Package schrodinger :: Package application :: Package desmond :: Module covalent_fep_prep

Module covalent_fep_prep

Objective: Given proteins with covalent congeneric R groups prep ligands for mapper

Basic approach is to cut out the residue that is bonded to the R group from the protein cap the termini and turn off CM1 charge assignment in mae. Also remove any "protein" atom types that will confuse the protein asl selection

Classes

[hide private]

Workflow

LigandGenerator
Will generate a list of ligands preped for a mapper job

PrepLigand

ProcessLigands
Supports calling mapper and generating mae files for running multisim

ProcessProteins
The idea here is to use the mapping generated from the ligands to generate mae's for the complex.

SetupFEPJob

Functions

[hide private]

convertResToAsl(input)

skip_cm1a(struct)
Skip cm1a charge assignment

Variables

[hide private]

MSJ_SOLVENT_TEMPLATE = '\nextern {\n command = "\nimport os\...

MSJ_COMPLEX_TEMPLATE = '\nextern {\n command = "\nimport os\...

__package__ = 'schrodinger.application.desmond'

Variables Details

[hide private]

MSJ_SOLVENT_TEMPLATE

Value:

'''
extern {
   command = "
import os
import copy
import schrodinger.application.desmond.cmj   as cmj
import schrodinger.application.desmond.struc as struc
import schrodinger.application.desmond.util  as util
...

MSJ_COMPLEX_TEMPLATE

Value:

'''
extern {
   command = "
import os
import copy
import schrodinger.application.desmond.cmj   as cmj
import schrodinger.application.desmond.struc as struc
import schrodinger.application.desmond.util  as util
...