Merge pull request #143 from martimunicoy/devel

1.3.1 Release

docs/releasehistory.rst

@@ -7,6 +7,21 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+
+1.3.1 - PELE Platform support
+-----------------------------
+
+This is a micro release of peleffy that includes minor adjustments for the PELE Platform and other small fixes.
+
+New features
+""""""""""""
+- `PR #142 <https://github.com/martimunicoy/peleffy/pull/142>`_: Minor adjustments to facilitate platform compatibility.
+
+Bugfixes
+""""""""
+- Minor error when parsing Impact templates.
+
+
 1.3.0 - BCE conformations and automatic heteromolecules extraction
 ------------------------------------------------------------------
 

peleffy/forcefield/parameters.py

@@ -506,6 +506,8 @@ def reindex_atom_idx(list_params, dict_index):
         with open(impact_template_path, 'r') as fd:
             type_info = 'tag'
             for line in fd.readlines():
+                if len(line.strip()) == 0:  # Skip empty lines
+                    continue
                 if not line.startswith('*'):
                     if 'NBON' in line:
                         type_info = 'nbon'
@@ -517,6 +519,8 @@ def reindex_atom_idx(list_params, dict_index):
                         type_info = 'phi'
                     elif 'IPHI' in line:
                         type_info = 'iphi'
+                    elif 'END' in line:
+                        break
                     else:
                         if type_info == 'tag':
                             tag.append(line)
@@ -594,7 +598,7 @@ def reindex_atom_idx(list_params, dict_index):
 
         # Impropers
         impropers_list = []
-        for line in iphi[:-1]:
+        for line in iphi:
             info = line.split()
             case = {'atom1_idx': index(info[0]),
                     'atom2_idx': index(info[1]),

peleffy/tests/test_parameters.py

@@ -290,13 +290,6 @@ def test_generate_OPLS2005ParameterWrapper(molecule,
         test_generate_OPLS2005ParameterWrapper(molecule,
                                                impact_template_path)
 
-        # Test with molecule with phase different than 0 or 180
-        # Load molecule, parameterize and generate Impact template
-        molecule = Molecule(smiles='c1c(c(n(n1)S(=O)(=O)C))O')
-        impact_template_path = get_data_file_path('tests/unlz')
-        test_generate_OpenForceFieldParameterWrapper(molecule,
-                                                     impact_template_path)
-
         # The molecule and Impact template do no represent the same chemical
         # entity
         with pytest.raises(ValueError):

peleffy/topology/conformer.py

@@ -16,10 +16,9 @@
 
 class BCEConformations(object):
     """
-    A class to produce a library of conformations from the output
-    of the BCE server.
+    A class to produce a library of conformations from a set of ligand PDB files.
     """
-    def __init__(self, topology_obj, bce_output_path):
+    def __init__(self, topology_obj, bce_output_path, from_bce=True):
         """
         Initializes a BCEConformations object.
 
@@ -29,11 +28,15 @@ def __init__(self, topology_obj, bce_output_path):
             A Topology object that contains the ligand's information
         bce_output_path: str
             Path where the output from the BCE server is stored
+        from_bce : bool
+            Whether the ligand clusters originate from the BCE server or not. Affects cluster search path in
+            _calculate_all_conformations method.
         """
         self._topology = topology_obj
         self._molecule = topology_obj.molecule
         self.bce_path = bce_output_path
         self.conformations_library = {}
+        self.from_bce = from_bce
 
     def calculate(self):
         """
@@ -44,9 +47,11 @@ def calculate(self):
         self._calculate_all_conformations()
 
     def _calculate_all_conformations(self):
-        clusters = sorted(glob.glob(os.path.join(self.bce_path,
-                                                 "CLUSTERS", "CL*",
-                                                 "cluster*.min.imaged.pdb")))
+        if self.from_bce:
+            clusters = sorted(glob.glob(os.path.join(self.bce_path, "CLUSTERS", "CL*", "cluster*.min.imaged.pdb")))
+        else:
+            clusters = sorted(glob.glob(os.path.join(self.bce_path, "*.pdb")))
+
         if not clusters:
             raise ValueError("Path to the BCE output does not contain a "
                              + "CLUSTERS folder, please check if the path "
@@ -56,7 +61,6 @@ def _calculate_all_conformations(self):
         for cluster in ordered_clusters:
             self.calculate_cluster_offsets(cluster)
 
-
     def calculate_cluster_offsets(self, cluster_pdb):
         """
         Calculate dihedral angles from PDB.
@@ -71,7 +75,8 @@ def calculate_cluster_offsets(self, cluster_pdb):
         # Use the input molecule as template since the cluster structures
         # probably will not have proper stereochemistry
         mol = molecule.Molecule(
-            cluster_pdb, connectivity_template=self._molecule.rdkit_molecule)
+            cluster_pdb, connectivity_template=self._molecule.rdkit_molecule,
+            allow_undefined_stereo=self._molecule.allow_undefined_stereo)
         cluster_coordinates = mol.get_conformer()
         topology_to_cluster = {
             i: x for i, x
@@ -136,7 +141,8 @@ def order_clusters_min_distances(self, clusters):
             # probably will not have proper stereochemistry
             cluster_molecules.append(molecule.Molecule(
                 cluster,
-                connectivity_template=self._molecule.rdkit_molecule))
+                connectivity_template=self._molecule.rdkit_molecule,
+                allow_undefined_stereo=self._molecule.allow_undefined_stereo))
         for i, cluster_mol in enumerate(cluster_molecules):
             for j, cluster_mol_2 in enumerate(cluster_molecules[i+1:],
                                               start=i+1):
@@ -179,6 +185,7 @@ def find_optimal_path_from_matrix(distances):
 
     return min_path
 
+
 def find_heuristic_path(graph, distances, start_node):
     """
     Given a graph, the corresponding distances matrix and a starting node,
@@ -222,13 +229,13 @@ def find_heuristic_path(graph, distances, start_node):
 def find_index_root(sorted_topology, topology):
     """
     It finds the index of the root atom in the original topology
-    that matches with the one from the topology that fullfills the Impact
+    that matches with the one from the topology that fulfills the Impact
     template rules.
 
     Parameters
     ----------
     sorted_topology : a peleffy.topology.Topology object
-        The topology sorted to fullfill the Impact template format
+        The topology sorted to fulfill the Impact template format
     topology : a peleffy.topology.Topology object
         The original topology object