H13 17 2.167 1.880 2.550 1.4814 1.0539 0.6999 + 1D2E DC8 18 2.503 1.631 2.468 -0.9418 -0.5438 0.2501 + 1D2E HV8 19 2.464 1.611 2.367 -0.9267 2.5401 -0.3600 + 1D2E HV9 20 2.511 1.537 2.524 1.0216 -1.8686 -2.2567 + 1D2E HV10 21 2.586 1.700 2.489 -1.4033 -0.5042 1.9301 + 2SOL OW 22 1.301 2.415 0.143 0.0259 -0.3388 -0.3830 + 2SOL HW1 23 1.376 2.435 0.086 0.8751 -1.5575 0.3373 + 2SOL HW2 24 1.227 2.458 0.099 0.9648 0.0657 -1.5847 + 3SOL OW 25 1.844 1.024 1.372 -0.3547 0.7708 -0.3814 + 3SOL HW1 26 1.932 1.004 1.342 -0.7314 0.1563 -1.0745 + 3SOL HW2 27 1.807 0.940 1.398 0.6962 1.5806 3.7611 + 4SOL OW 28 0.134 2.477 2.387 0.2543 -0.5893 -0.1143 + 4SOL HW1 29 0.078 2.445 2.317 -1.4512 -1.3337 1.6127 + 4SOL HW2 30 0.206 2.414 2.391 -0.0622 -0.9827 -0.6556 + 5SOL OW 31 2.540 2.723 0.044 0.2693 -0.1303 -0.1746 + 5SOL HW1 32 2.511 2.634 0.061 0.6917 -0.3596 -0.6468 + 5SOL HW2 33 2.470 2.778 0.076 -1.0497 -0.7037 -2.0500 + 6SOL OW 34 0.848 1.613 1.195 -0.1534 0.1471 -0.1685 + 6SOL HW1 35 0.855 1.657 1.110 1.7009 1.5924 0.7489 + 6SOL HW2 36 0.804 1.676 1.251 -1.1703 -0.7236 0.0052 + 7SOL OW 37 1.799 1.470 0.258 0.0384 0.1019 -0.0517 + 7SOL HW1 38 1.836 1.425 0.334 1.1122 1.1993 0.0758 + 7SOL HW2 39 1.757 1.548 0.294 0.5149 0.6030 -0.5813 + 8SOL OW 40 0.519 2.326 0.401 -0.2246 -0.4679 0.1500 + 8SOL HW1 41 0.497 2.240 0.436 3.1324 -1.6122 -0.6024 + 8SOL HW2 42 0.451 2.384 0.435 -0.6154 -2.8018 3.2885 + 9SOL OW 43 1.668 2.196 1.238 -0.4143 0.1958 0.2334 + 9SOL HW1 44 1.710 2.190 1.153 0.7751 -0.4050 0.8625 + 9SOL HW2 45 1.611 2.119 1.242 -1.7629 1.1361 -0.7113 + 10SOL OW 46 0.033 0.816 1.427 0.1914 -0.4187 -0.4052 + 10SOL HW1 47 -0.021 0.895 1.435 1.0489 0.3534 -2.4318 + 10SOL HW2 48 -0.010 0.765 1.359 1.1197 -0.5272 -0.9041 + 11SOL OW 49 0.286 0.940 1.750 -0.1867 -0.0617 -0.1851 + 11SOL HW1 50 0.207 0.993 1.762 0.4543 1.2552 -1.7497 + 11SOL HW2 51 0.269 0.860 1.798 -1.6248 1.1220 1.2571 + 12SOL OW 52 1.617 1.652 0.410 0.0025 0.4960 -0.0939 + 12SOL HW1 53 1.601 1.723 0.348 0.9445 0.9817 0.2227 + 12SOL HW2 54 1.658 1.695 0.485 1.3634 -0.5265 -0.2616 + 13SOL OW 55 0.828 0.435 1.657 0.2187 -0.1636 -0.5114 + 13SOL HW1 56 0.741 0.399 1.638 -0.6593 0.6452 1.9680 + 13SOL HW2 57 0.872 0.366 1.705 0.6888 -0.2758 -1.1016 + 14SOL OW 58 1.406 1.749 1.687 -0.1566 -0.0677 -0.0094 + 14SOL HW1 59 1.451 1.672 1.652 1.0515 0.4847 0.3180 + 14SOL HW2 60 1.360 1.716 1.765 -0.6525 -0.7159 -0.5707 + 15SOL OW 61 0.672 1.926 0.210 -0.3203 0.4018 -0.9451 + 15SOL HW1 62 0.602 1.865 0.185 0.0851 -0.0007 -1.1155 + 15SOL HW2 63 0.685 1.980 0.132 -0.0782 0.1252 -1.0991 + 16SOL OW 64 1.397 2.340 1.843 -0.1982 0.3554 0.1107 + 16SOL HW1 65 1.399 2.430 1.810 0.4784 0.4087 0.2952 + 16SOL HW2 66 1.408 2.286 1.765 -0.7882 0.4330 -0.0224 + 17SOL OW 67 1.151 0.184 0.244 0.4356 0.2119 -0.0824 + 17SOL HW1 68 1.056 0.185 0.232 0.3802 -2.7680 0.0602 + 17SOL HW2 69 1.169 0.256 0.304 -1.9317 -0.3731 1.3169 + 18SOL OW 70 2.058 2.493 0.351 -0.1566 -0.7531 0.2459 + 18SOL HW1 71 2.020 2.437 0.283 2.5652 -0.0355 -1.8814 + 18SOL HW2 72 2.090 2.569 0.303 1.6658 -0.2093 2.3666 + 19SOL OW 73 1.049 1.336 1.505 -0.7389 -0.3242 0.6421 + 19SOL HW1 74 1.073 1.250 1.538 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649SOL HW1 1964 1.307 0.141 2.524 -0.8543 0.8660 0.7174 + 649SOL HW2 1965 1.415 0.164 2.627 -0.2720 1.1395 0.0412 + 650SOL OW 1966 2.055 2.314 1.238 -0.0770 0.0946 -1.0472 + 650SOL HW1 1967 2.008 2.232 1.251 -0.3736 0.2633 -1.0473 + 650SOL HW2 1968 2.000 2.364 1.177 0.1186 0.2763 -1.0759 + 651SOL OW 1969 2.301 0.052 1.817 0.1422 0.6539 -0.0914 + 651SOL HW1 1970 2.320 -0.018 1.755 -2.5329 0.5475 -0.7959 + 651SOL HW2 1971 2.308 0.133 1.766 -1.1794 0.6202 -0.3327 + 652SOL OW 1972 0.566 1.280 0.446 0.4189 0.6402 -0.2041 + 652SOL HW1 1973 0.525 1.304 0.363 2.2279 1.3799 -0.8934 + 652SOL HW2 1974 0.517 1.329 0.512 -0.2184 1.0361 -0.9750 + 653SOL OW 1975 1.703 0.309 1.707 -0.1779 -0.0877 -0.2101 + 653SOL HW1 1976 1.639 0.374 1.680 0.7309 0.7614 -0.3124 + 653SOL HW2 1977 1.697 0.307 1.802 -2.7594 -2.4488 -0.4063 + 654SOL OW 1978 1.170 2.215 1.453 0.2107 -0.4290 -0.0408 + 654SOL HW1 1979 1.112 2.161 1.506 -0.4805 0.2852 -0.0561 + 654SOL HW2 1980 1.157 2.184 1.363 0.5457 -0.8910 0.0708 + 655SOL OW 1981 1.363 1.704 0.711 -0.1439 -0.4296 0.3475 + 655SOL HW1 1982 1.294 1.726 0.648 0.1767 -0.0657 0.1230 + 655SOL HW2 1983 1.330 1.737 0.794 -0.6369 -1.0438 0.4000 + 656SOL OW 1984 2.566 0.891 2.281 0.2081 -0.2780 0.3520 + 656SOL HW1 1985 2.511 0.903 2.358 2.0703 3.0449 1.1489 + 656SOL HW2 1986 2.653 0.870 2.316 0.9548 0.8315 -0.8370 + 657SOL OW 1987 1.810 2.341 2.557 0.1634 -0.3146 -0.5774 + 657SOL HW1 1988 1.898 2.346 2.520 0.5403 -0.4253 0.3077 + 657SOL HW2 1989 1.774 2.429 2.544 0.9933 0.1871 0.5433 + 658SOL OW 1990 0.119 1.495 0.438 0.3962 0.6096 -0.0030 + 658SOL HW1 1991 0.045 1.440 0.415 0.6576 0.3192 -0.1462 + 658SOL HW2 1992 0.140 1.471 0.529 0.0858 0.9464 0.1558 + 659SOL OW 1993 0.037 1.226 1.729 0.0921 0.1994 -0.4115 + 659SOL HW1 1994 0.064 1.235 1.637 2.3927 1.5222 0.3913 + 659SOL HW2 1995 -0.036 1.287 1.739 1.3742 1.7968 -0.7431 + 660SOL OW 1996 1.250 0.011 0.452 0.3662 0.5511 -0.3000 + 660SOL HW1 1997 1.217 0.072 0.517 1.9531 0.5050 0.5394 + 660SOL HW2 1998 1.217 0.046 0.368 -3.6961 -0.7604 0.7466 + 661SOL OW 1999 0.130 0.668 2.131 0.1484 -0.3017 0.3646 + 661SOL HW1 2000 0.180 0.711 2.061 -0.4036 0.9509 0.7373 + 661SOL HW2 2001 0.050 0.637 2.088 -0.0346 0.1700 0.3582 + 662SOL OW 2002 2.217 1.240 0.437 0.4417 0.0331 -0.1789 + 662SOL HW1 2003 2.123 1.253 0.454 0.1829 1.0828 -2.3128 + 662SOL HW2 2004 2.219 1.172 0.369 1.3297 -2.0999 2.0167 + 663SOL OW 2005 2.462 0.187 2.475 0.3621 -0.0321 -0.3132 + 663SOL HW1 2006 2.396 0.199 2.543 -0.5957 -1.0308 -1.0687 + 663SOL HW2 2007 2.522 0.121 2.510 0.3349 0.0656 -0.0871 + 664SOL OW 2008 0.208 0.108 0.804 0.5004 -0.5901 -0.1439 + 664SOL HW1 2009 0.210 0.158 0.885 2.5492 -0.2760 -0.3914 + 664SOL