Package schrodinger :: Package application :: Package desmond :: Module fep_scholar_util

Module fep_scholar_util

This file contains common utility methods and classes used in several FEP scripts.

Classes

MappingAnnotator
This annotator allows to show atom numbers for a selected subset of atoms.

MetaAtom
This is the meta atom class that mostly provides convinience functions.

FEPScholarMapper
This is a mapper class used by FEP Scholar GUI so that we don't need to use Canvas MCS for matching molecule atoms.

ScholarStructureItem
This class adds new function to the base structure_item class that allows to show some atoms and bonds with highlighting.

FEPStructureObject
This class holds all information about each ligand.

Functions

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DECREMENT(x)

get_chmmol_bonds_from_atoms(chmmol, atoms)
This function returns a list of bonds that connect atoms in a given list.

tuple

get_mutation_atoms_and_bonds(cmol, match, mut_atoms)
This function determines lists of atoms and bonds that should be highlighted to show mutations.

generate_default_pic(ligand1, ligand2)
Create default picture of two ligands, which only shows ligand structures and no mapping.

generate_mutation_pic(mapper, ligand1, ligand2)
Create mutations on ligand structures.

generate_mapping_pic(mapper, ligand1, ligand2)
Create atom mapping by displaying atom indices on ligand structures.

generate_core_pic(mapper, ligand1, ligand2)
Highlight core atoms and bonds in ligand structures.

generate_hot_atoms_pic(mapper, ligand1, ligand2)
Show 'hot' atoms on ligand structures.

list

make_fep_cmd(cd_params, jobname, struct_fname, opt=[])
Generates an FEP command list based on the specified parameters.

generate_scripts(cd_params, jobname, cmd)
Write the command line for submitting the job

Variables

[hide private]

__doc__ = ...

DISTANCE_CUTOFF = 0.4

MUTATION_COLOR = QtGui.QColor(255, 0, 0)

MCS_COLOR = QtGui.QColor(0, 255, 0)

CORE_COLOR = QtGui.QColor(0, 255, 0)

HOT_ATOMS_COLOR = QtGui.QColor(255, 140, 0)

IGNORE_HYDROGEN = 0
hash(x)

RESCALE = 2

FIXUP = True
hash(x)

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

get_chmmol_bonds_from_atoms(chmmol, atoms)

This function returns a list of bonds that connect atoms in a given list.

Parameters:

chmmol (canvas.ChmMol) - molecule structure
atoms (list) - list of atom indices

get_mutation_atoms_and_bonds(cmol, match, mut_atoms)

This function determines lists of atoms and bonds that should be highlighted to show mutations.

Parameters:

cmol (canvas2d.ChmMol) - Canvas ChmMol
match (list) - list of core atoms
mut_atoms (list) - list of 'mutated' atoms

Returns: tuple

tuple that contains list of atoms and list of bonds

generate_default_pic(ligand1, ligand2)

Create default picture of two ligands, which only shows ligand structures and no mapping.

Parameters:

ligand1 (fep_scholar_util.FEPStructureObject) - first ligand FEP structure object
ligand2 (fep_scholar_util.FEPStructureObject) - second ligand FEP structure object

generate_mutation_pic(mapper, ligand1, ligand2)

Create mutations on ligand structures.

Parameters:

mapper (fep_scholar_util.FEPScholarMapper) - FEP scholar mapper object
ligand1 (fep_scholar_util.FEPStructureObject) - first ligand FEP structure object
ligand2 (fep_scholar_util.FEPStructureObject) - second ligand FEP structure object

generate_mapping_pic(mapper, ligand1, ligand2)

Create atom mapping by displaying atom indices on ligand structures. For the second ligand we display corresponding atom indices from the first ligand.

Parameters:

mapper (fep_scholar_util.FEPScholarMapper) - FEP scholar mapper object
ligand1 (fep_scholar_util.FEPStructureObject) - first ligand FEP structure object
ligand2 (fep_scholar_util.FEPStructureObject) - second ligand FEP structure object

generate_core_pic(mapper, ligand1, ligand2)

Highlight core atoms and bonds in ligand structures.

Parameters:

mapper (fep_scholar_util.FEPScholarMapper) - FEP scholar mapper object
ligand1 (fep_scholar_util.FEPStructureObject) - first ligand FEP structure object
ligand2 (fep_scholar_util.FEPStructureObject) - second ligand FEP structure object

generate_hot_atoms_pic(mapper, ligand1, ligand2)

Show 'hot' atoms on ligand structures.

Parameters:

mapper (fep_scholar_util.FEPScholarMapper) - FEP scholar mapper object
ligand1 (fep_scholar_util.FEPStructureObject) - first ligand FEP structure object
ligand2 (fep_scholar_util.FEPStructureObject) - second ligand FEP structure object

make_fep_cmd(cd_params, jobname, struct_fname, opt=`[]`)

Generates an FEP command list based on the specified parameters.

Parameters:

cd_params (dict) - config dialog parameters
jobname (str) - the jobname
master_msj_fname (str) - the filename for the master msj file
struct_fname (str) - the filename for the input structure

Returns: list

a command list for launching the job

Variables Details

[hide private]

doc

Value:

"""
This file contains common utility methods and classes used in several 
FEP
scripts.

Copyright Schrodinger, LLC. All rights reserved.
"""

Module fep_scholar_util

get_chmmol_bonds_from_atoms(chmmol, atoms)

get_mutation_atoms_and_bonds(cmol, match, mut_atoms)

generate_default_pic(ligand1, ligand2)

generate_mutation_pic(mapper, ligand1, ligand2)

generate_mapping_pic(mapper, ligand1, ligand2)

generate_core_pic(mapper, ligand1, ligand2)

generate_hot_atoms_pic(mapper, ligand1, ligand2)

make_fep_cmd(cd_params, jobname, struct_fname, opt=[])

__doc__

make_fep_cmd(cd_params, jobname, struct_fname, opt=`[]`)

doc