3.1.4. Partial Charges And Other Electronic Properties

The script print_atom_elec_props.py demonstrates how to iterate over the atoms of molecules read from a specified input file and calculate the following electronic atom properties:

  • Sigma charge

  • Pi charge

  • Total partial charge

  • Lone-pair electronegativity

  • Pi electronegativity

  • Sigma electronegativity

  • Exerted inductive effect

  • Free valence electron count

  • Valence electron count

Synopsis

python print_atom_elec_props.py <file>

Code

 1import sys
 2import os
 3
 4import CDPL.Chem as Chem
 5import CDPL.MolProp as MolProp
 6
 7
 8# outputs the corresponding properties of each atom of the provided molecule
 9def outputProperties(mol: Chem.Molecule) -> None:
10    Chem.calcBasicProperties(mol, False)       # calculate basic molecular properties (if not yet done)
11    Chem.perceivePiElectronSystems(mol, False) # perceive pi electron systems and store info as Chem.MolecularGraph property
12                                               # (required for MHMO calculations)
13
14    # calculate sigma charges and electronegativities using the PEOE method and store values as atom properties
15    # (prerequisite for MHMO calculations)
16    MolProp.calcPEOEProperties(mol, False)  
17
18    # calculate pi charges, electronegativities and other properties by a modified Hueckel MO method and store values as properties
19    MolProp.calcMHMOProperties(mol, False)
20                
21    for atom in mol.atoms:
22        print('- Atom #%s' % str(atom.getIndex()))
23        print('\tSigma charge: %s' % str(MolProp.getPEOESigmaCharge(atom)))
24        print('\tPi charge: %s' % str(MolProp.getMHMOPiCharge(atom)))
25        print('\tTotal partial charge: %s' % str(MolProp.calcTotalPartialCharge(atom)))
26        print('\tLone-pair electronegativity: %s' % str(MolProp.calcLonePairElectronegativity(atom, mol)))
27        print('\tPi electronegativity: %s' % str(MolProp.calcPiElectronegativity(atom, mol)))
28        print('\tSigma electronegativity: %s' % str(MolProp.getPEOESigmaElectronegativity(atom)))
29        print('\tExerted inductive effect: %s' % str(MolProp.calcInductiveEffect(atom, mol)))
30        print('\tFree valence electron count: %s' % str(MolProp.calcFreeValenceElectronCount(atom, mol)))
31        print('\tValence electron count: %s' % str(MolProp.calcValenceElectronCount(atom)))
32
33def main() -> None:
34    if len(sys.argv) < 2:
35        sys.exit('Usage: %s <input mol. file>' % sys.argv[0])
36
37    # create reader for input molecules (format specified by file extension)
38    reader = Chem.MoleculeReader(sys.argv[1]) 
39   
40    # create an instance of the default implementation of the Chem.Molecule interface
41    mol = Chem.BasicMolecule()
42    
43    # read and process molecules one after the other until the end of input has been reached
44    try:
45        while reader.read(mol):
46            try:
47                outputProperties(mol)
48            except Exception as e:
49                sys.exit('Error: processing of molecule failed: ' + str(e))
50                
51    except Exception as e: # handle exception raised in case of severe read errors
52        sys.exit('Error: reading molecule failed: ' + str(e))
53
54    sys.exit(0)
55        
56if __name__ == '__main__':
57    main()

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