HW2 2010 0.178 0.170 0.738 -2.0571 -1.0902 0.5483 + 665SOL OW 2011 0.688 0.030 2.356 -0.4951 -0.6351 -0.2178 + 665SOL HW1 2012 0.621 0.074 2.304 -1.4467 -1.1756 0.5439 + 665SOL HW2 2013 0.707 -0.051 2.309 0.9217 0.3868 -1.3791 + 666SOL OW 2014 2.012 0.228 0.932 -0.1273 0.0440 -0.8108 + 666SOL HW1 2015 2.020 0.259 1.022 2.7098 2.3391 -1.8582 + 666SOL HW2 2016 1.920 0.242 0.910 -0.8508 -0.6802 1.8011 + 667SOL OW 2017 0.254 0.602 0.206 -0.2777 0.2089 0.2710 + 667SOL HW1 2018 0.337 0.603 0.160 -0.9415 2.8158 -0.8885 + 667SOL HW2 2019 0.219 0.691 0.194 -2.7644 -0.5998 1.5280 + 668SOL OW 2020 0.810 1.466 2.381 -0.3339 0.3876 0.0731 + 668SOL HW1 2021 0.795 1.487 2.473 -1.3659 -3.2456 0.7559 + 668SOL HW2 2022 0.730 1.492 2.336 0.0979 1.9848 0.2434 + 669SOL OW 2023 0.372 0.334 1.781 0.4688 -0.3945 -0.1436 + 669SOL HW1 2024 0.338 0.315 1.869 0.4578 -0.4945 -0.1697 + 669SOL HW2 2025 0.425 0.258 1.759 0.8655 -0.1511 -0.0229 + 670SOL OW 2026 1.416 0.205 1.914 0.3356 0.0535 0.1835 + 670SOL HW1 2027 1.477 0.139 1.946 0.0844 -1.0341 -1.6094 + 670SOL HW2 2028 1.419 0.275 1.980 0.5935 -1.7368 2.0590 + 671SOL OW 2029 0.956 0.262 1.823 0.1967 -0.1738 -0.6054 + 671SOL HW1 2030 1.041 0.222 1.805 1.1302 1.3631 0.3819 + 671SOL HW2 2031 0.974 0.326 1.891 -0.9691 3.2001 -3.4870 + 672SOL OW 2032 0.253 2.681 2.526 0.9734 -0.0279 -0.0833 + 672SOL HW1 2033 0.229 2.616 2.460 3.7716 0.5124 -1.6603 + 672SOL HW2 2034 0.228 2.765 2.487 -0.8405 -0.0194 1.1237 + 673SOL OW 2035 1.395 1.312 2.611 0.1721 -0.0562 -0.4947 + 673SOL HW1 2036 1.335 1.261 2.666 1.1401 -1.6737 -0.9359 + 673SOL HW2 2037 1.344 1.389 2.586 -0.9091 -0.2258 1.1280 + 674SOL OW 2038 2.304 1.781 0.785 -0.2557 0.3237 0.5125 + 674SOL HW1 2039 2.215 1.779 0.751 0.6807 -0.1041 -1.9383 + 674SOL HW2 2040 2.321 1.874 0.802 -0.8512 0.5024 0.1237 + 675SOL OW 2041 1.346 0.819 0.296 0.3251 0.2411 0.0937 + 675SOL HW1 2042 1.266 0.767 0.288 1.6657 -1.8369 0.3368 + 675SOL HW2 2043 1.363 0.850 0.207 -0.6735 0.5729 0.0172 + 676SOL OW 2044 0.910 0.626 0.594 -0.0137 0.1018 0.0326 + 676SOL HW1 2045 0.999 0.648 0.566 0.0136 1.5802 1.2731 + 676SOL HW2 2046 0.897 0.676 0.675 -1.5177 -1.0800 0.5374 + 677SOL OW 2047 1.236 1.201 1.303 0.5596 0.7748 -0.3037 + 677SOL HW1 2048 1.199 1.158 1.380 1.0679 -1.7925 -1.4855 + 677SOL HW2 2049 1.311 1.250 1.336 1.1933 -0.9035 0.7220 + 678SOL OW 2050 1.735 1.861 2.550 0.6114 0.5605 0.6581 + 678SOL HW1 2051 1.821 1.887 2.581 0.7719 0.1932 0.5269 + 678SOL HW2 2052 1.676 1.929 2.583 0.8594 0.4717 1.3010 + 679SOL OW 2053 0.587 0.484 0.181 -0.1348 -0.5588 -0.1883 + 679SOL HW1 2054 0.609 0.483 0.275 -2.6795 1.6171 0.4442 + 679SOL HW2 2055 0.613 0.398 0.149 -0.5164 -1.8061 2.8474 + 680SOL OW 2056 2.416 2.485 0.560 -0.0379 0.4661 -0.3382 + 680SOL HW1 2057 2.342 2.426 0.542 -0.1771 1.1710 -2.0466 + 680SOL HW2 2058 2.378 2.572 0.560 0.3073 0.6114 1.4934 + 2.74243 2.74243 2.74243 diff --git a/ensemble_md/tests/data/coord_swap/D-E.itp b/ensemble_md/tests/data/coord_swap/D-E.itp new file mode 100644 index 00000000..dc41c076 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/D-E.itp @@ -0,0 +1,229 @@ + + + +[ moleculetype ] +; Name nrexcl +D2E 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB + 1 ss 1 D2E S1 1 -0.117300 32.0600 + 2 cc 1 D2E C2 2 0.405700 12.0100 cc 0.404700 12.0100 + 3 nd 1 D2E N3 3 -0.633000 14.0100 + 4 cd 1 D2E C4 4 0.331200 12.0100 + 5 cc 1 D2E C5 5 -0.251400 12.0100 + 6 c3 1 D2E C6 6 -0.092000 12.0100 c3 -0.091000 12.0100 + 7 c3 1 D2E C7 7 -0.087100 12.0100 c3 -0.073400 12.0100 + 8 c3 1 D2E C9 8 -0.087100 12.0100 + 9 h4 1 D2E H1 9 0.043100 1.0080 + 10 h4 1 D2E H2 10 0.180000 1.0080 + 11 hc 1 D2E H3 11 0.049700 1.0080 hc 0.051700 1.0080 + 12 hc 1 D2E H5 12 0.043033 1.0080 DUM_hc 0.000000 1.0080 + 13 hc 1 D2E H6 13 0.043033 1.0080 hc 0.052200 1.0080 + 14 hc 1 D2E H7 14 0.043033 1.0080 hc 0.052200 1.0080 + 15 hc 1 D2E H11 15 0.043033 1.0080 hc 0.043033 1.0080 + 16 hc 1 D2E H12 16 0.043033 1.0080 hc 0.043033 1.0080 + 17 hc 1 D2E H13 17 0.043033 1.0080 hc 0.043033 1.0080 + 18 DUM_c3 1 D2E DC8 18 0.000000 12.0100 c3 -0.094100 12.0100 + 19 DUM_hc 1 D2E HV8 19 0.000000 1.0080 hc 0.034367 1.0080 + 20 DUM_hc 1 D2E HV9 20 0.000000 1.0080 hc 0.034367 1.0080 + 21 DUM_hc 1 D2E HV10 21 0.000000 1.0080 hc 0.034367 1.0080 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 0.175380 193853.088000 0.175380 193853.088000 + 1 5 1 0.175380 193853.088000 0.175380 193853.088000 + 2 3 1 0.131580 351221.696000 0.131580 351221.696000 + 2 6 1 0.150020 213501.152000 0.150020 213501.152000 + 3 4 1 0.137130 289474.224000 0.137130 289474.224000 + 4 5 1 0.137300 323205.632000 0.137300 323205.632000 + 6 7 1 0.153540 191535.152000 0.153540 191535.152000 + 6 8 1 0.153540 191535.152000 0.153540 191535.152000 + 4 9 1 0.108180 307348.272000 0.108180 307348.272000 + 5 10 1 0.108090 308544.896000 0.108090 308544.896000 + 6 11 1 0.109620 288905.200000 0.109620 288905.200000 + 7 12 1 0.109620 288905.200000 0.109620 288905.200000 + 7 13 1 0.109620 288905.200000 0.109620 288905.200000 + 7 14 1 0.109620 288905.200000 0.109620 288905.200000 + 8 15 1 0.109620 288905.200000 0.109620 288905.200000 + 8 16 1 0.109620 288905.200000 0.109620 288905.200000 + 8 17 1 0.109620 288905.200000 0.109620 288905.200000 + 7 18 1 0.153540 191535.152000 0.153540 191535.152000 + 18 19 1 0.109620 288905.200000 0.109620 288905.200000 + 18 20 1 0.109620 288905.200000 0.109620 288905.200000 + 18 21 1 0.109620 288905.200000 0.109620 288905.200000 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 7 1 + 1 8 1 + 3 7 1 + 3 8 1 + 4 6 1 + 5 6 1 + 1 11 1 + 1 9 1 + 2 10 1 + 2 9 1 + 2 12 1 + 2 13 1 + 2 14 1 + 2 15 1 + 2 16 1 + 2 17 1 + 3 11 1 + 3 10 1 + 7 15 1 + 7 16 1 + 7 17 1 + 8 12 1 + 8 13 1 + 8 14 1 + 9 10 1 + 11 12 1 + 11 13 1 + 11 14 1 + 11 15 1 + 11 16 1 + 11 17 1 + 2 18 1 + 18 8 1 + 6 19 1 + 6 20 1 + 6 21 1 + 18 11 1 + 13 19 1 + 13 20 1 + 13 21 1 + 14 19 1 + 14 20 1 + 14 21 