More robust phase_path order handling

choderalab · Dec 1, 2017 · d94cbcc · d94cbcc
1 parent 5d071df
commit d94cbcc
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Showing 4 changed files with 16 additions and 27 deletions.
diff --git a/Yank/experiment.py b/Yank/experiment.py
@@ -1657,15 +1657,13 @@ def _is_pipeline_solvent_with_receptor(field, solvent_id, error):
                 type: string
                 validator: file_exists
             validator: supported_system_files
-            coerce: sort_system_files_by_type
         phase2_path:
             required: no
             type: list
             schema:
                 type: string
                 validator: file_exists
             validator: supported_system_files
-            coerce: sort_system_files_by_type
         gromacs_include_dir:
             required: no
             type: string

diff --git a/Yank/pipeline.py b/Yank/pipeline.py
@@ -857,6 +857,7 @@ def get_system_files_paths(self, system_id):
         """
         Paths = collections.namedtuple('Paths', ['position_path', 'parameters_path'])
         system_dir = os.path.join(self.setup_dir, self.SYSTEMS_DIR, system_id)
+
         if 'receptor' in self.systems[system_id]:
             system_files_paths = [
                 Paths(position_path=os.path.join(system_dir, 'complex.inpcrd'),
@@ -872,13 +873,20 @@ def get_system_files_paths(self, system_id):
                       parameters_path=os.path.join(system_dir, 'solvent2.prmtop'))
             ]
         else:
-            system_files_paths = [
-                Paths(position_path=self.systems[system_id]['phase1_path'][0],
-                      parameters_path=self.systems[system_id]['phase1_path'][1]),
-                Paths(position_path=self.systems[system_id]['phase2_path'][0],
-                      parameters_path=self.systems[system_id]['phase2_path'][1])
-            ]
-
+            parameter_file_extensions = {'prmtop', 'top', 'xml'}
+            system_files_paths = []
+            for phase_path_name in ['phase1_path', 'phase2_path']:
+                file_paths = self.systems[system_id][phase_path_name]
+                assert len(file_paths) == 2
+
+                # Make sure that the position file is first.
+                first_file_extension = os.path.splitext(file_paths[0])[1][1:]
+                if first_file_extension in parameter_file_extensions:
+                    file_paths = list(reversed(file_paths))
+
+                # Append Paths object.
+                system_files_paths.append(Paths(position_path=file_paths[0],
+                                                parameters_path=file_paths[1]))
         return system_files_paths
 
     def is_molecule_setup(self, molecule_id):

diff --git a/Yank/schema/validator.py b/Yank/schema/validator.py
@@ -24,17 +24,6 @@ def _normalize_coerce_single_str_to_list(self, value):
         """Cast a single string to a list of string"""
         return [value] if isinstance(value, str) else value
 
-    def _normalize_coerce_sort_system_files_by_type(self, file_paths):
-        """Sort the system files path to have positions first and parameters second."""
-        file_extensions = [os.path.splitext(file_path)[1][1:] for file_path in file_paths]
-
-        # In all cases but for the pair (rst7, prmtop) we can just sort alphabetically.
-        sorted_file_paths = [file_path for ext, file_path in sorted(zip(file_extensions, file_paths))]
-        if 'rst7' not in file_extensions:
-            # reversed() return an iterator.
-            return list(reversed(sorted_file_paths))
-        return sorted_file_paths
-
     # ====================================================
     # DATA VALIDATORS
     # ====================================================
@@ -73,12 +62,6 @@ def _validator_int_or_all_string(self, field, value):
 
     def _validator_supported_system_files(self, field, file_paths):
         """Ensure the input system files are supported."""
-        # Check that this is a list of two file_paths.
-        if len(file_paths) != 2:
-            self._error(field, '{} must be a list of paths to the position '
-                               'and parameter files'.format(field))
-            return
-
         # Obtain the extension of the system files.
         file_extensions = {os.path.splitext(file_path)[1][1:] for file_path in file_paths}
 

diff --git a/Yank/tests/test_experiment.py b/Yank/tests/test_experiment.py
@@ -619,7 +619,7 @@ def test_validation_wrong_systems():
             {'receptor': 'rec', 'ligand': 'lig', 'solvent': 'solv3',
              'parameters': 'leaprc.ff14SB'}),
 
-        ("list of paths",
+        ("phase1_path: \[must be of list type\]",
             {'phase1_path': data_paths['bentol-complex'][0],
              'phase2_path': data_paths['bentol-solvent'],
              'ligand_dsl': 'resname BEN', 'solvent': 'solv'}),