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small_molecule_construction.py
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small_molecule_construction.py
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import networkx as nx
import numpy as np
import atomic_data
from itertools import groupby, combinations
from random import randint
import small_molecule_constants
from cif2system import PBC3DF_sym
import write_molecule_files as WMF
from ase import Atom, Atoms
from ase import neighborlist
from ase.geometry import get_distances
from ase.io import read
mass_key = atomic_data.mass_key
def add_small_molecules(FF, ff_string):
if ff_string == 'TraPPE':
SM_constants = small_molecule_constants.TraPPE
elif ff_string == 'TIP4P_2005_long':
SM_constants = small_molecule_constants.TIP4P_2005_long
FF.pair_data['special_bonds'] = 'lj 0.0 0.0 1.0 coul 0.0 0.0 0.0'
elif ff_string == 'TIP4P_cutoff':
SM_constants = small_molecule_constants.TIP4P_cutoff
FF.pair_data['special_bonds'] = 'lj/coul 0.0 0.0 1.0'
elif ff_string == 'TIP4P_2005_cutoff':
SM_constants = small_molecule_constants.TIP4P_cutoff
FF.pair_data['special_bonds'] = 'lj/coul 0.0 0.0 1.0'
elif ff_string == 'Ions':
SM_constants = small_molecule_constants.Ions
FF.pair_data['special_bonds'] = 'lj/coul 0.0 0.0 1.0'
# insert more force fields here if needed
else:
raise ValueError('the small molecule force field', ff_string, 'is not defined')
SG = FF.system['graph']
SMG = FF.system['SM_graph']
if len(SMG.nodes()) > 0 and len(SMG.edges()) == 0:
print('there are no small molecule bonds in the CIF, calculating based on covalent radii...')
atoms = Atoms()
offset = min(SMG.nodes())
for node,data in SMG.nodes(data=True):
#print(node, data)
atoms.append(Atom(data['element_symbol'], data['cartesian_position']))
atoms.set_cell(FF.system['box'])
unit_cell = atoms.get_cell()
cutoffs = neighborlist.natural_cutoffs(atoms)
NL = neighborlist.NewPrimitiveNeighborList(cutoffs, use_scaled_positions=False, self_interaction=False, skin=0.10) # shorten the cutoff a bit
NL.build([True, True, True], unit_cell, atoms.get_positions())
for i in atoms:
nbors = NL.get_neighbors(i.index)[0]
for j in nbors:
bond_length = get_distances(i.position, p2=atoms[j].position, cell=unit_cell, pbc=[True,True,True])
bond_length = np.round(bond_length[1][0][0], 3)
SMG.add_edge(i.index + offset, j + offset, bond_length=bond_length, bond_order='1.0', bond_type='S')
NMOL = len(list(nx.connected_components(SMG)))
print(NMOL, 'small molecules were recovered after bond calculation')
mol_flag = 1
max_ind = FF.system['max_ind']
index = max_ind
box = FF.system['box']
a,b,c,alpha,beta,gamma = box
pi = np.pi
ax = a
ay = 0.0
az = 0.0
bx = b * np.cos(gamma * pi / 180.0)
by = b * np.sin(gamma * pi / 180.0)
bz = 0.0
cx = c * np.cos(beta * pi / 180.0)
cy = (c * b * np.cos(alpha * pi /180.0) - bx * cx) / by
cz = (c ** 2.0 - cx ** 2.0 - cy ** 2.0) ** 0.5
unit_cell = np.asarray([[ax,ay,az],[bx,by,bz],[cx,cy,cz]]).T
inv_unit_cell = np.linalg.inv(unit_cell)
add_nodes = []
add_edges = []
comps = []
for comp in nx.connected_components(SMG):
mol_flag += 1
comp = sorted(list(comp))
ID_string = sorted([SMG.nodes[n]['element_symbol'] for n in comp])
ID_string = [(key, len(list(group))) for key, group in groupby(ID_string)]
ID_string = ''.join([str(e) for c in ID_string for e in c])
comps.append(ID_string)
for n in comp:
data = SMG.nodes[n]
SMG.nodes[n]['mol_flag'] = str(mol_flag)
