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, frozen_atoms: Optional[List[int]] = 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, frozen_atoms: Optional[List[int]] = 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

  • frozen_atoms – List of atom indices to be frozen, if provided this will take precedence over smarts and reference. The attached hydrogens will also be frozen if not included.

  • dist – The cutoff to use receptor distance cell

getClashResult(ligand: Structure, exclude_h: bool = False, ofac_threshold: float = 0.4, lig_no: int = 0) → ClashResolutionResult

Get the clash result for the provided ligand.

Parameters:

  • ligand – The ligand to resolve clashes for

  • exclude_h – Whether to exclude hydrogen atoms on the ligand

  • ofac_threshold – The cutoff to use for clash detection

  • lig_no – The sequence number of the ligand

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

Resolve as many clashes as possible, only considering ring spears, when ring spear count is not zero, the steric clash count is still used for finding the best conformer when ring spear count ties.

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

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

schrodinger.structutils.clash_resolution.get_atoms_from_smarts_or_mcs(st: Structure, smarts: str | None, reference_st: Structure | None) → set[int]

Get atoms from a structure based on the provided SMARTS pattern or the MCS with the reference structure.

Parameters:

  • st – The structure to get atoms from

  • smarts – The SMARTS pattern to match against the structure

  • reference_st – The reference structure to use for MCS

Returns:

The atom indices that are frozen