3.1.5. Physicochemical Properties
The script print_atom_physchem_props.py demonstrates how to iterate over the atoms of molecules read from a specified input file and calculate the following physicochemical atom properties:
Hybrid polarizability
Effective polarizability
Synopsis
python print_atom_physchem_props.py <file>
Code
1import sys
2
3import CDPL.Chem as Chem
4import CDPL.MolProp as MolProp
5
6
7# outputs the corresponding properties of each atom of the provided molecular graph
8def outputProperties(molgraph: Chem.MolecularGraph) -> None:
9 Chem.calcBasicProperties(molgraph, False) # calculate basic molecular properties (if not yet done)
10 Chem.calcTopologicalDistanceMatrix(molgraph, False) # calculate topological distance matrix and store as Chem.MolecularGraph property
11 # (required for effective polarizability calculations)
12 for atom in molgraph.atoms:
13 print('- Atom #%s' % str(molgraph.getAtomIndex(atom)))
14 print('\tHybrid polarizability: %s' % str(MolProp.getHybridPolarizability(atom, molgraph)))
15 print('\tEffective polarizability: %s' % str(MolProp.calcEffectivePolarizability(atom, molgraph)))
16
17def main() -> None:
18 if len(sys.argv) < 2:
19 sys.exit('Usage: %s <input mol. file>' % sys.argv[0])
20
21 # create reader for input molecules (format specified by file extension)
22 reader = Chem.MoleculeReader(sys.argv[1])
23
24 # create an instance of the default implementation of the Chem.Molecule interface
25 mol = Chem.BasicMolecule()
26
27 # read and process molecules one after the other until the end of input has been reached
28 try:
29 while reader.read(mol):
30 try:
31 outputProperties(mol)
32 except Exception as e:
33 sys.exit('Error: processing of molecule failed: ' + str(e))
34
35 except Exception as e: # handle exception raised in case of severe read errors
36 sys.exit('Error: reading molecule failed: ' + str(e))
37
38 sys.exit(0)
39
40if __name__ == '__main__':
41 main()