schrodinger.application.desmond.fep_protein

Class ProteinPrep

object --+ | ProteinPrep

This object will be used to prepare a protein for fep

Instance Methods

__init__(self, receptor_struct, wt_lig_struct, mut_lig_struct, mutation_dict, of, lof)
x.__init__(...) initializes x; see help(type(x)) for signature

initAllAtoms(self)
This will initialize the properties to all 0's

prep_it(self)
Preps structures

correct_gly_map(self, wt_struct, mut_struct)
This is used to correct the wt structure.

build_structure(self, struct)
This will build the mutant structure given a list of mutations

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

Properties

[hide private]

Inherited from object: __class__

init(self, receptor_struct, wt_lig_struct, mut_lig_struct, mutation_dict, of, lof)
(Constructor)

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

Parameters:

receptor_struct (structure object) - receptor structure
wt_lig_struct (structure object) - Structure of the wild type "ligand"
mut_lig_struct (structure object) - Structure of the mutated "ligand"
mutation_dict (a dict i.e. {'D:8': 'ALA', 'D:10': 'GLY', 'D:32': 'GLY', 'D:34': 'GLY'}) - dictionary of wt keys mutation values
of (string) - out put filename of the resulting receptor structure
of (string) - out put filename of the resulting ligand structure

Overrides: object.__init__

correct_gly_map(self, wt_struct, mut_struct)

This is used to correct the wt structure.

Parameters:

wt_struct (structure object) - structure object of the wild type
mut_struct (structure object) - structure object of the mutant

build_structure(self, struct)

This will build the mutant structure given a list of mutations

Parameters:

struct (structure object @rtype : structure object @return : The mutated structure) - input structure

Class ProteinPrep

__init__(self, receptor_struct, wt_lig_struct, mut_lig_struct, mutation_dict, of, lof) (Constructor)

correct_gly_map(self, wt_struct, mut_struct)

build_structure(self, struct)

init(self, receptor_struct, wt_lig_struct, mut_lig_struct, mutation_dict, of, lof)
(Constructor)