schrodinger.application.desmond.sid_plots.pl_lid module

Module with utilities to create a Ligand Interaction Diagrams (LID) from protein-ligand (PL) interaction data.

schrodinger.application.desmond.sid_plots.pl_lid.add_halogen_interaction(bond_data: str, lid_sketcher: schrodinger.ui._sketcher.LIDSelectOnlySketcher, lid_residues_by_label: dict, lig_atom_map: dict, sketcher_lig_atoms: schrodinger.ui._sketcher.sketcherAtom) → None

Add a halogen interaction to an LID sketcher.

Parameters

• bond_data –

  The halogen bond data in the form: (<freq>, <prot_label>, <prot_atom_idx>, <prot_coords>, <lig_atom_idx>)

  e.g. (0.0148, ‘B:ARG_13:O’, 180, [4.014, -2.630, 8.924], 2357)

• lid_sketcher – The Ligand Interaction Diagram (LID) sketcher object

• lid_residues_by_label – A dictionary mapping residue labels to their sketcher residue objects.

• lig_atom_map – A dictionary mapping structure atom indices to rdkit atom indices.

• sketcher_lig_atoms – All sketcher atoms for the ligand.

schrodinger.application.desmond.sid_plots.pl_lid.parseLabel(label)

schrodinger.application.desmond.sid_plots.pl_lid.get_adjusted_opacity(opacity: float) → float