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3 + 1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6 + 1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4 + 2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5 + 2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4 + 2 6 7 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 C7 + 2 6 8 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 C9 + 3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6 + 3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5 + 7 6 8 1 112.630048 500.992160 112.630048 500.992160 ; C7 C6 C9 + 1 5 10 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2 + 2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3 + 3 4 9 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1 + 4 5 10 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2 + 5 4 9 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1 + 6 7 12 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H5 + 6 7 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H6 + 6 7 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H7 + 6 8 15 1 109.680047 362.083360 109.680047 362.083360 ; C6 C9 H11 + 6 8 16 1 109.680047 362.083360 109.680047 362.083360 ; C6 C9 H12 + 6 8 17 1 109.680047 362.083360 109.680047 362.083360 ; C6 C9 H13 + 7 6 11 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 H3 + 8 6 11 1 109.680047 362.083360 109.680047 362.083360 ; C9 C6 H3 + 12 7 13 1 107.730046 299.574400 107.730046 299.574400 ; H5 C7 H6 + 12 7 14 1 107.730046 299.574400 107.730046 299.574400 ; H5 C7 H7 + 13 7 14 1 107.730046 299.574400 107.730046 299.574400 ; H6 C7 H7 + 15 8 16 1 107.730046 299.574400 107.730046 299.574400 ; H11 C9 H12 + 15 8 17 1 107.730046 299.574400 107.730046 299.574400 ; H11 C9 H13 + 16 8 17 1 107.730046 299.574400 107.730046 299.574400 ; H12 C9 H13 + 6 7 18 1 112.630048 500.992160 112.630048 500.992160 ; C6 C7 DC8 + 7 18 19 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC8 HV8 + 7 18 20 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC8 HV9 + 7 18 21 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC8 HV10 + 18 7 13 1 109.680047 362.083360 109.680047 362.083360 ; DC8 C7 H6 + 18 7 14 1 109.680047 362.083360 109.680047 362.083360 ; DC8 C7 H7 + 19 18 20 1 107.730046 299.574400 107.730046 299.574400 ; HV8 DC8 HV9 + 19 18 21 1 107.730046 299.574400 107.730046 299.574400 ; HV8 DC8 HV10 + 20 18 21 1 107.730046 299.574400 107.730046 299.574400 ; HV9 DC8 HV10 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 2 6 8 1 0 0 3 0 0 3 ; S1 C2 C6 C9 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 3 2 6 8 1 0 0 3 0 0 3 ; N3 C2 C6 C9 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 5 4 9 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 10 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 9 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 12 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H5 (AAAA->AAAD) + 2 6 7 13 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H6 (AAAA->AAAA) + 2 6 7 14 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 2 6 8 15 1 0 0.6508444 3 0 0 3 ; C2 C6 C9 H11 (AAAA->AAAA) + 2 6 8 16 1 0 0.6508444 3 0 0 3 ; C2 C6 C9 H12 (AAAA->AAAA) + 2 6 8 17 1 0 0.6508444 3 0 0 3 ; C2 C6 C9 H13 (AAAA->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 4 5 10 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 7 6 8 15 1 0 0.54392 3 0 0 3 ; C7 C6 C9 H11 (AAAA->AAAA) + 7 6 8 16 1 0 0.54392 3 0 0 3 ; C7 C6 C9 H12 (AAAA->AAAA) + 7 6 8 17 1 0 0.54392 3 0 0 3 ; C7 C6 C9 H13 (AAAA->AAAA) + 8 6 7 12 1 0 0.54392 3 0 0 3 ; C9 C6 C7 H5 (AAAA->AAAD) + 8 6 7 13 1 0 0.54392 3 0 0 3 ; C9 C6 C7 H6 (AAAA->AAAA) + 8 6 7 14 1 0 0.54392 3 0 0 3 ; C9 C6 C7 H7 (AAAA->AAAA) + 9 4 5 10 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 11 6 7 12 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H5 (AAAA->AAAD) + 11 6 7 13 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H6 (AAAA->AAAA) + 11 6 7 14 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 11 6 8 15 1 0 0.50208 3 0 0 3 ; H3 C6 C9 H11 (AAAA->AAAA) + 11 6 8 16 1 0 0.50208 3 0 0 3 ; H3 C6 C9 H12 (AAAA->AAAA) + 11 6 8 17 1 0 0.50208 3 0 0 3 ; H3 C6 C9 H13 (AAAA->AAAA) + 1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 2 6 8 1 0 0 3 0 0 3 ; S1 C2 C6 C9 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 2 6 7 18 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 DC8 (AAAD->AAAA) + 5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 3 2 6 8 1 0 0 3 0 0 3 ; N3 C2 C6 C9 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 18 7 6 8 1 0 0 3 0 2.17568 3 ; DC8 C7 C6 C9 (DAAA->AAAA) + 1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 5 4 9 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 10 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 9 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 13 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H6 (AAAA->AAAA) + 2 6 7 14 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 2 6 8 15 1 0 0 3 0 0.6508444 3 ; C2 C6 C9 H11 (AAAA->AAAA) + 2 6 8 16 1 0 0 3 0 0.6508444 3 ; C2 C6 C9 H12 (AAAA->AAAA) + 2 6 8 17 1 0 0 3 0 0.6508444 3 ; C2 C6 C9 H13 (AAAA->AAAA) + 3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 4 5 10 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 6 7 18 19 1 0 0 3 0 0.54392 3 ; C6 C7 DC8 HV8 (AADD->AAAA) + 6 7 18 20 1 0 0 3 0 0.54392 3 ; C6 C7 DC8 HV9 (AADD->AAAA) + 6 7 18 21 1 0 0 3 0 0.54392 3 ; C6 C7 DC8 HV10 (AADD->AAAA) + 7 6 8 15 1 0 0 3 0 0.54392 3 ; C7 C6 C9 H11 (AAAA->AAAA) + 7 6 8 16 1 0 0 3 0 0.54392 3 ; C7 C6 C9 H12 (AAAA->AAAA) + 7 6 8 17 1 0 0 3 0 0.54392 3 ; C7 C6 C9 H13 (AAAA->AAAA) + 18 7 6 11 1 0 0 3 0 0.54392 3 ; DC8 C7 C6 H3 (DAAA->AAAA) + 8 6 7 13 1 0 0 3 0 0.54392 3 ; C9 C6 C7 H6 (AAAA->AAAA) + 8 6 7 14 1 0 0 3 0 0.54392 3 ; C9 C6 C7 H7 (AAAA->AAAA) + 9 4 5 10 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 