perf: features.contact

deeprankcore/domain/forcefield/__init__.py

@@ -7,9 +7,10 @@
 from deeprankcore.tools.forcefield.patch import PatchParser
 from deeprankcore.tools.forcefield.residue import ResidueClassParser
 from deeprankcore.tools.forcefield.param import ParamParser
-from deeprankcore.models.error import UnknownAtomError
+from deeprankcore.models.forcefield.vanderwaals import VanderwaalsParam
 
-logging.getLogger(__name__)
+
+_log = logging.getLogger(__name__)
 
 
 _forcefield_directory_path = os.path.dirname(os.path.abspath(__file__))
@@ -58,17 +59,12 @@ def _find_matching_residue_class(self, residue: Residue):
         return None
 
     def get_vanderwaals_parameters(self, atom: Atom):
-        type_ = self._get_type(atom)
-
-        return self._vanderwaals_parameters[type_]
-
-    def _get_type(self, atom: Atom):
         atom_name = atom.name
 
         if atom.residue.amino_acid is None:
-            raise UnknownAtomError(f"no amino acid for {atom}")
-
-        residue_name = atom.residue.amino_acid.three_letter_code
+            _log.warning(f"no amino acid for {atom}; three letter code set to XXX")
+            residue_name = 'XXX'
+        else: residue_name = atom.residue.amino_acid.three_letter_code
 
         type_ = None
 
@@ -86,11 +82,12 @@ def _get_type(self, atom: Atom):
 
                     type_ = action["TYPE"]
 
-        if type_ is None:
-            raise UnknownAtomError(
-                f"not mentioned in top or patch: {top_key}")
+        if type_ is None: # pylint: disable=no-else-return
+            _log.warning(f"Atom {atom} is unknown to the forcefield; vanderwaals_parameters set to (0.0, 0.0, 0.0, 0.0)")
+            return VanderwaalsParam(0.0, 0.0, 0.0, 0.0)
+        else:
+            return self._vanderwaals_parameters[type_]
 
-        return type_
 
     def get_charge(self, atom: Atom):
         """
@@ -119,11 +116,11 @@ def get_charge(self, atom: Atom):
 
                     charge = float(action["CHARGE"])
 
-        if charge is None:
-            raise UnknownAtomError(
-                f"not mentioned in top or patch: {top_key}")
-
-        return charge
+        if charge is None: # pylint: disable=no-else-return
+            _log.warning(f"Atom {atom} is unknown to the forcefield; charge is set to 0.0")
+            return 0.0
+        else:
+            return charge
 
 
 atomic_forcefield = AtomicForcefield()

deeprankcore/feature/atom.py

@@ -2,7 +2,6 @@
 from deeprankcore.models.graph import Graph
 from deeprankcore.domain.forcefield import atomic_forcefield
 from deeprankcore.domain.features import nodefeats
-from deeprankcore.models.error import UnknownAtomError
 import logging
 
 
@@ -21,12 +20,4 @@ def add_features( # pylint: disable=unused-argument
 
             node.features[nodefeats.ATOMTYPE] = atom.element.onehot
             node.features[nodefeats.PDBOCCUPANCY] = atom.occupancy
-
-            try:
-                node.features[nodefeats.ATOMCHARGE] = atomic_forcefield.get_charge(atom)
-
-            except UnknownAtomError:
-                _log.warning(f"Ignoring atom {atom}, because it's unknown to the forcefield")
-
-                # set parameters to zero, so that the potential becomes zero
-                node.features[nodefeats.ATOMCHARGE] = 0.0
+            node.features[nodefeats.ATOMCHARGE] = atomic_forcefield.get_charge(atom)