Merge pull request #90 from martimunicoy/support_openff-1.3.0

Add support to openff 1.3.0
martimunicoy · Nov 28, 2020 · b3db6ac · b3db6ac
2 parents cd10f2a + 3b5d364
commit b3db6ac
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Showing 5 changed files with 68 additions and 10 deletions.
diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -15,10 +15,11 @@ This minor release integrates the parameterization of OBC charges and scale fact
 
 New features
 """"""""""""
-- `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: New method to retrieve atom degrees with RDKit.
 - `PR #86 <https://github.com/martimunicoy/peleffy/pull/86>`_: New method to check the input PDB prior building the molecule.
-- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: New method for the OPLS OBC parameters.
+- `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: New method to retrieve atom degrees with RDKit.
+- `PR #90 <https://github.com/martimunicoy/peleffy/pull/90>`_: Add support for openff-1.3.0.
 - `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New parameter to skip the stereochemistry assignment (and the checking from the OpenFF toolkit).
+- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: New method for the OPLS OBC parameters.
 - `PR #100 <https://github.com/martimunicoy/peleffy/pull/100>`_: New writer for the OPLS OBC parameters.
 - `PR #106 <https://github.com/martimunicoy/peleffy/pull/106>`_: New method to initialize a Molecule object directly from an RDKit and OpenFF molecular representations.
 - `PR #112 <https://github.com/martimunicoy/peleffy/pull/112>`_: New method to fix an input PDB file with no atomic element identifiers.
@@ -37,8 +38,9 @@ Tests added
 """""""""""
 - `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: Adds tests to validate the atom degrees getter.
 - `PR #86 <https://github.com/martimunicoy/peleffy/pull/86>`_: Adds tests to validate the PDB check up.
-- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Adds tests to validate the OPLS OBC parameters generator.
+- `PR #90 <https://github.com/martimunicoy/peleffy/pull/90>`_: General validation of supported force fields.
 - `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New test to check the behaviour of the allow_undefined_stereo parameter.
+- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Adds tests to validate the OPLS OBC parameters generator.
 - `PR #97 <https://github.com/martimunicoy/peleffy/pull/97>`_: Includes tests for the new Topology container class.
 - `PR #100 <https://github.com/martimunicoy/peleffy/pull/100>`_: Adds tests to validate the solvent template writers.
 - `PR #106 <https://github.com/martimunicoy/peleffy/pull/106>`_: Adds tests to check the RDKit and OpenFF molecular initializers.

diff --git a/peleffy/forcefield/selectors.py b/peleffy/forcefield/selectors.py
@@ -9,7 +9,8 @@ class ForceFieldSelector(object):
     It defines a force field selector.
     """
     _FF_TYPES = {'OPLS2005': ('OPLS2005'),
-                 'OpenFF': ('openff_unconstrained-1.2.1.offxml',
+                 'OpenFF': ('openff_unconstrained-1.3.0.offxml',
+                            'openff_unconstrained-1.2.1.offxml',
                             'openff_unconstrained-1.2.0.offxml',
                             'openff_unconstrained-1.1.1.offxml',
                             'openff_unconstrained-1.1.0.offxml',

diff --git a/peleffy/main.py b/peleffy/main.py
@@ -16,7 +16,7 @@
 from peleffy.utils import Logger, OutputPathHandler
 
 
-DEFAULT_OFF_FORCEFIELD = 'openff_unconstrained-1.2.1.offxml'
+DEFAULT_OFF_FORCEFIELD = 'openff_unconstrained-1.3.0.offxml'
 DEFAULT_RESOLUTION = int(30)
 DEFAULT_CHARGE_METHOD = 'am1bcc'
 AVAILABLE_CHARGE_METHODS = ['am1bcc', 'gasteiger', 'OPLS']

diff --git a/peleffy/tests/test_forcefields.py b/peleffy/tests/test_forcefields.py
@@ -397,3 +397,58 @@ def check(hybridff, molecule, ffld_file, reference_file):
         check(hybridff, molecule, ffld_file,
               get_data_file_path(
                   'tests/ETL_openff-1.2.1_opls2005_parameters2.json'))
+
+
+class TestForceFieldSelector(object):
+    """
+    It wraps all tests that check the force field selector class.
+    """
+
+    def test_get_by_name(self):
+        """It checks the get_by_name method."""
+
+        from peleffy.forcefield import ForceFieldSelector
+        from peleffy.forcefield import OpenForceField
+        from peleffy.forcefield import OPLS2005ForceField
+
+        selector = ForceFieldSelector()
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.0.0.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.0.1.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.1.0.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.1.1.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.2.0.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.2.1.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('openff_unconstrained-1.3.0.offxml')
+
+        assert isinstance(forcefield, OpenForceField), \
+            'Unexpected force field type'
+
+        forcefield = selector.get_by_name('OPLS2005')
+
+        assert isinstance(forcefield, OPLS2005ForceField), \
+            'Unexpected force field type'
diff --git a/peleffy/tests/test_main.py b/peleffy/tests/test_main.py
@@ -67,7 +67,7 @@ def test_peleffy_argparse(self):
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.2.1.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -156,7 +156,7 @@ def test_peleffy_argparse(self):
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.2.1.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -181,7 +181,7 @@ def test_peleffy_argparse(self):
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.2.1.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is True, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -206,7 +206,7 @@ def test_peleffy_argparse(self):
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.2.1.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -234,7 +234,7 @@ def test_peleffy_argparse(self):
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is True, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.2.1.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'