11 6 7 13 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H6 (AAAA->AAAA) + 11 6 7 14 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 11 6 8 15 1 0 0 3 0 0.50208 3 ; H3 C6 C9 H11 (AAAA->AAAA) + 11 6 8 16 1 0 0 3 0 0.50208 3 ; H3 C6 C9 H12 (AAAA->AAAA) + 11 6 8 17 1 0 0 3 0 0.50208 3 ; H3 C6 C9 H13 (AAAA->AAAA) + 13 7 18 19 1 0 0 3 0 0.50208 3 ; H6 C7 DC8 HV8 (AADD->AAAA) + 13 7 18 20 1 0 0 3 0 0.50208 3 ; H6 C7 DC8 HV9 (AADD->AAAA) + 13 7 18 21 1 0 0 3 0 0.50208 3 ; H6 C7 DC8 HV10 (AADD->AAAA) + 14 7 18 19 1 0 0 3 0 0.50208 3 ; H7 C7 DC8 HV8 (AADD->AAAA) + 14 7 18 20 1 0 0 3 0 0.50208 3 ; H7 C7 DC8 HV9 (AADD->AAAA) + 14 7 18 21 1 0 0 3 0 0.50208 3 ; H7 C7 DC8 HV10 (AADD->AAAA) + + diff --git a/ensemble_md/tests/data/coord_swap/D-E.top b/ensemble_md/tests/data/coord_swap/D-E.top new file mode 100644 index 00000000..80bdff14 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/D-E.top @@ -0,0 +1,32 @@ +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.83333333 + +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +ss 16 32.060000 0.00000000 A 0.35324134 1.1815616 +cc 6 12.010000 0.00000000 A 0.33152123 0.4133792 +nd 7 14.010000 0.00000000 A 0.33841679 0.3937144 +cd 6 12.010000 0.00000000 A 0.33152123 0.4133792 +c3 6 12.010000 0.00000000 A 0.33977095 0.4510352 +h4 1 1.008000 0.00000000 A 0.25363887 0.0673624 +hc 1 1.008000 0.00000000 A 0.2600177 0.0870272 +DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000 +DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000 +Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02 +Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 + +#include "D-E.itp" + +#include "water_and_ions.itp" + +[ system ] +; Name +Generic title in water + +[ molecules ] +; Compound #mols +D2E 1 +SOL 679 diff --git a/ensemble_md/tests/data/coord_swap/E-F.gro b/ensemble_md/tests/data/coord_swap/E-F.gro new file mode 100644 index 00000000..3f2cd882 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/E-F.gro @@ -0,0 +1,2065 @@ +Generic title in water + 2062 + 1E2F S1 1 1.952 1.797 1.011 -0.0830 0.2466 0.2945 + 1E2F C2 2 2.086 1.903 0.973 -0.6149 -0.9035 -0.3208 + 1E2F N3 3 2.098 1.937 0.846 -0.6339 -0.1459 -0.3594 + 1E2F C4 4 1.994 1.884 0.776 0.0706 0.4255 -0.6396 + 1E2F C5 5 1.893 1.822 0.848 0.7358 0.2670 0.6656 + 1E2F C6 6 2.164 1.964 1.092 -0.1281 0.0489 -0.5463 + 1E2F C7 7 2.198 2.120 1.071 0.4240 0.1092 0.4091 + 1E2F C8 8 2.079 2.211 1.061 -0.2247 -0.3262 0.2310 + 1E2F C9 9 2.285 1.888 1.132 -0.3697 0.5676 0.8556 + 1E2F H1 10 1.991 1.903 0.670 1.5157 1.6500 -0.4567 + 1E2F H2 11 1.803 1.775 0.812 1.9627 -1.3853 -0.2590 + 1E2F H3 12 2.088 1.958 1.171 2.5532 -2.7543 1.8395 + 1E2F H6 13 2.251 2.129 0.975 -1.2029 -0.7839 -0.5667 + 1E2F H7 14 2.268 2.156 1.148 -0.0099 2.3664 -0.2612 + 1E2F H8 15 2.104 2.291 0.989 -3.4495 -1.9141 -2.6726 + 1E2F H9 16 2.060 2.264 1.155 1.5763 -2.1528 1.6019 + 1E2F H10 17 1.988 2.155 1.036 -1.0987 1.7188 -1.2041 + 1E2F H11 18 2.361 1.897 1.053 -0.4416 -0.4131 0.6793 + 1E2F H12 19 2.264 1.782 1.150 -0.5678 0.8391 2.1753 + 1E2F H13 20 2.323 1.913 1.231 -2.4723 0.6469 1.6446 + 1E2F DC10 21 2.273 2.141 0.939 -1.1945 0.3946 -0.3470 + 1E2F HV4 22 2.251 1.905 1.122 0.2250 0.9627 0.2351 + 1E2F HV14 23 2.356 2.068 0.944 -1.7086 0.0820 4.1037 + 1E2F HV15 24 2.321 2.236 0.916 -2.3764 0.8326 -0.9547 + 1E2F HV16 25 2.223 2.100 0.851 -0.3318 0.4626 -0.8747 + 2SOL OW 26 0.598 1.481 2.715 -0.1987 0.0572 -0.5238 + 2SOL HW1 27 0.583 1.420 2.643 1.2050 0.9606 -1.5639 + 2SOL HW2 28 0.573 1.431 2.793 -0.9585 -1.1781 -1.5536 + 3SOL OW 29 0.066 1.146 0.603 -0.0175 -0.1987 0.2260 + 3SOL HW1 30 0.105 1.118 0.520 0.3384 -2.0501 1.0020 + 3SOL HW2 31 -0.004 1.082 0.619 -0.2993 0.3441 1.1781 + 4SOL OW 32 0.797 2.719 1.234 0.9363 0.3331 0.3389 + 4SOL HW1 33 0.712 2.758 1.213 0.8348 0.1336 0.3808 + 4SOL HW2 34 0.792 2.699 1.327 0.7495 -0.3817 0.1718 + 5SOL OW 35 1.033 2.007 0.040 -0.0522 -0.8901 0.3952 + 5SOL HW1 36 1.039 2.084 0.095 1.4910 0.9027 -2.2674 + 5SOL HW2 37 0.940 1.984 0.038 -0.5057 0.9701 1.0774 + 6SOL OW 38 0.970 1.370 0.143 -0.0748 0.1856 0.0417 + 6SOL HW1 39 0.947 1.463 0.140 2.7052 0.8322 -0.6327 + 6SOL HW2 40 0.917 1.335 0.215 0.0175 2.5787 1.2754 + 7SOL OW 41 0.399 0.824 1.205 -0.6078 -0.4655 -0.9464 + 7SOL HW1 42 0.397 0.729 1.192 2.2860 -0.6907 0.1152 + 7SOL HW2 43 0.345 0.839 1.283 0.5621 -1.4550 0.0588 + 8SOL OW 44 0.618 1.825 2.273 0.3813 0.1183 -0.2058 + 8SOL HW1 45 0.639 1.849 2.183 0.3642 -0.7343 -0.4428 + 8SOL HW2 46 0.539 1.875 2.293 -0.9883 -1.5372 -1.4919 + 9SOL OW 47 2.579 1.892 0.902 0.1169 -0.1196 -0.5277 + 9SOL HW1 48 2.502 1.926 0.948 1.4163 0.8264 0.9618 + 9SOL HW2 49 2.566 1.918 0.811 -2.6862 -2.4014 -0.7408 + 10SOL OW 50 1.641 1.905 1.550 -0.5693 0.0783 0.3188 + 10SOL HW1 51 1.681 1.903 1.463 1.3879 -1.3120 1.2460 + 10SOL HW2 52 1.603 1.992 1.557 1.5963 1.1281 -0.8967 + 11SOL OW 53 0.342 2.019 2.017 0.7326 0.7808 -0.1826 + 11SOL HW1 54 0.262 2.070 2.028 0.8990 1.1273 -0.6014 + 11SOL HW2 55 0.409 2.070 2.062 0.5201 -0.0032 1.0347 + 12SOL OW 56 1.225 1.696 0.705 -0.4140 0.0323 -0.5150 + 12SOL HW1 57 1.174 1.776 0.701 -0.8231 -0.3007 -1.9308 + 12SOL HW2 58 1.207 1.651 0.622 1.2689 -0.6286 -0.5284 + 13SOL OW 59 0.458 0.827 2.024 -0.0815 0.2185 0.0224 + 13SOL HW1 60 0.503 0.764 2.079 -0.6757 1.2056 1.6265 + 13SOL HW2 61 0.510 0.830 1.943 -0.0358 -2.2646 -0.0214 + 14SOL OW 62 0.810 1.862 1.145 0.0598 -0.0022 -0.2090 + 14SOL HW1 63 0.784 1.868 1.237 0.9019 1.0565 -0.0333 + 14SOL HW2 64 0.767 1.937 1.103 -0.1619 -0.3683 -0.6414 + 15SOL OW 65 1.887 2.617 2.124 0.2034 -0.1614 0.3965 + 15SOL HW1 66 1.938 2.540 2.099 -0.5494 -0.3087 -0.7106 + 15SOL HW2 67 1.870 2.606 2.218 2.7192 0.1961 0.8736 + 16SOL OW 68 0.657 2.195 2.744 -0.7489 0.4828 0.3548 + 16SOL HW1 69 0.664 2.170 2.836 -0.6884 1.7073 0.6937 + 16SOL HW2 70 0.725 2.144 2.700 0.8379 1.6721 1.3887 + 17SOL OW 71 2.152 2.709 0.489 0.4722 