Merge pull request #171 from martimunicoy/ffld_error

Ffld error

docs/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'Open Force Field for PELE'
-copyright = '2020, Barcelona Supercomputing Center'
+copyright = '2022, Barcelona Supercomputing Center'
 author = 'Martí Municoy'
 
 
@@ -85,7 +85,7 @@ def add_source_parser(_old_add_source_parser, self, *args, **kwargs):
 
 #import peleffy
 #version = peleffy.__version__
-version = '1.4.1'
+version = '1.4.3'
 
 pygments_style = 'sphinx'
 

docs/releasehistory.rst

@@ -8,6 +8,16 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
+1.4.3 - Minor improvements for CLI arguments and ffld_server
+------------------------------------------------------------
+
+This is a micro release of peleffy that contains minor improvements for the CLI interface and the usage of the ffld_server.
+
+New features
+""""""""""""
+- `PR #171 <https://github.com/martimunicoy/peleffy/pull/171>`_: improvements for the CLI interface. Also, ffld_server will not raise an exception but any warning or error found will be raised by peleffy's logger
+
+
 1.4.2 - Compatibility fixes for latest RDKit and Schrodinger versions
 ---------------------------------------------------------------------
 

peleffy/forcefield/__init__.py

@@ -1,2 +1,2 @@
 from .forcefield import *
-from .selectors import ForceFieldSelector
+from .selectors import *

peleffy/forcefield/selectors.py

@@ -4,11 +4,14 @@
 """
 
 
+_ALL_ = ["ForceFieldSelector", "ChargeCalculatorSelector"]
+
+
 class ForceFieldSelector(object):
     """
     It defines a force field selector.
     """
-    _FF_TYPES = {'OPLS2005': ('OPLS2005'),
+    _FF_TYPES = {'OPLS2005': ('OPLS2005', ),
                  'OpenFF': ('openff_unconstrained-2.0.0.offxml',
                             'openff_unconstrained-1.3.0.offxml',
                             'openff_unconstrained-1.2.1.offxml',
@@ -69,11 +72,16 @@ def get_list(self):
 
         Returns
         -------
-        forcefields : dict
-            The complete list of available force fields grouped by
-            force field type
+        forcefields : list[str]
+            The complete list of available force fields
         """
-        return self._FF_TYPES
+        forcefields = []
+
+        for ff_type in self._FF_TYPES:
+            forcefields.extend([ff_name.lower() for ff_name in
+                                self._FF_TYPES[ff_type]])
+
+        return forcefields
 
 
 class ChargeCalculatorSelector(object):
@@ -131,8 +139,7 @@ def get_list(self):
 
         Returns
         -------
-        forcefields : dict
-            The complete list of available force fields grouped by
-            force field type
+        charge_methods : list[str]
+            The complete list of available charge methods
         """
-        return self._FF_TYPES
+        return list(self._AVAILABLE_TYPES.keys())

peleffy/main.py

@@ -17,10 +17,9 @@
 from peleffy.forcefield.selectors import ChargeCalculatorSelector
 
 
-DEFAULT_OFF_FORCEFIELD = 'openff_unconstrained-1.3.0.offxml'
+DEFAULT_OFF_FORCEFIELD = 'openff_unconstrained-2.0.0.offxml'
 DEFAULT_RESOLUTION = int(30)
-DEFAULT_CHARGE_METHOD = 'am1bcc'
-AVAILABLE_CHARGE_METHODS = ChargeCalculatorSelector()._AVAILABLE_TYPES.keys()
+DEFAULT_CHARGE_METHOD = None  # Use FF's default
 IMPACT_TEMPLATE_PATH = 'DataLocal/Templates/OFF/Parsley/HeteroAtoms/'
 ROTAMER_LIBRARY_PATH = 'DataLocal/LigandRotamerLibs/'
 SOLVENT_TEMPLATE_PATH = 'DataLocal/OBC/'
@@ -41,9 +40,12 @@ def parse_args(args):
     parsed_args : argparse.Namespace
         It contains the command-line arguments that are supplied by the user
     """
-    parser = ap.ArgumentParser()
+    import peleffy
+
+    parser = ap.ArgumentParser(prog="PELE Force Field Yielder (peleffy)")
     parser.add_argument("pdb_file", metavar="PDB FILE", type=str,
-                        help="Path PDB file to parameterize")
+                        help="Path PDB file to parameterize",
+                        default=None)
     parser.add_argument("-f", "--forcefield", metavar="NAME",
                         type=str, help="OpenForceField's forcefield name. " +
                         "Default is " + str(DEFAULT_OFF_FORCEFIELD),
@@ -66,8 +68,7 @@ def parse_args(args):
                         "DataLocal hierarchy", action='store_true')
     parser.add_argument('-c', '--charge_method', metavar="NAME",
                         type=str, help="The name of the method to use to " +
-                        "compute charges", default=DEFAULT_CHARGE_METHOD,
-                        choices=AVAILABLE_CHARGE_METHODS)
+                        "compute charges", default=DEFAULT_CHARGE_METHOD)
     parser.add_argument('--charges_from_file', metavar="PATH",
                         type=str, help="The path to the file with charges",
                         default=None)
@@ -92,6 +93,9 @@ def parse_args(args):
                         action='store_true',
                         help="Generate Impact template compatible with " +
                              "PELE\'s AMBER implementation")
+    parser.add_argument('-v', '--version',
+                        action='version',
+                        version='%(prog)s {}'.format(peleffy.__version__))
 
