Merge pull request #50 from martimunicoy/devel

0.3.1 release
martimunicoy · Sep 22, 2020 · 64330ae · 64330ae
2 parents 3a94344 + 5294dde
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diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -8,6 +8,31 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
+0.3.1 - Current development
+---------------------------
+
+This is a micro release that includes general bug fixes and stability improvements. It is still a preliminary version of the Open Force Field to PELE package which is under development.
+
+New features
+""""""""""""
+- `PR #55 <https://github.com/martimunicoy/offpele/pull/55>`_: Standard output prints follow the logging hierarchy and can be modified by the user.
+- `PR #59 <https://github.com/martimunicoy/offpele/pull/59>`_: Set alternative conformers to the offpele's molecule representation.
+
+Bugfixes
+""""""""
+- `PR #48 <https://github.com/martimunicoy/offpele/pull/48>`_: Fixes CLI's default output paths.
+- `PR #52 <https://github.com/martimunicoy/offpele/pull/52>`_: Molecule connectivity can be assigned from an RDKit molecular template when loading it from a PDB file without connectivity.
+- `PR #58 <https://github.com/martimunicoy/offpele/pull/58>`_: Fixes unconsistencies between PDB residue name and molecule tag.
+
+Tests added
+"""""""""""
+- `PR #48 <https://github.com/martimunicoy/offpele/pull/48>`_: Adds tests to validate the assignment of the default output paths.
+- `PR #52 <https://github.com/martimunicoy/offpele/pull/52>`_: Adds tests to validate the initialization using a connectivity template.
+- `PR #55 <https://github.com/martimunicoy/offpele/pull/55>`_: Adds tests for the new Logger class.
+- `PR #58 <https://github.com/martimunicoy/offpele/pull/58>`_: Adds tests to validate consistency between PDB residue name and molecule tag.
+- `PR #59 <https://github.com/martimunicoy/offpele/pull/59>`_: Adds tests for the new conformer setter.
+
+
 0.3.0 - Rotamers, OPLS2005, SMILES and stability improvements
 -------------------------------------------------------------
 

diff --git a/offpele/data/ligands/BNZ_without_connectivity.pdb b/offpele/data/ligands/BNZ_without_connectivity.pdb
@@ -0,0 +1,35 @@
+HEADER    HYDROLASE                               16-AUG-14   4W52
+REMARK   4 4W52 COMPLIES WITH FORMAT V. 3.30,
+REMARK 888
+REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
+TITLE     T4 LYSOZYME L99A WITH BENZENE BOUND
+EXPDTA    X-RAY DIFFRACTION
+REMARK   2 RESOLUTION.    1.50 ANGSTROMS
+REMARK   3  R VALUE : 0.165000
+REMARK   3  FREE R VALUE : 0.182000
+REMARK 200  TEMPERATURE           (KELVIN) : 100.00
+REMARK 200  PH                             : 7.50
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350   BIOMT1  1   1.000000 0.000000 0.000000   0.000000
+REMARK 350   BIOMT2  1   0.000000 1.000000 0.000000   0.000000
+REMARK 350   BIOMT3  1   0.000000 0.000000 1.000000   0.000000
+CRYST1   60.350   60.350   96.610  90.00  90.00 120.00 P 32 2 1      6
+HET    BNZ  L   1      12
+HETNAM     BNZ BENZENE
+FORMUL   1  BNZ    C6 H6
+MODEL        1
+HETATM    1  C1  BNZ L   1     -32.969   6.196   2.877  0.70 15.06           C
+HETATM    2  C2  BNZ L   1     -32.945   7.046   3.973  0.70 12.84           C
+HETATM    3  C3  BNZ L   1     -33.719   6.798   5.113  0.70 12.24           C
+HETATM    4  C4  BNZ L   1     -34.540   5.680   5.143  0.70 13.09           C
+HETATM    5  C5  BNZ L   1     -34.545   4.825   4.044  0.70 12.54           C
+HETATM    6  C6  BNZ L   1     -33.787   5.069   2.915  0.70 14.23           C
+HETATM    7  H1  BNZ L   1     -32.360   6.413   2.012  1.00  0.00           H
+HETATM    8  H2  BNZ L   1     -32.318   7.925   3.961  1.00  0.00           H
+HETATM    9  H3  BNZ L   1     -33.672   7.473   5.955  1.00  0.00           H
+HETATM   10  H4  BNZ L   1     -35.158   5.487   6.007  1.00  0.00           H
+HETATM   11  H5  BNZ L   1     -35.156   3.935   4.055  1.00  0.00           H
+HETATM   12  H6  BNZ L   1     -33.823   4.399   2.069  1.00  0.00           H
+ENDMDL
+END
diff --git a/offpele/main.py b/offpele/main.py
@@ -13,7 +13,7 @@
 import argparse as ap
 
 import offpele
-from offpele.utils import check_if_path_exists, create_path
+from offpele.utils import check_if_path_exists, create_path, Logger
 
