schrodinger.application.bioluminate.protein_protein_docking_shared module

schrodinger.application.bioluminate.protein_protein_docking_shared.get_residues_for_asl(st, asl)

For a given input structure, st {schrodinger.Structure} and an asl expressions that defines a residue subset, asl {string}, return the list of residues that are in the asl expression. This will be a list of tuples contraining the chain name {string} and the combination of residue number and inscode {string} of each residue Note: list is sorted to create more reproducible results

class schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair(rec_asl: str = None, lig_asl: str = None, dmin: float = 0.0, dmax: float = 5.0)

Bases: object

Object used to store the pairs of residues and the allowable distaances between them that make up a piper distance constraint.

__init__(rec_asl: str = None, lig_asl: str = None, dmin: float = 0.0, dmax: float = 5.0)

Initialize with:

Parameters

• rec_asl – REQUIRED ASL espression corresponding to exactly one residue on the receptor

• lig_asl – REQUIRED ASL espression corresponding to exactly one residue on the ligand

• dmin – minimum allowed distance between any two atoms on the residues defined by rec_asl and lig_asl

• dmax – maximum allowed distance between any two atoms on the residues defined by rec_asl and lig_asl

toDict()

setResidues(rec_st: schrodinger.structure._structure.Structure, lig_st: schrodinger.structure._structure.Structure)

This must be called to set link the asl expresion given in the initializer to a set of structures

Parameters

• rec_st – receptor structure

• lig_st – receptor structure

If the ASL expression provided in the initializer does not correspond to exactly one residue in rec_st and lig_st respectively than a RuntimeError is raised

getPiperDict()

Return the dictionary that will be used to create the piper-backend-formatted json file. This format is different than the json format used to pass constraint objects to the schrodinger-wrapper for Prime as that json file must include distance and energy-based constraints.

class schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint(constraint_type=None, asl=None, protein_type=None, attraction=None, required=None, distance_pairs=None)

Bases: object

Container for managing constraints

ATTRACTION = 'attraction'

REPULSION = 'repulsion'

DISTANCE = 'distance'

RECEPTOR = 'receptor'

LIGAND = 'ligand'

ANTIBODY = 'antibody'

ANTIGEN = 'antigen'

__init__(constraint_type=None, asl=None, protein_type=None, attraction=None, required=None, distance_pairs=None)

at_surface

Property holding the list of strings that can be added to a command line list to identify residues in attraction/masking scripts.

isEnergy()

Return True if this is an ENERGY-based constraint

isDistance()

Return True if this is an DISTANCE-based constraint

setResidues(rec_st, lig_st)

Uses self.asl with st_file and to set the commandline_residues property.

getPiperDict()

Return the dictionary that will be used to create the piper-backend-formatted json file. This format is different than the json format used to pass constraint objects to the schrodinger-wrapper for Prime as that json file must include This is used only for the distance constraints ( energy constraints are passed to piper using command-line options) so it will raise a NotImplementedError if used with an energy constraint

static read_constraints_file(fname)

Reads a constraints file and returns the python representation as loaded from the json module.

static write(constraints, ofile)

Writes a list of constraints to a JSON formatted file.