0.1073 0.3339 + 17SOL HW1 72 2.102 2.722 0.409 1.3294 -1.1404 -0.4020 + 17SOL HW2 73 2.181 2.618 0.485 -0.3064 -0.2240 2.5347 + 18SOL OW 74 1.771 2.224 2.196 -0.3461 -0.0837 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1.2523 + 642SOL HW2 1948 2.015 2.107 0.384 -0.0198 -0.3132 0.5251 + 643SOL OW 1949 0.494 0.552 2.404 -0.3506 -0.1026 -0.6606 + 643SOL HW1 1950 0.439 0.630 2.400 -0.8715 -0.3666 1.3859 + 643SOL HW2 1951 0.436 0.483 2.437 0.8851 -0.6426 0.4024 + 644SOL OW 1952 2.250 0.941 1.561 0.4017 0.2978 -0.8820 + 644SOL HW1 1953 2.158 0.929 1.538 0.5027 0.1711 -1.2045 + 644SOL HW2 1954 2.256 0.908 1.651 0.0303 0.7389 -0.6928 + 645SOL OW 1955 1.430 1.424 1.865 0.0260 -0.3983 0.1991 + 645SOL HW1 1956 1.520 1.390 1.865 0.4634 0.7493 -3.6003 + 645SOL HW2 1957 1.380 1.359 1.816 -0.5011 0.7453 -0.8074 + 646SOL OW 1958 1.096 2.293 0.211 0.2145 0.4647 -0.1690 + 646SOL HW1 1959 1.086 2.387 0.226 0.8886 0.2241 1.8008 + 646SOL HW2 1960 1.110 2.256 0.299 1.3766 -1.2929 -1.0948 + 647SOL OW 1961 1.138 2.576 0.185 0.1287 -1.1136 -0.0638 + 647SOL HW1 1962 1.156 2.665 0.155 0.8001 -0.9427 0.8643 + 647SOL HW2 1963 1.042 2.571 0.189 0.1007 -0.3339 0.2066 + 648SOL OW 1964 1.196 1.193 2.289 0.6224 0.1188 -0.4001 + 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0.307 0.342 1.685 0.2669 -0.7919 0.6374 + 654SOL HW1 1983 0.383 0.400 1.683 -0.4845 0.2264 1.4535 + 654SOL HW2 1984 0.341 0.259 1.718 1.2749 -0.6968 -0.1888 + 655SOL OW 1985 0.327 1.425 1.766 -0.4186 0.5984 -0.0733 + 655SOL HW1 1986 0.361 1.400 1.680 -1.3326 1.2218 -0.6071 + 655SOL HW2 1987 0.398 1.478 1.804 -0.5012 1.3168 -0.9135 + 656SOL OW 1988 2.213 2.115 0.107 -0.6958 0.0802 -0.1435 + 656SOL HW1 1989 2.276 2.178 0.142 -2.0562 1.2353 0.2022 + 656SOL HW2 1990 2.154 2.098 0.180 -0.2300 -1.7161 -0.1902 + 657SOL OW 1991 1.676 0.657 0.595 -0.6615 0.0928 0.0403 + 657SOL HW1 1992 1.669 0.636 0.502 1.2993 -0.1219 -0.0694 + 657SOL HW2 1993 1.610 0.725 0.610 -0.5875 0.5323 -1.6253 + 658SOL OW 1994 1.171 2.656 2.521 0.0141 -0.0368 -0.1326 + 658SOL HW1 1995 1.263 2.631 2.528 0.5644 2.2611 0.8161 + 658SOL HW2 1996 1.126 2.598 2.584 0.6825 -1.7875 -1.2726 + 659SOL OW 1997 2.035 2.647 0.856 -0.0560 0.1448 0.3169 + 659SOL HW1 1998 2.094 2.589 0.903 0.3070 -1.1101 -1.6888 + 659SOL HW2 1999 2.092 2.712 0.814 -0.1695 -0.4472 -0.7603 + 660SOL OW 2000 1.540 2.670 1.115 0.3387 -0.6244 0.4942 + 660SOL HW1 2001 1.621 2.668 1.064 -0.3166 3.5117 -0.6950 + 660SOL HW2 2002 1.564 2.710 1.198 0.1693 -2.1277 1.2643 + 661SOL OW 2003 2.669 1.683 0.050 -0.0756 -0.1601 0.4565 + 661SOL HW1 2004 2.620 1.744 -0.004 1.0147 1.5820 1.4242 + 661SOL HW2 2005 2.754 1.675 0.007 0.3106 0.1610 1.1664 + 662SOL OW 2006 0.809 0.564 1.332 0.0751 -0.4044 0.2610 + 662SOL HW1 2007 0.821 0.547 1.239 1.8264 0.5757 0.3171 + 662SOL HW2 2008 0.734 0.509 1.357 1.1097 -2.4693 -1.1810 + 663SOL OW 2009 1.508 0.293 0.649 -0.2797 -0.2379 0.4333 + 663SOL HW1 2010 1.471 0.245 0.723 -1.5710 0.0332 -0.0314 + 663SOL HW2 2011 1.540 0.375 0.687 3.0697 -2.0055 1.4386 + 664SOL OW 2012 2.740 2.055 2.456 -0.0800 0.8544 -0.2189 + 664SOL HW1 2013 2.834 2.051 2.476 0.0330 -1.9546 -1.3295 + 664SOL HW2 2014 2.730 2.137 2.407 2.1866 -0.0309 -2.1593 + 665SOL OW 2015 2.287 2.500 1.234 -0.4870 -0.4547 0.1811 + 665SOL HW1 2016 2.290 2.431 1.301 -0.5207 1.1893 1.8757 + 665SOL HW2 2017 2.276 2.581 1.284 1.3774 0.9623 -1.7300 + 666SOL OW 2018 1.801 0.625 1.838 0.1126 0.0241 0.2998 + 666SOL HW1 2019 1.818 0.591 1.750 -1.0256 -0.9556 0.4522 + 666SOL HW2 2020 1.837 0.559 1.897 -0.1256 0.1432 0.5787 + 667SOL OW 2021 0.866 0.927 0.187 -0.8330 -0.3887 0.2560 + 667SOL HW1 2022 0.807 0.974 0.244 0.2661 0.7072 0.4807 + 667SOL HW2 2023 0.875 0.983 0.110 -0.7856 -0.9582 -0.1526 + 668SOL OW 2024 2.186 0.158 1.492 -0.4723 0.2082 -0.1040 + 668SOL HW1 2025 2.104 0.149 1.445 0.7066 -2.1853 -1.7033 + 668SOL HW2 2026 2.185 0.247 1.527 -3.6044 0.2521 -0.3624 + 669SOL OW 2027 0.707 1.897 2.526 0.2920 -0.5340 0.6892 + 669SOL HW1 2028 0.778 1.956 2.499 0.0137 -0.2274 0.6211 + 669SOL HW2 2029 0.678 1.856 2.444 -1.4229 1.3680 0.3332 + 670SOL OW 2030 2.009 0.970 0.321 -0.1410 -0.3020 -0.2139 + 670SOL HW1 2031 2.078 0.949 0.258 -0.6278 -1.4851 -0.3568 + 670SOL HW2 2032 2.027 0.914 0.396 0.3708 1.0293 0.6576 + 671SOL OW 2033 2.451 0.170 2.550 -0.2021 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-0.7787 + 677SOL OW 2051 0.556 0.303 2.679 0.0862 0.6623 0.0138 + 677SOL HW1 2052 0.590 0.387 2.710 -0.5464 0.4873 1.1416 + 677SOL HW2 2053 0.498 0.326 2.606 -0.0471 1.1989 0.2914 + 678SOL OW 2054 1.651 2.635 0.743 -0.5354 0.2362 0.5330 + 678SOL HW1 2055 1.564 2.672 0.760 -0.7256 -0.2045 0.4958 + 678SOL HW2 2056 1.690 2.627 0.830 0.7152 3.5503 0.2947 + 679SOL OW 2057 1.090 0.890 1.165 0.3284 0.3651 -0.5159 + 679SOL HW1 2058 1.176 0.883 1.205 0.6105 -0.0364 -1.1992 + 679SOL HW2 2059 1.038 0.938 1.229 0.7870 -0.2714 0.3459 + 680SOL OW 2060 0.940 0.232 1.046 0.0243 -0.6081 -0.6255 + 680SOL HW1 2061 0.936 0.140 1.071 -3.0605 -0.1196 0.6415 + 680SOL HW2 2062 0.987 0.274 1.118 -1.6444 -0.5957 0.4533 + 2.75904 2.75904 2.75904 diff --git a/ensemble_md/tests/data/coord_swap/E-F.itp b/ensemble_md/tests/data/coord_swap/E-F.itp new file mode 100644 index 00000000..153a2aa1 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/E-F.itp @@ -0,0 +1,293 @@ + + + +[ moleculetype ] +; Name nrexcl +E2F 3 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18 hc 1 E2F H11 18 0.043033 1.0080 DUM_hc 0.000000 1.0080 + 19 hc 1 E2F H12 19 0.043033 1.0080 DUM_hc 0.000000 1.0080 + 20 hc 1 E2F H13 20 0.043033 1.0080 DUM_hc 0.000000 1.0080 + 21 DUM_c3 1 E2F DC10 21 0.000000 12.0100 c3 -0.092600 12.0100 + 22 DUM_hc 1 E2F HV4 22 0.000000 1.0080 hc 0.058700 1.0080 + 23 DUM_hc 1 E2F HV14 23 0.000000 1.0080 hc 0.035200 1.0080 + 24 DUM_hc 1 E2F HV15 24 0.000000 1.0080 hc 0.035200 1.0080 + 25 DUM_hc 1 E2F HV16 25 0.000000 1.0080 hc 0.035200 1.0080 