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

__str__()

Return str(self).

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.protein_protein_docking_shared', '__doc__': '\n Object used to store the pairs of residues and the allowable distaances\n between them that make up a piper distance constraint.\n ', '__init__': <function PIPERDistanceConstraintPair.__init__>, '__str__': <function PIPERDistanceConstraintPair.__str__>, 'toDict': <function PIPERDistanceConstraintPair.toDict>, 'setResidues': <function PIPERDistanceConstraintPair.setResidues>, '_setOneComponent': <function PIPERDistanceConstraintPair._setOneComponent>, 'getPiperDict': <function PIPERDistanceConstraintPair.getPiperDict>, '__dict__': <attribute '__dict__' of 'PIPERDistanceConstraintPair' objects>, '__weakref__': <attribute '__weakref__' of 'PIPERDistanceConstraintPair' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.protein_protein_docking_shared'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

__str__()

Return str(self).

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.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.protein_protein_docking_shared', '__doc__': ' Container for managing constraints ', 'ATTRACTION': 'attraction', 'REPULSION': 'repulsion', 'DISTANCE': 'distance', 'RECEPTOR': 'receptor', 'LIGAND': 'ligand', 'ANTIBODY': 'antibody', 'ANTIGEN': 'antigen', '__init__': <function PIPERConstraint.__init__>, 'isEnergy': <function PIPERConstraint.isEnergy>, 'isDistance': <function PIPERConstraint.isDistance>, '__str__': <function PIPERConstraint.__str__>, 'setResidues': <function PIPERConstraint.setResidues>, 'getPiperDict': <function PIPERConstraint.getPiperDict>, 'read_constraints_file': <staticmethod object>, 'write': <staticmethod object>, '__dict__': <attribute '__dict__' of 'PIPERConstraint' objects>, '__weakref__': <attribute '__weakref__' of 'PIPERConstraint' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.protein_protein_docking_shared'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

static write(constraints, ofile)

Writes a list of constraints to a JSON formatted file.