 
 DEFAULT_OFF_FORCEFIELD = 'openff_unconstrained-1.2.0.offxml'
@@ -73,12 +73,22 @@ def parse_args():
                         action='store_true',
                         help="Use OPLS to set the parameters for bonds "
                         + "and angles")
+    parser.add_argument('-s', '--silent',
+                        dest="silent",
+                        action='store_true',
+                        help="Activate silent mode")
+    parser.add_argument('-d', '--debug',
+                        dest="debug",
+                        action='store_true',
+                        help="Activate debug mode")
 
     parser.set_defaults(as_datalocal=False)
     parser.set_defaults(with_solvent=False)
     parser.set_defaults(include_terminal_rotamers=False)
     parser.set_defaults(use_OPLS_nb_params=False)
     parser.set_defaults(use_OPLS_bonds_and_angles=False)
+    parser.set_defaults(silent=False)
+    parser.set_defaults(debug=False)
 
     args = parser.parse_args()
 
@@ -109,16 +119,16 @@ def handle_output_paths(molecule, output, as_datalocal):
         The output path for the solvent template
     """
     from pathlib import Path
-    name = molecule.name
+    tag = molecule.tag
     output_path = Path(output)
     check_if_path_exists(output_path)
 
     rotlib_path = output_path
     impact_path = output_path
     solvent_path = output_path
 
-    rotlib_name = name.upper() + '.rot.assign'
-    impact_name = name.lower() + 'z'
+    rotlib_name = tag.upper() + '.rot.assign'
+    impact_name = tag.lower() + 'z'
     solvent_name = 'ligandParams.txt'
 
     if as_datalocal:
@@ -177,27 +187,24 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
         Whether to save output files following PELE's DataLocal hierarchy or
         not
     """
-    print('-' * 60)
-    print('Open Force Field parameterizer for PELE', offpele.__version__)
-    print('-' * 60)
-    print(' - General:')
-    print('   - Input PDB:', pdb_file)
-    print('   - Output path:', output)
-    print('   - Write solvent parameters:', with_solvent)
-    print('   - DataLocal-like output:', as_datalocal)
-    print(' - Parameterization:')
-    print('   - Force field:', forcefield)
-    print('   - Charges method:', charges_method)
-    print('   - Use OPLS nonbonding parameters:', use_OPLS_nb_params)
-    print('   - Use OPLS bonds and angles:', use_OPLS_bonds_and_angles)
-    print(' - Rotamer library:')
-    print('   - Resolution:', resolution)
-    print('   - Exclude terminal rotamers:', exclude_terminal_rotamers)
-    print('-' * 60)
-
-    # Supress OpenForceField toolkit warnings
-    import logging
-    logging.getLogger().setLevel(logging.ERROR)
+    log = Logger()
+    log.info('-' * 60)
+    log.info('Open Force Field parameterizer for PELE', offpele.__version__)
+    log.info('-' * 60)
+    log.info(' - General:')
+    log.info('   - Input PDB:', pdb_file)
+    log.info('   - Output path:', output)
+    log.info('   - Write solvent parameters:', with_solvent)
+    log.info('   - DataLocal-like output:', as_datalocal)
+    log.info(' - Parameterization:')
+    log.info('   - Force field:', forcefield)
+    log.info('   - Charges method:', charges_method)
+    log.info('   - Use OPLS nonbonding parameters:', use_OPLS_nb_params)
+    log.info('   - Use OPLS bonds and angles:', use_OPLS_bonds_and_angles)
+    log.info(' - Rotamer library:')
+    log.info('   - Resolution:', resolution)
+    log.info('   - Exclude terminal rotamers:', exclude_terminal_rotamers)
+    log.info('-' * 60)
 
     from offpele.topology import Molecule
     from offpele.template import Impact
@@ -226,8 +233,8 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
         solvent = OBC2(molecule)
         solvent.to_json_file(solvent_out)
 
-    print(' - All files were generated successfully')
-    print('-' * 60)
+    log.info(' - All files were generated successfully')
+    log.info('-' * 60)
 
 
 def main():
@@ -247,6 +254,19 @@ def main():
 
     exclude_terminal_rotamers = not args.include_terminal_rotamers
 
+    # Supress OpenForceField toolkit warnings
+    import logging
+    logging.getLogger().setLevel(logging.ERROR)
+
+    # Set offpele logger to the corresponding level
+    logger = Logger()
+    if args.silent:
+        logger.set_level('CRITICAL')
+    elif args.debug:
+        logger.set_level('DEBUG')
+    else:
+        logger.set_level('INFO')
+
     run_offpele(args.pdb_file, args.forcefield, args.resolution,
                 args.charges_method, args.use_OPLS_nb_params,
                 args.use_OPLS_bonds_and_angles, exclude_terminal_rotamers,

diff --git a/offpele/solvent/solvent.py b/offpele/solvent/solvent.py
@@ -7,6 +7,7 @@
 
 from offpele.utils import get_data_file_path, warning_on_one_line
 from offpele.utils.toolkits import OpenForceFieldToolkitWrapper
+from offpele.utils import Logger
 
 
 class _SolventWrapper(object):
@@ -42,7 +43,8 @@ def _initialize_from_molecule(self):
         """
         Initializes a SolventWrapper object using an offpele's Molecule.
         """
-        print(' - Loading solvent parameters')
+        logger = Logger()
+        logger.info(' - Loading solvent parameters')
 
         off_toolkit = OpenForceFieldToolkitWrapper()
 
