1import sys
2import os
3
4import CDPL.Chem as Chem
5import CDPL.ForceField as ForceField
6
7
8# calculates and outputs the MMFF94 charges of the atoms of the provided molecular graph
9def calcAndOutputCharges(mol: Chem.Molecule) -> None:
10 Chem.calcImplicitHydrogenCounts(mol, False) # calculate implicit hydrogen counts and set corresponding property for all atoms
11 Chem.makeHydrogenComplete(mol) # make all implicit hydrogens explicit
12 Chem.perceiveHybridizationStates(mol, False) # perceive atom hybridization states and set corresponding property for all atoms
13 Chem.perceiveSSSR(mol, False) # perceive smallest set of smallest rings and store as Chem.MolecularGraph property
14 Chem.setRingFlags(mol, False) # perceive cycles and set corresponding atom and bond properties
15 Chem.setAromaticityFlags(mol, False) # perceive aromaticity and set corresponding atom and bond properties
16
17 ForceField.perceiveMMFF94AromaticRings(mol, False) # perceive aromatic rings according to the MMFF94 aroamticity model and store data as Chem.MolecularGraph property
18 ForceField.assignMMFF94AtomTypes(mol, False, False) # perceive MMFF94 atom types (tolerant mode) set corresponding property for all atoms
19 ForceField.assignMMFF94BondTypeIndices(mol, False, False) # perceive MMFF94 bond types (tolerant mode) set corresponding property for all bonds
20 ForceField.calcMMFF94AtomCharges(mol, False, False) # calculate MMFF94 atom charges (tolerant mode) set corresponding property for all atoms
21
22 print('- MMFF94 partial charges')
23
24 for atom in mol.atoms:
25 print('Atom #%s: %s' % (str(atom.getIndex()), str(ForceField.getMMFF94Charge(atom))))
26
27def main() -> None:
28 if len(sys.argv) < 2:
29 sys.exit('Usage: %s <input mol. file>' % sys.argv[0])
30
31 # create reader for input molecules (format specified by file extension)
32 reader = Chem.MoleculeReader(sys.argv[1])
33
34 # create an instance of the default implementation of the Chem.Molecule interface
35 mol = Chem.BasicMolecule()
36
37 # read and process molecules one after the other until the end of input has been reached
38 try:
39 while reader.read(mol):
40 try:
41 calcAndOutputCharges(mol)
42 except Exception as e:
43 sys.exit('Error: processing of molecule failed: ' + str(e))
44
45 except Exception as e: # handle exception raised in case of severe read errors
46 sys.exit('Error: reading molecule failed: ' + str(e))
47
48 sys.exit(0)
49
50if __name__ == '__main__':
51 main()