ample.modelling.rosetta_model module¶

Created on 21 Feb 2013

@author: jmht

class RosettaModel(optd=None, rosetta_dir=None)[source]¶

Bases: object

Class to run Rosetta modelling

Methods

ab_initio_cmd(wdir, nstruct, seed)	Return the command to run rosetta as a list suitable for subprocess
find_binary(name)	Find a rosetta binary on different platforms separate from object as it’s currently used by the NMR stuff - which is in dire need of refactoring.
fragment_cmd()	Return the command to make the fragments as a list
generate_fragments(amoptd)	Run the script to generate the fragments
generate_seeds(nseeds)	Generate a list of nseed seeds
get_bin_dir()	Determine the binary directory for the version
get_version()	Return the Rosetta version as a string
idealize_cmd(pdbin)	Return command to idealize pdbin
idealize_pdbout(pdbin[, directory])	Return the path to the pdb generated by idealize for pdbin
set_from_dict(optd)	Set the values from a dictionary
setup_domain_restraints()	Create the file for restricting the domain termini and return the path to the file
split_jobs(njobs, nproc)	Return a list of number of jobs to run on each processor
tm_make_files()	Generate the various files needed for modelling transmembrane proteins

ab_initio_model
idealize_models
mr_cmd
nmr_remodel
remodel
remodel_proc_map
run_scripts
set_paths
tm2_make_patch
tm_set_paths

ab_initio_cmd(wdir, nstruct, seed)[source]¶

Return the command to run rosetta as a list suitable for subprocess wdir: directory to run in nstruct: number of structures to process seed: seed for this processor

ab_initio_model(monitor)[source]¶

find_binary(name)[source]¶

Find a rosetta binary on different platforms separate from object as it’s currently used by the NMR stuff - which is in dire need of refactoring.

fragment_cmd()[source]¶

Return the command to make the fragments as a list

generate_fragments(amoptd)[source]¶

Run the script to generate the fragments

generate_seeds(nseeds)[source]¶

Generate a list of nseed seeds

Parameters:	nseeds : int The number of seeds required

get_bin_dir()[source]¶

Determine the binary directory for the version

get_version()[source]¶

Return the Rosetta version as a string

idealize_cmd(pdbin)[source]¶

Return command to idealize pdbin

idealize_models(models, monitor)[source]¶

idealize_pdbout(pdbin, directory=None)[source]¶

Return the path to the pdb generated by idealize for pdbin

mr_cmd(template, alignment, nstruct, seed)[source]¶

nmr_remodel(nmr_model_in=None, ntimes=None, alignment_file=None, remodel_fasta=None, monitor=None)[source]¶

remodel(id_pdbs, ntimes, alignment_file, monitor=None)[source]¶

remodel_proc_map(id_pdbs, ntimes)[source]¶

run_scripts(job_scripts, job_time=None, job_name=None, monitor=None)[source]¶

set_from_dict(optd)[source]¶

Set the values from a dictionary

set_paths(optd=None, rosetta_dir=None)[source]¶

setup_domain_restraints()[source]¶

Create the file for restricting the domain termini and return the path to the file

split_jobs(njobs, nproc)[source]¶

Return a list of number of jobs to run on each processor

tm2_make_patch(run_dir)[source]¶

tm_make_files()[source]¶

Generate the various files needed for modelling transmembrane proteins

REM the fasta as it needs to reside in this directory or the script may fail due to problems with parsing directory names with ‘funny’ characters

tm_set_paths(optd)[source]¶

class RosettaScoreData[source]¶

Bases: object

class RosettaScoreParser(directory)[source]¶

Bases: object

Methods

maxsub
maxsubSorted
parseFile
rms
rmsSorted

maxsub(name)[source]¶

maxsubSorted(reverse=True)[source]¶

parseFile(score_file)[source]¶

rms(name)[source]¶

rmsSorted(reverse=True)[source]¶

align_clustalw(query_seq, template_seq, logger, clustalw_exe=None)[source]¶

align_mafft(query_seq, template_seq, logger, mafft_exe=None)[source]¶