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=None, lig_asl=None, dmin=0.0, dmax=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=None, lig_asl=None, dmin=0.0, dmax=5.0)

Initialize with: rec_asl {string} REQUIRED ASL espression corresponding to eactly

one residue on the receptor
lig_asl {string} REQUIRED ASL espression corresponding to eactly
one residue on the ligand
dmin {float} minimum allowed distance between any two atoms on the
residues defined by rec_asl and lig_asl
dmax {float} maximum allowed distance between any two atoms on the
residues defined by rec_asl and lig_asl
toDict()
setResidues(rec_st, lig_st)

This must be called to set link the asl expresion given in the initializer to a set of structures rec_st { schrodinger.Structure} receptor structure lig_st { schrodinger.Structure} 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 = None

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.