schrodinger.application.bioluminate.protein_protein_docking_shared module¶
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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
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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.
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__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
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toDict
()¶
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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
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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.
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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
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ATTRACTION
= 'attraction'¶
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REPULSION
= 'repulsion'¶
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DISTANCE
= 'distance'¶
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RECEPTOR
= 'receptor'¶
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LIGAND
= 'ligand'¶
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ANTIBODY
= 'antibody'¶
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ANTIGEN
= 'antigen'¶
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__init__
(constraint_type=None, asl=None, protein_type=None, attraction=None, required=None, distance_pairs=None)¶
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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.
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isEnergy
()¶ Return True if this is an ENERGY-based constraint
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isDistance
()¶ Return True if this is an DISTANCE-based constraint
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setResidues
(rec_st, lig_st)¶ Uses
self.asl
withst_file
and to set the commandline_residues property.
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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
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static
read_constraints_file
(fname)¶ Reads a constraints file and returns the python representation as loaded from the json module.
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static
write
(constraints, ofile)¶ Writes a list of constraints to a JSON formatted file.
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