PELE-451 Minor adjustments to facilitate platform compatibility

.github/workflows/conda.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest]
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
     name: Python ${{ matrix.python-version }} at ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2

.github/workflows/master.yml

@@ -11,32 +11,37 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.7
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: 3.7
+          conda-channels: anaconda, omnia, conda-forge, martimunicoy
 
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        python -m pip install --upgrade pip
-        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+      - name: Install doc dependencies
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
 
-    - name: Build sphinx documentation
-      shell: bash -l {0}
-      run: |
-        cd docs/
-        make github
+      - name: Install latest peleffy version
+        run: conda install peleffy
 
-    # https://github.com/peaceiris/actions-gh-pages
-    - name: Deploy documentation
-      if: success()
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-          publish_branch: gh-pages
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: docs/html/
-          user_name: 'Martí Municoy'
-          user_email: 'martimunicoy@gmail.com'
+      - name: Build sphinx documentation
+        shell: bash
+        run: |
+          cd docs/
+          make github
+
+      # https://github.com/peaceiris/actions-gh-pages
+      - name: Deploy documentation
+        if: success()
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+            publish_branch: gh-pages
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            publish_dir: docs/html/
+            user_name: 'Martí Municoy'
+            user_email: 'martimunicoy@gmail.com'

README.md

@@ -1,4 +1,4 @@
-| **About** | [![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Python](https://img.shields.io/badge/python-3.6%2C%203.7-blue.svg)](https://martimunicoy.github.io/peleffy) [![Release](https://img.shields.io/github/release/martimunicoy/peleffy.svg?include_prereleases)](https://github.com/martimunicoy/peleffy/releases/) |
+| **About** | [![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Python](https://img.shields.io/badge/python-3.6%2C%203.7%2C%203.8-blue.svg)](https://martimunicoy.github.io/peleffy) [![Release](https://img.shields.io/github/release/martimunicoy/peleffy.svg?include_prereleases)](https://github.com/martimunicoy/peleffy/releases/) |
 | :------ | :------- |
 | **Status** | [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/martimunicoy/peleffy.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/martimunicoy/peleffy/context:python) [![Test](https://github.com/martimunicoy/peleffy/workflows/Test/badge.svg)](https://github.com/martimunicoy/peleffy/actions?query=workflow%3ATest) [![codecov](https://codecov.io/gh/martimunicoy/peleffy/branch/master/graph/badge.svg)](https://codecov.io/gh/martimunicoy/peleffy) |
 | **Installation** | [![Conda](https://img.shields.io/conda/v/martimunicoy/peleffy.svg)](https://anaconda.org/martimunicoy/peleffy) [![PyPI](https://img.shields.io/pypi/v/peleffy)](https://pypi.org/project/peleffy/) |

devtools/conda/meta.yaml

@@ -13,13 +13,11 @@ build:
 
 requirements:
   build:
-    # Note that rdkit does not support Python 3.8 yet
-    - python 3.6|3.7
+    - python
     - setuptools
 
   run:
-    # Note that rdkit does not support Python 3.8 yet
-    - python 3.6|3.7
+    - python
     - numpy
     - matplotlib
     - pytest

docs/requirements.txt

@@ -1,3 +1,5 @@
 Sphinx==3.1.2
 sphinx-rtd-theme==0.5.0
 m2r==0.2.1
+docutils==0.16
+peleffy

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