Move read_top function

ensemble_md/replica_exchange_EE.py

@@ -1591,7 +1591,7 @@ def process_top(self):
             df_top = pd.DataFrame()
             for f, file_name in enumerate(self.top):
                 # Read file
-                input_file = coordinate_swap.read_top(file_name, self.resname_list[f])
+                input_file = gmx_parser.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_file)
@@ -1623,9 +1623,9 @@ def process_top(self):
                 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[A], self.resname_list[A])
+                    input_A = gmx_parser.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[B], self.resname_list[B])
+                    input_B = gmx_parser.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]

ensemble_md/tests/test_coordinate_swap.py

@@ -380,12 +380,3 @@ def test_determine_connection():
     select_cmpr_df = cmpr_df[(cmpr_df['Swap A'] == 'E2F') & (cmpr_df['Swap B'] == 'D2E')]
     for col in ['Anchor Atom Name A', 'Anchor Atom Name B', 'Alignment Atom A', 'Alignment Atom B', 'Angle Atom A', 'Angle Atom B', 'Missing Atom Name']:  # noqa: E501
         assert test_df[col].to_list()[0] == select_cmpr_df[col].to_list()[0]
-
-
-def test_read_top():
-    top_files = ['A-B.top', 'B-C.top', 'C-D.top', 'D-E.top', 'E-F.top']
-    resname_list = ['A2B', 'B2C', 'C2D', 'D2E', 'E2F']
-
-    for resname, top_file in zip(resname_list, top_files):
-        top = coordinate_swap.read_top(f'{input_path}/coord_swap/{top_file}', resname)
-        assert len(top) > 0

ensemble_md/tests/test_gmx_parser.py

@@ -120,3 +120,12 @@ def test_compare_MDPs():
 
     assert result_1 == dict_1
     assert result_2 == dict_2
+
+
+def test_read_top():
+    top_files = ['A-B.top', 'B-C.top', 'C-D.top', 'D-E.top', 'E-F.top']
+    resname_list = ['A2B', 'B2C', 'C2D', 'D2E', 'E2F']
+
+    for resname, top_file in zip(resname_list, top_files):
+        top = gmx_parser.read_top(f'{input_path}/coord_swap/{top_file}', resname)
+        assert len(top) > 0

ensemble_md/utils/coordinate_swap.py

@@ -1444,58 +1444,3 @@ def determine_connection(main_only, other_only, main_name, other_name, df_top, m
     df['Missing Atom Name'] = miss_sep_reformat
 
     return df
-
-
-def read_top(file_name, resname):
-    """
-    Reads 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.
-
-    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 = []
-    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""'))
-    file_dir, file_name = os.path.split(file_name)
-    for file in itp_files:
-        if os.path.exists(f'{file_dir}/{file}'):
-            input_file = open(f'{file_dir}/{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}')

ensemble_md/utils/gmx_parser.py

@@ -353,3 +353,58 @@ def compare_MDPs(mdp_list, print_diff=False):
             print()
 
     return diff_params
+
+
+def read_top(file_name, resname):
+    """
+    Reads 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.
+
+    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 = []
+    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""'))
+    file_dir, file_name = os.path.split(file_name)
+    for file in itp_files:
+        if os.path.exists(f'{file_dir}/{file}'):
+            input_file = open(f'{file_dir}/{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}')