moleculekit.tools.atomtyper module

moleculekit.tools.atomtyper.atomtypingValidityChecks(mol)
moleculekit.tools.atomtyper.getFeatures(mol)
moleculekit.tools.atomtyper.getPDBQTAtomType(atype, aidx, mol, aromaticNitrogen=False)
moleculekit.tools.atomtyper.getPDBQTAtomTypesAndCharges(mol, aromaticNitrogen=False, validitychecks=True)
moleculekit.tools.atomtyper.parallel(func, listobj, n_cpus=- 1, *args)
moleculekit.tools.atomtyper.prepareProteinForAtomtyping(mol, guessBonds=True, protonate=True, pH=7, segment=True, verbose=True)

Prepares a Molecule object for atom typing.

Parameters
  • mol (Molecule object) – The protein to prepare

  • guessBonds (bool) – Drops the bonds in the molecule and guesses them from scratch

  • protonate (bool) – Protonates the protein for the given pH and optimizes hydrogen networks

  • pH (float) – The pH for protonation

  • segment (bool) – Automatically guesses the segments of a protein by using the guessed bonds

  • verbose (bool) – Set to False to turn of the printing

Returns

mol – The prepared Molecule

Return type

Molecule object