openpharmacophore.LigandReceptorPharmacophore

class openpharmacophore.LigandReceptorPharmacophore(binding_site, ligand)[source]

Bases: object

Class to store, and extract pharmacophores from protein-ligand complexes.

The pharmacophores can be extracted from a PDB structure or from a molecular dynamics trajectory.

Parameters:

binding_site (ComplexBindingSite) – Binding site from which the pharmacophore will be extracted
ligand (Ligand) – The ligand in the binding site.

Methods

extract

Extract one or multiple pharmaophores at different frames

Attributes

`CHARGE_DIST_MAX`
`HBOND_ANG_MIN`
`HBOND_DIST_MAX`
`HYD_DIST_MAX`
`HYD_MERGE_DIST`
`PISTACK_ANG_DEV`
`PISTACK_DIST_MAX`
`PISTACK_OFFSET_MAX`
`pharmacophores`

extract(frames=None, feat_types=frozenset({'aromatic ring', 'hb acceptor', 'hb donor', 'hydrophobicity', 'negative charge', 'positive charge'}))[source]

Extract one or multiple pharmaophores at different frames

Parameters:

frames (Iterable[int], optional) – Iterable with the frames for which pharmacophores will be extracted.
feat_types (set[str], optional) – Only pharmacophoric points with this feature types will be extracted.