if ID_string == 'H2O1':
SMG.nodes[n]['force_field_type'] = SMG.nodes[n]['element_symbol'] + '_w'
else:
SMG.nodes[n]['force_field_type'] = SMG.nodes[n]['element_symbol'] + '_' + ID_string
# add COM sites where relevant, extend this list as new types are added
if ID_string in ('O2', 'N2'):
coords = []
anchor = SMG.nodes[comp[0]]['fractional_position']
for n in comp:
data = SMG.nodes[n]
data['mol_flag'] = str(mol_flag)
fcoord = data['fractional_position']
mic = PBC3DF_sym(fcoord, anchor)
fcoord += mic[1]
ccoord = np.dot(unit_cell, fcoord)
coords.append(ccoord)
ccom = np.average(coords, axis=0)
fcom = np.dot(inv_unit_cell, ccom)
index += 1
if ID_string == 'O2':
fft = 'O_com'
elif ID_string == 'N2':
fft = 'N_com'
ndata = {'element_symbol':'NA', 'mol_flag':mol_flag, 'index':index, 'force_field_type':fft, 'cartesian_position':ccom, 'fractional_position':fcom, 'charge':0.0, 'replication':np.array([0.0,0.0,0.0]), 'duplicated_version_of':None}
edata = {'sym_code':None, 'length':None, 'bond_type':None}
add_nodes.append([index, ndata])
add_edges.extend([(index, comp[0], edata), (index, comp[1], edata)])
for n, data in add_nodes:
SMG.add_node(n, **data)
for e0, e1, data in add_edges:
SMG.add_edge(e0, e1, **data)
ntypes = max([FF.atom_types[ty] for ty in FF.atom_types])
maxatomtype_wsm = max([FF.atom_types[ty] for ty in FF.atom_types])
maxbondtype_wsm = max([bty for bty in FF.bond_data['params']])
maxangletype_wsm = max([aty for aty in FF.angle_data['params']])
nbonds = max([i for i in FF.bond_data['params']])
nangles = max([i for i in FF.angle_data['params']])
try:
ndihedrals = max([i for i in FF.dihedral_data['params']])
except ValueError:
ndihedrals = 0
try:
nimpropers = max([i for i in FF.improper_data['params']])
except ValueError:
nimpropers = 0
new_bond_types = {}
new_angle_types = {}
new_dihedral_types = {}
new_improper_types = {}
for subG, ID_string in zip([SMG.subgraph(c).copy() for c in nx.connected_components(SMG)], comps):
constants = SM_constants[ID_string]
# add new atom types
for name,data in sorted(subG.nodes(data=True), key=lambda x:x[0]):
fft = data['force_field_type']
chg = constants['pair']['charges'][fft]
data['charge'] = chg
SG.add_node(name, **data)
try:
FF.atom_types[fft] += 0
except KeyError:
ntypes += 1
FF.atom_types[fft] = ntypes
style = constants['pair']['style']
vdW = constants['pair']['vdW'][fft]
FF.pair_data['params'][FF.atom_types[fft]] = (style, vdW[0], vdW[1])
FF.pair_data['comments'][FF.atom_types[fft]] = [fft, fft]
FF.atom_masses[fft] = mass_key[data['element_symbol']]
if 'hybrid' not in FF.pair_data['style'] and style != FF.pair_data['style']:
FF.pair_data['style'] = ' '.join(['hybrid', FF.pair_data['style'], style])
elif 'hybrid' in FF.pair_data['style'] and style in FF.pair_data['style']:
pass
elif 'hybrid' in FF.pair_data['style'] and style not in FF.pair_data['style']:
FF.pair_data['style'] += ' ' + style
# add new bonds
used_bonds = []
ty = nbonds
for e0,e1,data in subG.edges(data=True):
bonds = constants['bonds']
fft_i = SG.nodes[e0]['force_field_type']
fft_j = SG.nodes[e1]['force_field_type']
# make sure the order corresponds to that in the molecule dictionary
bond = tuple(sorted([fft_i, fft_j]))
try:
style = bonds[bond][0]
if bond not in used_bonds:
ty = ty + 1
new_bond_types[bond] = ty
FF.bond_data['params'][ty] = list(bonds[bond])
FF.bond_data['comments'][ty] = list(bond)
used_bonds.append(bond)
if 'hybrid' not in FF.bond_data['style'] and style != FF.bond_data['style']:
