Module fep_edge_data

Classes

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ResData
A class to store the molecule number, chain, name, and number of a residue

FEPTorsions

FEPTorsionsContainer
Class that stores torsions for a single ligand.

FEPEdgeData
FEPEdgeData contains all the data related to an FEP perturbation.

PRMEdgeData
PRMEdgeData is an object that stores Protein Residue Mutation related data.

Functions

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tag_protein(proteinA, proteinB)
This is function was adopted from: scisol.leadoptmap.protein_fep_mapper.tag_protein This proceeds in several steps for mutation of protein A -> protein B Loop over all other atoms in the two full length proteins and assign 1:1 atom mapping.

Variables

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SOLVENT_NAMES = {'covalent_ligand': 'Frag. Solvent', 'prm_affi...

COMPLEX_NAMES = {'covalent_ligand': 'Complex', 'prm_affinity':...

MAP_MARKER = 'i_fep_mapping'

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

tag_protein(proteinA, proteinB)


This is function was adopted from:
    scisol.leadoptmap.protein_fep_mapper.tag_protein
This proceeds in several steps for mutation of protein A -> protein B
Loop over all other atoms in the two full length proteins and assign
1:1 atom mapping. For the mutated residue, it might put some wrong
numbers in, but it is fine as the correct value will later overwrite
them.

@param proteinA : protein A
@type proteinA : structure
@param proteinB : protein B
@type proteinB : structure

Variables Details

[hide private]

SOLVENT_NAMES

Value:

{'covalent_ligand': 'Frag. Solvent',
 'prm_affinity': 'ProteinA',
 'prm_ligand_selectivity': 'Apo',
 'prm_stability': 'Frag. Solvent',
 'small_molecule': 'Solvent'}

COMPLEX_NAMES

Value:

{'covalent_ligand': 'Complex',
 'prm_affinity': 'ProteinA-ProteinB Complex',
 'prm_ligand_selectivity': 'Holo',
 'prm_stability': 'Protein',
 'small_molecule': 'Complex'}