HOTFIX: Improve Sybyl atom types, add cyano and CO2 test

helpers/molecule.py

@@ -43,7 +43,11 @@ def __init__(
         else:
             raise Exception('Invalide type(atoms): {0}'.format(type(atoms)))
 
-        self.atoms = validated_atoms_dict(atoms_dict)
+        try:
+            self.atoms = validated_atoms_dict(atoms_dict)
+        except AssertionError:
+            raise AssertionError('In: {0}'.format(atoms_dict))
+
         self.bonds = set(map(frozenset, bonds))
         validate_bond_dict(self.atoms, self.bonds)
         self.name = name if name is not None else md5((str(sorted(self.atoms.values())) + str(sorted(bonds))).encode()).hexdigest()
@@ -384,9 +388,22 @@ def print_to_io(*args):
             print(*args, file=io)
 
         def sibyl_atom_type(atom: Atom) -> str:
-            if atom.element in {'C', 'N', 'O', 'S', 'P'}:
+            if atom.element is None:
+                return 'Du'
+            elif atom.element == 'D':
+                return 'H'
+            elif atom.element == 'P':
+                return 'P.3'
+            elif atom.element.upper() in {'RU', 'CO'}:
+                return atom.element.title() + '.oh'
+            elif atom.element in {'C', 'O', 'N', 'S'}:
                 if atom.element == 'C':
-                    valence = atom.valence - 1
+                    if atom.valence >= 4:
+                        valence = 3
+                    elif atom.valence == 1:
+                        valence = 1
+                    else:
+                        valence = atom.valence - 1
                 elif atom.element == 'O':
                     valence = atom.valence + 1
                 elif atom.element == 'S':
@@ -400,12 +417,18 @@ def sibyl_atom_type(atom: Atom) -> str:
                         valence = 2
                 else:
                     valence = atom.valence
+                assert valence > 0, (atom, valence)
                 return '{element}.{valence}'.format(
-                    element=atom.element,
+                    element=atom.element.title(),
                     valence=valence,
                 )
+            elif atom.element.upper() in {'TI', 'CR'}:
+                if atom.valence <= 4:
+                    return atom.element.title() + '.th'
+                else:
+                    return atom.element.title() + '.oh'
             else:
-                return atom.element
+                return atom.element.title()
 
         print_to_io('@<TRIPOS>MOLECULE')
         print_to_io(self.name)

pdbs/cyano.pdb

@@ -0,0 +1,9 @@
+HEADER    UNCLASSIFIED                            04-Mar-18
+TITLE     ALL ATOM STRUCTURE FOR MOLECULE UNK                                   
+AUTHOR    GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2018-01-17 10:59:17
+AUTHOR   2  http://compbio.biosci.uq.edu.au/atb
+HETATM    1    C 4GGB    0       0.637   0.000   0.000  1.00  0.00           C
+HETATM    2    N 4GGB    0      -0.546   0.000   0.000  1.00  0.00           N
+CONECT    1    2
+CONECT    2    1
+END

test_electron_assignment.py

@@ -0,0 +1,43 @@
+from sys import stderr
+import unittest
+
+from fragment_capping.helpers.types_helpers import Atom
+from fragment_capping.helpers.molecule import Molecule, molecule_from_pdb_str
+
+class Test_Capping(unittest.TestCase):
+    def test_carbon_dioxide(self) -> None:
+        with open('pdbs/carbon_dioxide.pdb') as fh:
+            input_molecule = molecule_from_pdb_str(
+                fh.read(),
+                name='carbon_dioxide',
+            )
+
+        input_molecule.assign_bond_orders_and_charges_with_ILP(
+            enforce_octet_rule=True,
+        )
+
+        input_molecule.write_graph(
+            '',
+            output_size=(400, 400),
+            graph_kwargs={'include_atom_index': True},
+        )
+
+    def test_cyano(self) -> None:
+        with open('pdbs/cyano.pdb') as fh:
+            input_molecule = molecule_from_pdb_str(
+                fh.read(),
+                name='cyano',
+            )
+
+        input_molecule.assign_bond_orders_and_charges_with_ILP(
+            enforce_octet_rule=True,
+        )
+
+        input_molecule.write_graph(
+            '',
+            output_size=(400, 400),
+            graph_kwargs={'include_atom_index': True},
+        )
+
+if __name__ == '__main__':
+    unittest.main(warnings='ignore', verbosity=2)