josejimenezluna/delfta

Add checks: hydrogens present, types of atoms

Closed this issue · 5 comments

cisert commented

delfta/delfta/calculator.py

Line 54 in ca79d57

def _preprocess(self, mols):

  • mol.addhs()
  • check for atom types that are not included in QMugs
cisert commented
  • print an INFO when adding hydrogens
  • print a WARNING when unsupported atom types are present, and skip calculation for that molecule
cisert commented
  • check for charges → QMugs only contains uncharged molecules, so let's stick to that
josejimenezluna commented

only missing the check for charges now

josejimenezluna commented

@cisert the atom object in pybel has both a formalcharge and a partialcharge attribute.

https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html

Which should we be checking?

cisert commented

@josejimenezluna: formal charge :) (difference between #protons and #electrons)