Class PIPERConstraint

object --+
         |
        PIPERConstraint

Container for managing constraints

Instance Methods

[hide private]

__init__(self, constraint_type=None, asl=None, protein_type=None, attraction=None, required=None, distance_pairs=None)
x.__init__(...) initializes x; see help(type(x)) for signature

isEnergy(self)
Return True if this is an ENERGY-based constraint

isDistance(self)
Return True if this is an DISTANCE-based constraint

__str__(self)
str(x)

setResidues(self, rec_st, lig_st)
Uses self.asl with st_file and to set the commandline_residues property.

getPiperDict(self)
Return the dictionary that will be used to create the piper-backend-formatted json file.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Static Methods

[hide private]

read_constraints_file(fname)
Reads a constraints file and returns the python representation as loaded from the json module.

write(constraints, ofile)
Writes a list of constraints to a JSON formatted file.

Class Variables

[hide private]

ATTRACTION = 'attraction'

REPULSION = 'repulsion'

DISTANCE = 'distance'

RECEPTOR = 'receptor'

LIGAND = 'ligand'

ANTIBODY = 'antibody'

ANTIGEN = 'antigen'

Instance Variables

[hide private]

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, constraint_type=None, asl=None, protein_type=None, attraction=None, required=None, distance_pairs=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

getPiperDict(self)

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

Class PIPERConstraint

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

__str__(self) (Informal representation operator)

getPiperDict(self)

init(self, constraint_type=None, asl=None, protein_type=None, attraction=None, required=None, distance_pairs=None)
(Constructor)

str(self)
(Informal representation operator)