Package schrodinger :: Package application :: Package desmond :: Module fep_protein_prep

Module fep_protein_prep

Classes

Tagger

ProteinPrep
This object will be used to prepare a protein for fep

Workflow
Will take a list of proteins and a mutation dictionary and return a set of "lig" "rec" legs and msj for running the sims.

Functions

[hide private]

get_mutations(a_line)
This will get the mutations from a line using the bioluminate/prime syntax

submit_to_residue_scanning(complex_struct, mutation_file, rec_asl, host='localhost', njobs=1, jobname='temp_mut', cutoff_dist=0.0)

get_lig_asl_for_fep(struct)
Will generate the ligand asl.

get_marked_atoms_asl_for_fep(struct)
Will generate asl if atoms are marked with REF_MARKER.

_keyify(x)
This is used to create a key out of the chain:resnum string

sort_mut_dict(a_dict)
Need to sort the dictionary based on res number so that when we add the codes 98,99, 198,199, 298,299 , etc.

get_CB_atom(atoms, struct)
Gets the CB atom

get_MUT_HA2_atom(atoms, struct)
This will find the HA2 atom in the mutated structure

get_HA_atoms(atoms, struct)
This will get the Hydrogen atoms attached to the CA

flip_closest_atom(ref, list_of_atoms)
This will make sure we assign the correct H attached to the CA the appropriate code.

get_resname(struct, chain, resnum)
Will return the pdbresname of the residue in the structure

get_mut_struct_dict(mut_struct_file, mutation_list)

convertResToAsl(input)

append_mut_dict(lig_rec, mut_st_dict, mutation_list, idx)

sanitize_structure(struct)
Remove all fep codes

Variables

[hide private]

ATOM_MARKER = 'i_fep_subst'

RES_MARKER = 'i_fep_residue'

PRO_MARKER = 'i_fep_protein'

LIG_MARKER = 'i_fep_ligand'

REST_MARKER = 'i_rest_hotregion'

REF_MARKER = 'i_fep_ref'

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

get_mutations(a_line)

This will get the mutations from a line using the bioluminate/prime syntax

Parameters:

a_line (string) - The line containing mutations

Returns:

a dictionary @rtype : dict

submit_to_residue_scanning(complex_struct, mutation_file, rec_asl, host=`'localhost'`, njobs=1, jobname=`'temp_mut'`, cutoff_dist=0.0)

Parameters:

complex_struct (string) - filename for the complex structure
mutation_file (string) - filename containing the mutations
rec_asl (string) - asl for defining the receptor
host (string) - The host to run on
njobs (int) - number of jobs (processors)
jobname (string) - name of the job
cutoff_dist (float) - distance to use for cutoff in prime backend

get_lig_asl_for_fep(struct)

Will generate the ligand asl.

Parameters:

struct (structure) - a structure

get_marked_atoms_asl_for_fep(struct)

Will generate asl if atoms are marked with REF_MARKER.

Parameters:

struct (structure) - a structure

sort_mut_dict(a_dict)

Need to sort the dictionary based on res number so that when we add the codes 98,99, 198,199, 298,299 , etc. are in order of increasing atom number... This will sort the dictionary based on the resid by first keyifying the input

Parameters:

a_dict (a dictionary @rtype : a list of tuples @return : list) - a input dictionary

get_CB_atom(atoms, struct)

Gets the CB atom

Parameters:

atoms (list of ints) - a list of atom indexes to check
struct (structure object @return : found Hydrogen atom object @rtype : atom object) - structure object we search

get_MUT_HA2_atom(atoms, struct)

This will find the HA2 atom in the mutated structure

Parameters:

atoms (list of ints) - a list of atom indexes to check
struct (structure object @return : found Hydrogen atom object @rtype : atom object) - structure object we search

get_HA_atoms(atoms, struct)

This will get the Hydrogen atoms attached to the CA

Parameters:

atoms (list of ints) - a list of atom indexes to check
struct (structure object @return : The list of found Hydrogen atom objects @rtype : list of atom objects) - structure object we search

flip_closest_atom(ref, list_of_atoms)

This will make sure we assign the correct H attached to the CA the appropriate code. We also make sure that the other hydrogen is assigned 1 and not 2.

Parameters:

ref (atom object) - atom object used which will be tagged
list_of_atom (list) - list of atoms used to measure distance to ref

get_resname(struct, chain, resnum)

Will return the pdbresname of the residue in the structure

Parameters:

struct (structure) - structure to use
chain (string) - chain name
resnum (string) - residue number

get_mut_struct_dict(mut_struct_file, mutation_list)

Parameters:

mut_struct_file (string) - filename of mutant structure generated from prime
mutation_list (list) - list of mutations

append_mut_dict(lig_rec, mut_st_dict, mutation_list, idx)

Parameters:

lig_rec (structure) - ligand receptor
mut_st_dict (dict) - dictionary of mutations
mutation_list (list) - list of mutations
idx (int) - index

sanitize_structure(struct)

Remove all fep codes

Parameters:

struct (structure) - structure object

Module fep_protein_prep

get_mutations(a_line)

submit_to_residue_scanning(complex_struct, mutation_file, rec_asl, host='localhost', njobs=1, jobname='temp_mut', cutoff_dist=0.0)

get_lig_asl_for_fep(struct)

get_marked_atoms_asl_for_fep(struct)

sort_mut_dict(a_dict)

get_CB_atom(atoms, struct)

get_MUT_HA2_atom(atoms, struct)

get_HA_atoms(atoms, struct)

flip_closest_atom(ref, list_of_atoms)

get_resname(struct, chain, resnum)

get_mut_struct_dict(mut_struct_file, mutation_list)

append_mut_dict(lig_rec, mut_st_dict, mutation_list, idx)

sanitize_structure(struct)

submit_to_residue_scanning(complex_struct, mutation_file, rec_asl, host=`'localhost'`, njobs=1, jobname=`'temp_mut'`, cutoff_dist=0.0)