Utilities

pmapper.utils.get_rms

Calculates best RMSD between two pharmacophores.

pmapper.utils.load_multi_conf_mol

Convenience function which loads all conformers of a molecule into a list of pharmacophore objects.

pmapper.utils.get_rms(p1, p2)

Calculates best RMSD between two pharmacophores.

Parameters
  • p1 – the first Pharmacophore class object

  • p2 – the second Pharmacophore class object

Returns

best RMSD value between two pharmacophores. Value -1 will be returned if two pharmacophores have different sets of features, e.g. aaHD and aaHDD

Return type

float

pmapper.utils.load_multi_conf_mol(mol, smarts_features=None, factory=None, bin_step=1, cached=False)

Convenience function which loads all conformers of a molecule into a list of pharmacophore objects.

Parameters
  • mol – RDKit Mol

  • smarts_features – dictionary of SMARTS of features obtained with load_smarts function from pmapper.util module. Default: None.

  • factory – RDKit MolChemicalFeatureFactory loaded with load_factory function from pmapper.util module. Default: None.

  • bin_step – binning step

  • cached – whether or not to cache intermediate computation results. This substantially increases speed of repeated computation of a hash or fingerprints.

Returns

list of pharmacophore objects

Note: if both arguments smarts_features and factory are None the default patterns will be used.