FF.bond_data['style'] = ' '.join(['hybrid', FF.bond_data['style'], style])
elif 'hybrid' in FF.bond_data['style'] and style in FF.bond_data['style']:
pass
elif 'hybrid' in FF.bond_data['style'] and style not in FF.bond_data['style']:
FF.bond_data['style'] += ' ' + style
if ty in FF.bond_data['all_bonds']:
FF.bond_data['count'] = (FF.bond_data['count'][0] + 1, FF.bond_data['count'][1] + 1)
FF.bond_data['all_bonds'][ty].append((e0,e1))
else:
FF.bond_data['count'] = (FF.bond_data['count'][0] + 1, FF.bond_data['count'][1] + 1)
FF.bond_data['all_bonds'][ty] = [(e0,e1)]
except KeyError:
pass
# add new angles
used_angles = []
ty = nangles
for name,data in subG.nodes(data=True):
angles = constants['angles']
nbors = list(subG.neighbors(name))
for comb in combinations(nbors, 2):
j = name
i, k = comb
fft_i = subG.nodes[i]['force_field_type']
fft_j = subG.nodes[j]['force_field_type']
fft_k = subG.nodes[k]['force_field_type']
angle = sorted((fft_i, fft_k))
angle = (angle[0], fft_j, angle[1])
try:
style = angles[angle][0]
FF.angle_data['count'] = (FF.angle_data['count'][0] + 1, FF.angle_data['count'][1])
if angle not in used_angles:
ty = ty + 1
new_angle_types[angle] = ty
FF.angle_data['count'] = (FF.angle_data['count'][0], FF.angle_data['count'][1] + 1)
FF.angle_data['params'][ty] = list(angles[angle])
FF.angle_data['comments'][ty] = list(angle)
used_angles.append(angle)
if 'hybrid' not in FF.angle_data['style'] and style != FF.angle_data['style']:
FF.angle_data['style'] = ' '.join(['hybrid', FF.angle_data['style'], style])
elif 'hybrid' in FF.angle_data['style'] and style in FF.angle_data['style']:
pass
elif 'hybrid' in FF.angle_data['style'] and style not in FF.angle_data['style']:
FF.angle_data['style'] += ' ' + style
if ty in FF.angle_data['all_angles']:
FF.angle_data['all_angles'][ty].append((i,j,k))
else:
FF.angle_data['all_angles'][ty] = [(i,j,k)]
except KeyError:
pass
# add new dihedrals
FF.bond_data['count'] = (FF.bond_data['count'][0], len(FF.bond_data['params']))
FF.angle_data['count'] = (FF.angle_data['count'][0], len(FF.angle_data['params']))
if 'tip4p' in FF.pair_data['style']:
for ty,pair in FF.pair_data['comments'].items():
fft = pair[0]
if fft == 'O_w':
FF.pair_data['O_type'] = ty
if fft == 'H_w':
FF.pair_data['H_type'] = ty
for ty, bond in FF.bond_data['comments'].items():
if sorted(bond) == ['H_w', 'O_w']:
FF.pair_data['H2O_bond_type'] = ty
for ty, angle in FF.angle_data['comments'].items():
if angle == ['H_w', 'O_w', 'H_w']:
FF.pair_data['H2O_angle_type'] = ty
if 'long' in FF.pair_data['style']:
FF.pair_data['M_site_dist'] = 0.1546 # only TIP4P/2005 is implemented
elif 'cut' in FF.pair_data['style'] and ff_string == 'TIP4P_2005_cutoff':
FF.pair_data['M_site_dist'] = 0.1546
elif 'cut' in FF.pair_data['style'] and ff_string == 'TIP4P_cutoff':
FF.pair_data['M_site_dist'] = 0.1500
def update_potential(potential_data, new_potential_params, potential_coeff):
write_instyles = False
add_styles = set([new_potential_params[ty]['style'] for ty in new_potential_params])
for ABS in add_styles:
if ABS not in potential_data['style'] and 'hybrid' in potential_data['style']:
potential_data['style'] = potential_data['style'] + ' ' + ABS
write_instyles = True
if ABS not in potential_data['style'] and 'hybrid' not in potential_data['style']:
potential_data['style'] = 'hybrid ' + potential_data['style'] + ' ' + ABS
write_instyles = True
else:
pass
if write_instyles:
