Package schrodinger :: Package application :: Package desmond :: Module covalent_fep_prep :: Class LigandGenerator

Class LigandGenerator

object --+
         |
        LigandGenerator

Will generate a list of ligands preped for a mapper job

Instance Methods

[hide private]

__init__(self, proteins, covalent_ligand_asl=None, receptor_residue_asl=None)
Takes a list of protein cts, and asl's indicating the covalent ligand in the proteins

dump_raw_ligands(self, file_name)
More for debugging

set_indices(self, asl, ct)
Will set the atom indices

generate_ligands(self, neighbor=0)
Will generate new ct's from covalent ligand fragemnts in protein.

create_ligand(self, ct, idx)

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, proteins, covalent_ligand_asl=None, receptor_residue_asl=None)
(Constructor)

Takes a list of protein cts, and asl's indicating the covalent ligand in the proteins

Overrides: object.__init__

generate_ligands(self, neighbor=0)

Will generate new ct's from covalent ligand fragemnts in protein.

Parameters:

neighbor - number of residues to flank ligand default 0

Class LigandGenerator

__init__(self, proteins, covalent_ligand_asl=None, receptor_residue_asl=None) (Constructor)

generate_ligands(self, neighbor=0)

init(self, proteins, covalent_ligand_asl=None, receptor_residue_asl=None)
(Constructor)