Update tests

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] + '/'
@@ -1541,27 +1536,27 @@ 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')
         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
+        # 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):

ensemble_md/tests/test_coordinate_swap.py

@@ -1,60 +1,87 @@
-####################################################################
-#                                                                  #
-#    ensemble_md,                                                  #
-#    a python package for running GROMACS simulation ensembles     #
-#                                                                  #
-#    Written by Wei-Tse Hsu <wehs7661@colorado.edu>                #
-#    Copyright (c) 2022 University of Colorado Boulder             #
-#                                                                  #
-####################################################################
-"""
-Unit tests for the module coordinate_swap.py.
-"""
-from ensemble_md.utils import coordinate_swap
-import numpy as np
-import pandas as pd
-
-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) == [2.74964, 2.74964, 2.74964]
-    assert coordinate_swap.get_dimensions(test_file2) == [2.74243, 2.74243, 2.74243]
-
-def test_find_common():
-    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')
-    test_df = coordinate_swap.find_common(test_file1, test_file2, 'C2D', 'D2E')
-    df = pd.read_csv('ensemble_md/tests/data/coord_swap/find_common.csv')
-
-    for index, row in df.iterrows():
-        test_row = test_df[test_df['Name'] == row['Name']]
-        assert row['Atom Name Number'] == int(test_row['Atom Name Number'].to_list()[0])
-        assert row['Element'] == test_row['Element'].to_list()[0]
-        assert row['Direction'] == test_row['Direction'].to_list()[0]
-        assert row['Swap'] == test_row['Swap'].to_list()[0]
-        assert row['File line'] == int(test_row['File line'].to_list()[0])
-        assert row['Final Type'] == test_row['Final Type'].to_list()[0]
-
-def test_rotate_point_around_axis():
-    initial_point = np.array([0.16, 0.19, -0.05])
-    vertex = np.array([0, 0, 0])
-    axis = np.array([0.15, 0.82, 0.14])
-    angle = 0.13
-    rotated_point = [0.1693233, 0.18548463, -0.0335421]
-    assert coordinate_swap.rotate_point_around_axis(initial_point, vertex, axis, angle) == rotated_point
-
-def test_find_rotation_angle():
-    initial_point = np.array([0.16, 0.19, -0.05])
-    vertex = np.array([0, 0, 0])
-    axis = np.array([0.15, 0.82, 0.14])
-    rotated_point = [0.1693233, 0.18548463, -0.0335421]
-    angle = 0.13
-    test_angle = coordinate_swap.find_rotation_angle(initial_point, vertex, rotated_point, axis)
-    assert np.isclose(angle, test_angle, 10**(-5))
-
-def test_compute_angle():
-    vec1_start = [0.13, 0.15, 0.16]
-    vec1_end = [0.16, 0.18, 0.17]
-    vec2_start = [0.13, 0.15, 0.16]
-    vec2_end = [0.11, 0.23, 0.05]
-    assert np.isclose(coordinate_swap.compute_angle([vec1_start, vec1_end, vec2_start, vec2_end]), 0.991836017536949, atol=10**(-4))
+####################################################################
+#                                                                  #
+#    ensemble_md,                                                  #
+#    a python package for running GROMACS simulation ensembles     #
+#                                                                  #
+#    Written by Wei-Tse Hsu <wehs7661@colorado.edu>                #
+#    Copyright (c) 2022 University of Colorado Boulder             #
+#                                                                  #
+####################################################################
+"""
+Unit tests for the module coordinate_swap.py.
+"""
+from ensemble_md.utils import coordinate_swap
+import numpy as np
+import pandas as pd
+import os
+
+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_find_common():
+    test_file1 = open(f'{input_path}/coord_swap/input_A.gro', 'r')
+    test_file2 = open(f'{input_path}/coord_swap/input_B.gro', 'r')
+    test_df = coordinate_swap.find_common(test_file1, test_file2, 'C2D', 'D2E')
+    df = pd.read_csv(f'{input_path}/coord_swap/find_common.csv')
+
+    for index, row in df.iterrows():
+        test_row = test_df[test_df['Name'] == row['Name']]
+        assert row['Atom Name Number'] == int(test_row['Atom Name Number'].to_list()[0])
+        assert row['Element'] == test_row['Element'].to_list()[0]
+        assert row['Direction'] == test_row['Direction'].to_list()[0]
+        assert row['Swap'] == test_row['Swap'].to_list()[0]
+        assert row['File line'] == int(test_row['File line'].to_list()[0])
+        assert row['Final Type'] == test_row['Final Type'].to_list()[0]
+
+def test_rotate_point_around_axis():
+    initial_point = np.array([0.16, 0.19, -0.05])
+    vertex = np.array([0, 0, 0])
+    axis = np.array([0.15, 0.82, 0.14])
+    angle = 0.13
+    rotated_point = [0.1693233, 0.18548463, -0.0335421]
+    assert coordinate_swap.rotate_point_around_axis(initial_point, vertex, axis, angle) == rotated_point
+
+def test_find_rotation_angle():
+    initial_point = np.array([0.16, 0.19, -0.05])
+    vertex = np.array([0, 0, 0])
+    axis = np.array([0.15, 0.82, 0.14])
+    rotated_point = [0.1693233, 0.18548463, -0.0335421]
+    angle = 0.13
+    test_angle = coordinate_swap.find_rotation_angle(initial_point, vertex, rotated_point, axis)
+    assert np.isclose(angle, test_angle, 10**(-5))
+
+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.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)

ensemble_md/utils/coordinate_swap.py

@@ -980,8 +980,8 @@ 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
     -------