instyles = {ty:' ' + new_potential_params[ty]['style'] for ty in new_potential_params}
else:
instyles = {ty:'' for ty in new_potential_params}
potential_data['infile_add_lines'] = []
for ty,data in new_potential_params.items():
strparams = ' '.join([str(p) for p in data['params']])
potential_data['infile_add_lines'].append(potential_coeff + str(ty) + instyles[ty] + ' ' + strparams + ' ' + data['comments'])
def include_molecule_file(FF, maxIDs, add_molecule):
max_atom_ty, max_bond_ty, max_angle_ty, max_dihedral_ty, max_improper_ty = maxIDs
molname, model, N = add_molecule
if molname in ('water', 'Water', 'H2O', 'h2o'):
molfile, LJ_params, bond_params, angle_params, molnames, mass_dict, M_site_dist, extra_types = WMF.water(max_atom_ty, max_bond_ty, max_angle_ty, model=model)
dihedral_params = None
improper_params = None
FF.pair_data['special_bonds'] = 'lj/coul 0.0 0.0 1.0'
FF.pair_data['O_type'] = max_atom_ty + 1
FF.pair_data['H_type'] = max_atom_ty + 2
FF.pair_data['H2O_bond_type'] = max_bond_ty + 1
FF.pair_data['H2O_angle_type'] = max_angle_ty + 1
FF.pair_data['M_site_dist'] = M_site_dist
add_LJ_style = LJ_params['style']
if add_LJ_style not in FF.pair_data['style']:
FF.pair_data['style'] = FF.pair_data['style'] + ' ' + add_LJ_style
if 'hybrid' not in FF.pair_data['style']:
FF.pair_data['style'] = 'hybrid ' + FF.pair_data['style']
for aty, param in LJ_params.items():
if aty not in ('style', 'comments'):
FF.pair_data['params'][aty] = param
FF.pair_data['comments'][aty] = LJ_params['comments'][aty]
if bond_params != None:
update_potential(FF.bond_data, bond_params, 'bond_coeff ')
if angle_params != None:
update_potential(FF.angle_data, angle_params, 'angle_coeff ')
if dihedral_params != None:
update_potential(FF.dihedral_params, dihedral_params, 'dihedral_coeff ')
if improper_params != None:
update_potential(FF.improper_data, improper_params, 'improper_coeff ')
infile_add_lines = ['molecule ' + ' '.join(molnames)]
for atom in mass_dict:
infile_add_lines.append('mass ' + str(atom) + ' ' + str(mass_dict[atom]))
seed0 = randint(1,10000)
seed1 = randint(1,10000)
if N > 0:
create_line = ' '.join([str(N), str(seed0), 'NULL', 'mol', molnames[0], str(seed1), 'units', 'box'])
infile_add_lines.append('create_atoms 0 random ' + create_line)
return molfile, infile_add_lines, extra_types
def read_RASPA_pdb(file):
with open(file, 'r') as pdb:
pdb = pdb.read()
pdb = pdb.split('\n')
atoms = Atoms()
for line in pdb:
s = line.split()
if len(s) > 0 and s[0] == 'ATOM':
atoms.append(Atom(s[2], np.array([float(c) for c in s[4:7]])))
return atoms
def read_small_molecule_file(sm_file, system):
fm = sm_file.split('.')[-1]
max_ind = max(system['graph'])
ind = max_ind + 1
if fm not in ('pdb', 'xyz', 'cif'):
raise ValueError('only xyz and RASPA pdb formats are supported for small molecule files')
if fm == 'pdb':
print('assuming small molecule file is in RASPA pdb format, if not, too bad...')
atoms = read_RASPA_pdb(sm_file)
else:
atoms = read(sm_file, format=fm)
atoms.set_cell(system['box'])
SMG = nx.Graph()
for atom in atoms:
SMG.add_node(ind, element_symbol=atom.symbol, mol_flag='1', index=ind, force_field_type='', cartesian_position=atom.position,
fractional_position=atom.scaled_position, charge=0.0, replication=np.array([0.0,0.0,0.0]), duplicated_version_of=None)
ind += 1
system['SM_graph'] = nx.compose(SMG, system['SM_graph']) # don't want to overwrite extra framework species already in the cif