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 0.175380 193853.088000 0.175380 193853.088000 + 1 5 1 0.175380 193853.088000 0.175380 193853.088000 + 2 3 1 0.131580 351221.696000 0.131580 351221.696000 + 2 6 1 0.150020 213501.152000 0.150020 213501.152000 + 3 4 1 0.137130 289474.224000 0.137130 289474.224000 + 4 5 1 0.137300 323205.632000 0.137300 323205.632000 + 6 7 1 0.153540 191535.152000 0.153540 191535.152000 + 6 9 1 0.153540 191535.152000 0.153540 191535.152000 + 7 8 1 0.153540 191535.152000 0.153540 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548.355040 123.870053 548.355040 ; N3 C2 C6 + 3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5 + 6 7 8 1 112.630048 500.992160 112.630048 500.992160 ; C6 C7 C8 + 7 6 9 1 112.630048 500.992160 112.630048 500.992160 ; C7 C6 C9 + 1 5 11 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2 + 2 6 12 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3 + 3 4 10 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1 + 4 5 11 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2 + 5 4 10 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1 + 6 7 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H6 + 6 7 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 C7 H7 + 6 9 18 1 109.680047 362.083360 109.680047 362.083360 ; C6 C9 H11 + 6 9 19 1 109.680047 362.083360 109.680047 362.083360 ; C6 C9 H12 + 6 9 20 1 109.680047 362.083360 109.680047 362.083360 ; C6 C9 H13 + 7 6 12 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 H3 + 7 8 15 1 109.680047 362.083360 109.680047 362.083360 ; C7 C8 H8 + 7 8 16 1 109.680047 362.083360 109.680047 362.083360 ; C7 C8 H9 + 7 8 17 1 109.680047 362.083360 109.680047 362.083360 ; C7 C8 H10 + 8 7 13 1 109.680047 362.083360 109.680047 362.083360 ; C8 C7 H6 + 8 7 14 1 109.680047 362.083360 109.680047 362.083360 ; C8 C7 H7 + 9 6 12 1 109.680047 362.083360 109.680047 362.083360 ; C9 C6 H3 + 13 7 14 1 107.730046 299.574400 107.730046 299.574400 ; H6 C7 H7 + 15 8 16 1 107.730046 299.574400 107.730046 299.574400 ; H8 C8 H9 + 15 8 17 1 107.730046 299.574400 107.730046 299.574400 ; H8 C8 H10 + 16 8 17 1 107.730046 299.574400 107.730046 299.574400 ; H9 C8 H10 + 18 9 19 1 107.730046 299.574400 107.730046 299.574400 ; H11 C9 H12 + 18 9 20 1 107.730046 299.574400 107.730046 299.574400 ; H11 C9 H13 + 19 9 20 1 107.730046 299.574400 107.730046 299.574400 ; H12 C9 H13 + 6 7 21 1 112.630048 500.992160 112.630048 500.992160 ; C6 C7 DC10 + 8 7 21 1 112.630048 500.992160 112.630048 500.992160 ; C8 C7 DC10 + 2 6 22 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 HV4 + 7 6 22 1 109.680047 362.083360 109.680047 362.083360 ; C7 C6 HV4 + 7 21 23 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC10 HV14 + 7 21 24 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC10 HV15 + 7 21 25 1 109.680047 362.083360 109.680047 362.083360 ; C7 DC10 HV16 + 21 7 14 1 109.680047 362.083360 109.680047 362.083360 ; DC10 C7 H7 + 12 6 22 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 HV4 + 23 21 24 1 107.730046 299.574400 107.730046 299.574400 ; HV14 DC10 HV15 + 23 21 25 1 107.730046 299.574400 107.730046 299.574400 ; HV14 DC10 HV16 + 24 21 25 1 107.730046 299.574400 107.730046 299.574400 ; HV15 DC10 HV16 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 C9 (AAAA->AAAD) + 1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 C9 (AAAA->AAAD) + 1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 2 6 7 8 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 C8 (AAAA->AAAA) + 5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 C9 (AAAA->AAAD) + 3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 C9 (AAAA->AAAD) + 4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 8 7 6 9 1 0 2.17568 3 0 0 3 ; C8 C7 C6 C9 (AAAA->AAAD) + 1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 5 4 10 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 11 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 10 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 13 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H6 (AAAA->AAAD) + 2 6 7 13 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H6 (AAAA->AAAD) + 2 6 7 14 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 2 6 9 18 1 0 0.6508444 3 0 0 3 ; C2 C6 C9 H11 (AAAA->AADD) + 2 6 9 19 1 0 0.6508444 3 0 0 3 ; C2 C6 C9 H12 (AAAA->AADD) + 2 6 9 20 1 0 0.6508444 3 0 0 3 ; C2 C6 C9 H13 (AAAA->AADD) + 3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 4 5 11 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 6 7 8 15 1 0 0.54392 3 0 0 3 ; C6 C7 C8 H8 (AAAA->AAAA) + 6 7 8 16 1 0 0.54392 3 0 0 3 ; C6 C7 C8 H9 (AAAA->AAAA) + 6 7 8 17 1 0 0.54392 3 0 0 3 ; C6 C7 C8 H10 (AAAA->AAAA) + 7 6 9 18 1 0 0.54392 3 0 0 3 ; C7 C6 C9 H11 (AAAA->AADD) + 7 6 9 19 1 0 0.54392 3 0 0 3 ; C7 C6 C9 H12 (AAAA->AADD) + 7 6 9 20 1 0 0.54392 3 0 0 3 ; C7 C6 C9 H13 (AAAA->AADD) + 8 7 6 12 1 0 0.54392 3 0 0 3 ; C8 C7 C6 H3 (AAAA->AAAA) + 9 6 7 13 1 0 0.54392 3 0 0 3 ; C9 C6 C7 H6 (AAAA->DAAD) + 9 6 7 14 1 0 0.54392 3 0 0 3 ; C9 C6 C7 H7 (AAAA->DAAA) + 10 4 5 11 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 12 6 7 13 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H6 (AAAA->AAAD) + 12 6 7 14 1 0 0.50208 3 0 0 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 12 6 9 18 1 0 0.50208 3 0 0 3 ; H3 C6 C9 H11 (AAAA->AADD) + 12 6 9 19 1 0 0.50208 3 0 0 3 ; H3 C6 C9 H12 (AAAA->AADD) + 12 6 9 20 1 0 0.50208 3 0 0 3 ; H3 C6 C9 H13 (AAAA->AADD) + 13 7 8 15 1 0 0.50208 3 0 0 3 ; H6 C7 C8 H8 (AAAA->DAAA) + 13 7 8 16 1 0 0.50208 3 0 0 3 ; H6 C7 C8 H9 (AAAA->DAAA) + 13 7 8 17 1 0 0.50208 3 0 0 3 ; H6 C7 C8 H10 (AAAA->DAAA) + 14 7 8 15 1 0 0.50208 3 0 0 3 ; H7 C7 C8 H8 (AAAA->AAAA) + 14 7 8 16 1 0 0.50208 3 0 0 3 ; H7 C7 C8 H9 (AAAA->AAAA) + 14 7 8 17 1 0 0.50208 3 0 0 3 ; H7 C7 C8 H10 (AAAA->AAAA) + 1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA) + 1 2 6 7 1 0 0 3 0 0 3 ; S1 C2 