     parser.set_defaults(as_datalocal=False)
     parser.set_defaults(with_solvent=False)
@@ -101,6 +105,29 @@ def parse_args(args):
     parser.set_defaults(for_amber=False)
 
     parsed_args = parser.parse_args(args)
+
+    # Check force field
+    from peleffy.forcefield import ForceFieldSelector
+
+    selector = ForceFieldSelector()
+    available_ffs = selector.get_list()
+
+    if parsed_args.forcefield.lower() not in available_ffs:
+        raise ValueError('Force field ' +
+                         '\'{}\' '.format(parsed_args.forcefield) +
+                         'is unknown')
+
+    # Check charge method
+    if parsed_args.charge_method is not None:
+        from peleffy.forcefield import ChargeCalculatorSelector
+
+        selector = ChargeCalculatorSelector()
+        available_charge_methods = selector.get_list()
+
+        if parsed_args.charge_method.lower() not in available_charge_methods:
+            raise ValueError('Charge method ' +
+                             '\'{}\' '.format(parsed_args.charge_method) +
+                             'is unknown')
 
     return parsed_args
 
@@ -157,11 +184,14 @@ def run_peleffy(pdb_file,
             + '   - Charge file: {}'.format(charges_from_file)
         charge_method = 'dummy'
     else:
-        charge_method_str = charge_method
+        if charge_method is None:
+            charge_method_str = "-"
+        else:
+            charge_method_str = charge_method
 
     log = Logger()
     log.info('-' * 60)
-    log.info('Open Force Field parameterizer for PELE', peleffy.__version__)
+    log.info('PELE Force Field Yielder', peleffy.__version__)
     log.info('-' * 60)
     log.info(' - General:')
     log.info('   - Input PDB:', pdb_file)

peleffy/tests/test_main.py

@@ -63,11 +63,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -152,23 +152,20 @@ def test_peleffy_argparse(self):
             'Unexpected for_amber settings were parsed'
 
         # Test unexpected charge method
-        with pytest.raises(SystemExit) as pytest_wrapped_e:
+        with pytest.raises(ValueError):
             parsed_args = parse_args(['toluene.pdb', '-c', 'unexpected'])
 
-        assert pytest_wrapped_e.type == SystemExit
-        assert pytest_wrapped_e.value.code == 2
-
         # Test as_datalocal argument
         parsed_args = parse_args(['methane.pdb',
                                   '--as_datalocal'])
 
         assert parsed_args.as_datalocal is True, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -193,11 +190,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -224,11 +221,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is True, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -253,11 +250,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -282,11 +279,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -311,11 +308,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is True, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -340,11 +337,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -369,11 +366,11 @@ def test_peleffy_argparse(self):
 
         assert parsed_args.as_datalocal is False, \
             'Unexpected as_datalocal settings were parsed'
-        assert parsed_args.charge_method == 'am1bcc', \
+        assert parsed_args.charge_method == None, \
             'Unexpected charge_method settings were parsed'
         assert parsed_args.debug is False, \
             'Unexpected debug settings were parsed'
-        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+        assert parsed_args.forcefield == 'openff_unconstrained-2.0.0.offxml', \
             'Unexpected forcefield settings were parsed'
         assert parsed_args.include_terminal_rotamers is False, \
             'Unexpected include_terminal_rotamers settings were parsed'
@@ -441,6 +438,3 @@ def test_PDB_checks(self):
         complex_path = get_data_file_path('complexes/complex_test.pdb')
         with pytest.raises(ValueError):
             _ = run_peleffy(complex_path, chain = 'C')
-
-
-

peleffy/utils/toolkits.py

@@ -1322,6 +1322,10 @@ def run_ffld_server(self, molecule):
         ffld_output : str
             The ffld_server output
         """
+        from peleffy.utils import Logger
+
+        # Initialize logger
+        logger = Logger()
 
         ffld_server_exec = self.path_to_ffld_server()
 
@@ -1338,9 +1342,9 @@ def run_ffld_server(self, molecule):
                                                   "parameters.txt"])
 
                 if errors:
-                    raise SystemError('FFLD_SERVER has failed with the ' +
-                                      'following error message: \n ' +
-                                      '{}'.format(errors.decode("utf-8")))
+                    logger.warning('FFLD_SERVER has produced the ' +
+                                   'following error message: \n ' +
+                                   '{}'.format(errors.decode("utf-8")))
 
                 with open('parameters.txt') as parameters_file:
                     return parameters_file.read()

peleffy/utils/utils.py

@@ -420,6 +420,9 @@ def __init__(self):
 
             # Add stream handler
             self.set_stdout_handler()
+
+            # Disable backwards propagation
+            self._logger.propagate = False
         else:
             self._logger = logging.getLogger('peleffy_log')