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

ab_initio_cmd()[source]¶

Return the command to run rosetta as a list suitable for subprocess

ab_initio_model(processed_models=None)[source]¶

Run the ab initio modelling and return a list of models.

Parameters:	processed_models (list, optional) – A list of pdb models that should have been checked for suitability. NB - currently only required by NMR remodelling
Returns:	The list of created ab initio pdb models
Return type:	list

cmd_add_restraints(cmd)[source]¶

Add any restraints and files to the ROSETTA command-line options

create_broker_definition_file()[source]¶

create_multimer_constraints_file()[source]¶

create_multimer_flagsfile(broker_file=None, symmetry_file=None, constraints_file=None)[source]¶

create_multimer_symmetry_file()[source]¶

do_multimer_modelling()[source]¶

do_nmr_remodel(models)[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, start=1000000, end=4000000)[source]¶

Generate a list of nseed seeds

Parameters:	nseeds (int) – The number of seeds required start (int) – Beginning of random range nseeds – End of random range

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)[source]¶

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

Return the path to the pdb generated by idealize for pdbin

model_from_flagsfile(flagsfile, rosetta_executable=None, job_time=43200, consolidate_pdbs=True)[source]¶

Run ROSETTA modelling from a flagsfile

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

static process_cmd_list(cmds)[source]¶

Create a string from a list of commands

process_multimer_models(modelsin)[source]¶

Merge the multi-chain pdbs into a single chain

remodel(id_pdbs, ntimes, alignment_file)[source]¶

remodel_proc_map(id_pdbs, ntimes)[source]¶

run_scripts(collector, run_dir=None, 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(work_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]¶

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

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