C6 C7 (AAAA->AAAA) + 1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA) + 2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA) + 2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA) + 2 6 7 8 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 C8 (AAAA->AAAA) + 2 6 7 21 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 DC10 (AAAD->AAAA) + 2 6 7 21 1 0 0.6508444 3 0 0 3 ; C2 C6 C7 DC10 (AAAD->AAAA) + 5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA) + 3 2 6 7 1 0 0 3 0 0 3 ; N3 C2 C6 C7 (AAAA->AAAA) + 4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA) + 5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA) + 1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA) + 1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA) + 1 2 6 22 1 0 0 3 0 0 3 ; S1 C2 C6 HV4 (AAAD->AAAA) + 1 2 6 22 1 0 0 3 0 0 3 ; S1 C2 C6 HV4 (AAAD->AAAA) + 1 5 4 10 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA) + 2 1 5 11 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA) + 2 3 4 10 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA) + 2 6 7 14 1 0 0 3 0 0.6508444 3 ; C2 C6 C7 H7 (AAAA->AAAA) + 3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA) + 3 2 6 22 1 0 0 3 0 0 3 ; N3 C2 C6 HV4 (AAAD->AAAA) + 3 2 6 22 1 0 0 3 0 0 3 ; N3 C2 C6 HV4 (AAAD->AAAA) + 3 4 5 11 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA) + 6 7 8 15 1 0 0 3 0 0.54392 3 ; C6 C7 C8 H8 (AAAA->AAAA) + 6 7 8 16 1 0 0 3 0 0.54392 3 ; C6 C7 C8 H9 (AAAA->AAAA) + 6 7 8 17 1 0 0 3 0 0.54392 3 ; C6 C7 C8 H10 (AAAA->AAAA) + 6 7 21 23 1 0 0 3 0 0.54392 3 ; C6 C7 DC10 HV14 (AADD->AAAA) + 6 7 21 23 1 0 0.54392 3 0 0 3 ; C6 C7 DC10 HV14 (AADD->AAAA) + 6 7 21 24 1 0 0 3 0 0.54392 3 ; C6 C7 DC10 HV15 (AADD->AAAA) + 6 7 21 24 1 0 0.54392 3 0 0 3 ; C6 C7 DC10 HV15 (AADD->AAAA) + 6 7 21 25 1 0 0 3 0 0.54392 3 ; C6 C7 DC10 HV16 (AADD->AAAA) + 6 7 21 25 1 0 0.54392 3 0 0 3 ; C6 C7 DC10 HV16 (AADD->AAAA) + 8 7 6 12 1 0 0 3 0 0.54392 3 ; C8 C7 C6 H3 (AAAA->AAAA) + 8 7 6 22 1 0 0 3 0 0.54392 3 ; C8 C7 C6 HV4 (AAAD->AAAA) + 8 7 6 22 1 0 0.54392 3 0 0 3 ; C8 C7 C6 HV4 (AAAD->AAAA) + 8 7 21 23 1 0 0 3 0 0.54392 3 ; C8 C7 DC10 HV14 (AADD->AAAA) + 8 7 21 23 1 0 0.54392 3 0 0 3 ; C8 C7 DC10 HV14 (AADD->AAAA) + 8 7 21 24 1 0 0 3 0 0.54392 3 ; C8 C7 DC10 HV15 (AADD->AAAA) + 8 7 21 24 1 0 0.54392 3 0 0 3 ; C8 C7 DC10 HV15 (AADD->AAAA) + 8 7 21 25 1 0 0 3 0 0.54392 3 ; C8 C7 DC10 HV16 (AADD->AAAA) + 8 7 21 25 1 0 0.54392 3 0 0 3 ; C8 C7 DC10 HV16 (AADD->AAAA) + 21 7 6 12 1 0 0 3 0 0.54392 3 ; DC10 C7 C6 H3 (DAAA->AAAA) + 21 7 6 12 1 0 0.54392 3 0 0 3 ; DC10 C7 C6 H3 (DAAA->AAAA) + 21 7 6 22 1 0 0 3 0 0.54392 3 ; DC10 C7 C6 HV4 (DAAD->AAAA) + 21 7 6 22 1 0 0.54392 3 0 0 3 ; DC10 C7 C6 HV4 (DAAD->AAAA) + 21 7 8 15 1 0 0 3 0 0.54392 3 ; DC10 C7 C8 H8 (DAAA->AAAA) + 21 7 8 15 1 0 0.54392 3 0 0 3 ; DC10 C7 C8 H8 (DAAA->AAAA) + 21 7 8 16 1 0 0 3 0 0.54392 3 ; DC10 C7 C8 H9 (DAAA->AAAA) + 21 7 8 16 1 0 0.54392 3 0 0 3 ; DC10 C7 C8 H9 (DAAA->AAAA) + 21 7 8 17 1 0 0 3 0 0.54392 3 ; DC10 C7 C8 H10 (DAAA->AAAA) + 21 7 8 17 1 0 0.54392 3 0 0 3 ; DC10 C7 C8 H10 (DAAA->AAAA) + 10 4 5 11 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA) + 12 6 7 14 1 0 0 3 0 0.50208 3 ; H3 C6 C7 H7 (AAAA->AAAA) + 22 6 7 14 1 0 0 3 0 0.50208 3 ; HV4 C6 C7 H7 (DAAA->AAAA) + 22 6 7 14 1 0 0.50208 3 0 0 3 ; HV4 C6 C7 H7 (DAAA->AAAA) + 14 7 8 15 1 0 0 3 0 0.50208 3 ; H7 C7 C8 H8 (AAAA->AAAA) + 14 7 8 16 1 0 0 3 0 0.50208 3 ; H7 C7 C8 H9 (AAAA->AAAA) + 14 7 8 17 1 0 0 3 0 0.50208 3 ; H7 C7 C8 H10 (AAAA->AAAA) + 14 7 21 23 1 0 0 3 0 0.50208 3 ; H7 C7 DC10 HV14 (AADD->AAAA) + 14 7 21 23 1 0 0.50208 3 0 0 3 ; H7 C7 DC10 HV14 (AADD->AAAA) + 14 7 21 24 1 0 0 3 0 0.50208 3 ; H7 C7 DC10 HV15 (AADD->AAAA) + 14 7 21 24 1 0 0.50208 3 0 0 3 ; H7 C7 DC10 HV15 (AADD->AAAA) + 14 7 21 25 1 0 0 3 0 0.50208 3 ; H7 C7 DC10 HV16 (AADD->AAAA) + 14 7 21 25 1 0 0.50208 3 0 0 3 ; H7 C7 DC10 HV16 (AADD->AAAA) + + diff --git a/ensemble_md/tests/data/coord_swap/E-F.top b/ensemble_md/tests/data/coord_swap/E-F.top new file mode 100644 index 00000000..0659a83b --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/E-F.top @@ -0,0 +1,32 @@ +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.83333333 + +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +ss 16 32.060000 0.00000000 A 0.35324134 1.1815616 +cc 6 12.010000 0.00000000 A 0.33152123 0.4133792 +nd 7 14.010000 0.00000000 A 0.33841679 0.3937144 +cd 6 12.010000 0.00000000 A 0.33152123 0.4133792 +c3 6 12.010000 0.00000000 A 0.33977095 0.4510352 +h4 1 1.008000 0.00000000 A 0.25363887 0.0673624 +hc 1 1.008000 0.00000000 A 0.2600177 0.0870272 +DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000 +DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000 +Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02 +Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 + +#include "E-F.itp" + +#include "water_and_ions.itp" + +[ system ] +; Name +Generic title in water + +[ molecules ] +; Compound #mols +E2F 1 +SOL 679 diff --git a/ensemble_md/tests/data/coord_swap/params.yaml b/ensemble_md/tests/data/coord_swap/params.yaml new file mode 100644 index 00000000..0c7820ce --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/params.yaml @@ -0,0 +1,27 @@ +n_sim: 5 # Number of replica simulations +n_iter: 1000 # Number of iterations +s: 9 # Shift in λ ranges [e.g. s = 2 if λ_2 = [2, 3, 4] & λ_3 = [4, 5, 6]] +nst_sim: 10000 # Number of simulation steps for each homogeneous replica +proposal: 'exhaustive' +mdp: 'expanded.mdp' +add_swappables: [[6, 9], [6, 10], [6, 11], [7, 9], [7, 10], [7, 11], [8, 9], [8, 10], [8, 11], [15, 18], [15, 19], [15, 20], [16, 18], [16, 19], [16, 20], [17, 18], [17, 19], [17, 20], [24, 27], [24, 28], [24, 29], [25, 27], [25, 28], [25, 29], [26, 27], [26, 28], [26, 29], [33, 36], [33, 37], [33, 38], [34, 36], [34, 37], [34, 38], [35, 36], [35, 37], [35, 38], [42, 45], [42, 46], [42, 