schrodinger.structutils.clash_resolution module

class schrodinger.structutils.clash_resolution.ClashResolutionResult(spears: int, clashes: int, no: int, conformer: Structure)

Bases: object

Result of the clash resolution.

Parameters:

  • spears – The number of ring spears

  • clashes – The number of steric clashes

  • no – The sequence number of the generated conformer (0 if no conformer was needed)

  • conformer – The conformer structure

spears: int
clashes: int
no: int
conformer: Structure
__init__(spears: int, clashes: int, no: int, conformer: Structure) → None
class schrodinger.structutils.clash_resolution.ReceptorLigandClashResolver(receptor: Structure, exclude_asl: Optional[str] = None, reference: Optional[Structure] = None, smarts: Optional[str] = None, dist: float = 4.0)

Bases: object

A class to provide logic for resolving clashes between a receptor and a constrained ligand.

Constraints on the ligand are based on keeping the atoms in the smarts or maximum common substructure with a reference ligand frozen, with smarts taking precedence.

__init__(receptor: Structure, exclude_asl: Optional[str] = None, reference: Optional[Structure] = None, smarts: Optional[str] = None, dist: float = 4.0)
Parameters:

  • receptor – The receptor structure

  • exclude_asl – ASL to exclude atoms from the receptor

  • reference – A reference structure to use for the MCS

  • smarts – SMARTS to use for the frozen atoms

  • dist – The cutoff to use receptor distance cell

getBestClashResolutionResult(ligand: Structure, exclude_h: bool = False, max_conformers: int = 1000, ofac_threshold: float = 0.4) → ClashResolutionResult

Resolve as many clashes as possible considering the ring spears to be more important to be resolved.

Parameters:

  • ligand – The ligand to resolve clashes for

  • exclude_h – Whether to exclude hydrogen atoms on the ligand

  • max_conformers – The maximum number of conformers to generate

  • ofac_threshold – The cutoff to use for clash detection

resolveClashes(ligand: Structure, exclude_h: bool = False, max_conformers: int = 1000, ofac_threshold: float = 0.4) → Structure

Resolve as many clashes as possible considering the ring spears to be more important to be resolved.

Parameters:

  • ligand – The ligand to resolve clashes for

  • exclude_h – Whether to exclude hydrogen atoms on the ligand

  • max_conformers – The maximum number of conformers to generate

  • ofac_threshold – The cutoff to use for clash detection