@@ -82,15 +84,15 @@ def to_dict(self):
         data['SolventParameters']['General']['surface_area_penalty'] = \
             round(self.surface_area_penalty.value_in_unit(
                 unit.kilocalorie / (unit.angstrom**2 * unit.mole)), 8)
-        data['SolventParameters'][self.molecule.name] = dict()
+        data['SolventParameters'][self.molecule.tag] = dict()
 
         atom_names = self.molecule.get_pdb_atom_names()
 
         for atom, name in zip(self.molecule.rdkit_molecule.GetAtoms(),
                               atom_names):
             name = name.replace(' ', '_')
             index = atom.GetIdx()
-            data['SolventParameters'][self.molecule.name][name] = \
+            data['SolventParameters'][self.molecule.tag][name] = \
                 {'radius': round(self.radii[tuple((index, ))].value_in_unit(
                                  unit.angstrom), 5),
                  'scale': round(self.scales[tuple((index, ))], 5)}

diff --git a/offpele/tests/test_main.py b/offpele/tests/test_main.py
@@ -4,9 +4,11 @@
 
 import pytest
 
+import os
 import tempfile
-from offpele.main import run_offpele
+from offpele.main import run_offpele, handle_output_paths
 from offpele.utils import get_data_file_path, temporary_cd
+from offpele.topology import Molecule
 
 
 FORCEFIELD_NAME = 'openff_unconstrained-1.2.0.offxml'
@@ -18,6 +20,9 @@ class TestMain(object):
     """
 
     def test_offpele_default_call(self):
+        """
+        It checks the default call of offpele's main function.
+        """
         LIGAND_PATH = 'ligands/BNZ.pdb'
         ligand_path = get_data_file_path(LIGAND_PATH)
 
@@ -26,6 +31,9 @@ def test_offpele_default_call(self):
                 run_offpele(ligand_path, output=tmpdir)
 
     def test_offpele_custom_call(self):
+        """
+        It checks the custom call of offpele's main function.
+        """
         LIGAND_PATH = 'ligands/BNZ.pdb'
         ligand_path = get_data_file_path(LIGAND_PATH)
 
@@ -38,3 +46,81 @@ def test_offpele_custom_call(self):
                             output=tmpdir,
                             with_solvent=True,
                             as_datalocal=True)
+
+    def test_default_output_paths(self):
+        """
+        It checks the default output paths that are used for each parameter
+        file from offpele.
+        """
+
+        def from_PosixPath_to_string(paths):
+            """
+            Convert PosixPaths to strings
+            """
+            return map(str, paths)
+
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+
+        rotlib_path, impact_path, solvent_path = \
+            handle_output_paths(molecule, '', False)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'BNZ.rot.assign', 'Unexpected default ' \
+            + 'rotamer library path'
+        assert impact_path == 'bnzz', 'Unexpected default Impact ' \
+            + 'template path'
+        assert solvent_path == 'ligandParams.txt', 'Unexpected default ' \
+            + 'solvent parameters path'
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            with temporary_cd(tmpdir):
+                # To avoid the complain about unexistent folder
+                os.mkdir('output')
+                rotlib_path, impact_path, solvent_path = \
+                    handle_output_paths(molecule, 'output', False)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'output/BNZ.rot.assign', 'Unexpected default ' \
+            + 'rotamer library path'
+        assert impact_path == 'output/bnzz', 'Unexpected default Impact ' \
+            + 'template path'
+        assert solvent_path == 'output/ligandParams.txt', 'Unexpected ' \
+            + 'default solvent parameters path'
+
+        rotlib_path, impact_path, solvent_path = \
+            handle_output_paths(molecule, '', True)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'DataLocal/LigandRotamerLibs/' \
+            + 'BNZ.rot.assign', 'Unexpected default rotamer library path'
+        assert impact_path == 'DataLocal/Templates/OFF/Parsley/' \
+            + 'HeteroAtoms/bnzz', 'Unexpected default Impact template'
+        assert solvent_path == 'DataLocal/OBC/ligandParams.txt', \
+            'Unexpected default solvent parameters path'
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            with temporary_cd(tmpdir):
+                # To avoid the complain about unexistent folder
+                os.mkdir('output')
+                rotlib_path, impact_path, solvent_path = \
+                    handle_output_paths(molecule, 'output', True)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'output/DataLocal/LigandRotamerLibs/' \
+            + 'BNZ.rot.assign', 'Unexpected default rotamer library path'
+        assert impact_path == 'output/DataLocal/Templates/OFF/Parsley/' \
+            + 'HeteroAtoms/bnzz', 'Unexpected default Impact template path'
+        assert solvent_path == 'output/DataLocal/OBC/ligandParams.txt', \
+            'Unexpected default solvent parameters path'