47], [43, 45], [43, 46], [43, 47], [44, 45], [44, 46], [44, 47]] +n_ckpt: 25 +N_cutoff: -1 +w_combine: False # The method for combining weights. Choices include "None" [unspecified], exp_avg, ... +runtime_args: {'-ntomp': '5', '-ntmpi': '1'} +grompp_args: {'-maxwarn': '2'} +gro: ['A-B.gro', 'B-C.gro', 'C-D.gro', 'D-E.gro', 'E-F.gro'] +top: ['A-B.top', 'B-C.top', 'C-D.top', 'D-E.top', 'E-F.top'] +gmx_executable: 'gmx' +verbose: True +modify_coords: 'default' +resname_list: ['A2B', 'B2C', 'C2D', 'D2E', 'E2F'] +swap_rep_pattern: [[[0,1],[1,0]], [[1,1],[2,0]], [[2,1],[3,0]], [[3,1],[4,0]]] + +msm: False +free_energy: True +df_spacing: 1 +df_method: "MBAR" +err_method: "propagate" +n_bootstrap: 50 +seed : null diff --git a/ensemble_md/tests/test_coordinate_swap.py b/ensemble_md/tests/test_coordinate_swap.py new file mode 100644 index 00000000..81021a53 --- /dev/null +++ b/ensemble_md/tests/test_coordinate_swap.py @@ -0,0 +1,20 @@ +#################################################################### +# # +# ensemble_md, # +# a python package for running GROMACS simulation ensembles # +# # +# Written by Wei-Tse Hsu # +# Copyright (c) 2022 University of Colorado Boulder # +# # +#################################################################### +""" +Unit tests for the module coordinate_swap.py. +""" +from ensemble_md.utils import coordinate_swap + +def test_get_dimenstion(): + test_file1 = open('ensemble_md/tests/data/coord_swap/input_A.gro', 'r') + test_file2 = open('ensemble_md/tests/data/coord_swap/input_B.gro', 'r') + assert coordinate_swap.get_dimensions(test_file1) == [] + assert coordinate_swap.get_dimensions(test_file2) == [] + From 0aa3ef9cca077355fdd1a80697a98ed363d08f81 Mon Sep 17 00:00:00 2001 From: ajfriedman22 Date: Wed, 18 Sep 2024 16:52:23 -0600 Subject: [PATCH 21/68] fix error in coordinate_swap find_common function --- ensemble_md/utils/coordinate_swap.py | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 9f31b34e..94f632dc 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -72,21 +72,23 @@ def find_common(molA_file, molB_file, nameA, nameB): split_line = line.split(' ') while ("" in split_line): split_line.remove("") - if len(split_line[1]) > 5: - split_line = sep_merge(split_line) - if nameA in split_line[0]: - nameA_list.append(split_line[1]) - lineA_list.append(l) + if len(split_line) > 2: + if len(split_line[1]) > 5: + split_line = sep_merge(split_line) + if nameA in split_line[0]: + nameA_list.append(split_line[1]) + lineA_list.append(l) for l, line in enumerate(molB_file): # noqa: E741 split_line = line.split(' ') while ("" in split_line): split_line.remove("") - if len(split_line[1]) > 5: - split_line = sep_merge(split_line) - if nameB in split_line[0]: - nameB_list.append(split_line[1]) - lineB_list.append(l) + if len(split_line) > 2: + if len(split_line[1]) > 5: + split_line = sep_merge(split_line) + if nameB in split_line[0]: + nameB_list.append(split_line[1]) + lineB_list.append(l) # Determine the atom names present in both molecules common_atoms_all = list(set(nameA_list) & set(nameB_list)) From 046d236a8bdaa9a9c10639d485a8b91c56b4b0c2 Mon Sep 17 00:00:00 2001 From: ajfriedman22 Date: Thu, 19 Sep 2024 10:23:50 -0600 Subject: [PATCH 22/68] Fix error in pbc shift function in coordinate_swap --- ensemble_md/utils/coordinate_swap.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py index 94f632dc..dc88645b 100644 --- a/ensemble_md/utils/coordinate_swap.py +++ b/ensemble_md/utils/coordinate_swap.py @@ -276,10 +276,10 @@ def perform_shift_1D(mol, box_dimensions, broken_pairs_init, prev_shift_atom): fixed = False for x in range(3): # Loop through x, y, and z for shift_dir in [1, -1]: - mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] + (shift_dir[0] * box_dimensions[x]) # positive shift # noqa: E501 + mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] + (shift_dir * box_dimensions[x]) # positive shift # noqa: E501 dist_check = md.compute_distances(mol, atom_pairs=[atom_pair], periodic=False) if dist_check > 0.2: # Didn't work so reverse and try again - mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] - (shift_dir[0] * box_dimensions[x]) + mol.xyz[0, broken_atom, x] = mol.xyz[0, broken_atom, x] - (shift_dir * box_dimensions[x]) else: # Yay fixed break fixed = True break From b221831237de4ab36c62bab92fa5464f8e858f27 Mon Sep 17 00:00:00 2001 From: ajfriedman22 Date: Thu, 19 Sep 2024 11:25:31 -0600 Subject: [PATCH 23/68] add tests --- .../tests/data/coord_swap/find_common.csv | 20 + ensemble_md/tests/data/coord_swap/input_A.gro | 2062 +++++++++++++++++ ensemble_md/tests/data/coord_swap/input_A.trr | Bin 0 -> 273108 bytes ensemble_md/tests/data/coord_swap/input_B.gro | 2061 ++++++++++++++++ ensemble_md/tests/data/coord_swap/input_B.trr | Bin 0 -> 272976 bytes .../tests/data/coord_swap/output_A.gro | 2062 +++++++++++++++++ .../tests/data/coord_swap/output_B.gro | 2061 ++++++++++++++++ ensemble_md/tests/test_coordinate_swap.py | 44 +- 8 files changed, 8308 insertions(+), 2 deletions(-) create mode 100644 ensemble_md/tests/data/coord_swap/find_common.csv create mode 100644 ensemble_md/tests/data/coord_swap/input_A.gro create mode 100644 ensemble_md/tests/data/coord_swap/input_A.trr create mode 100644 ensemble_md/tests/data/coord_swap/input_B.gro create mode 100644 ensemble_md/tests/data/coord_swap/input_B.trr create mode 100644 ensemble_md/tests/data/coord_swap/output_A.gro create mode 100644 ensemble_md/tests/data/coord_swap/output_B.gro diff --git a/ensemble_md/tests/data/coord_swap/find_common.csv b/ensemble_md/tests/data/coord_swap/find_common.csv new file mode 100644 index 00000000..92c92eb5 --- /dev/null +++ b/ensemble_md/tests/data/coord_swap/find_common.csv @@ -0,0 +1,20 @@ +,index,Name,Atom Name Number,Element,Direction,Swap,File line,Final Type +0,0,C8,8,C,R2D,A2B,9,dummy 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