Created on 21 Feb 2013
@author: jmht
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 |
cmd_add_restraints (cmd) |
Add any restraints and files to the ROSETTA command-line options |
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
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.
generate_seeds
(nseeds)[source]¶Generate a list of nseed seeds
Parameters: |
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idealize_pdbout
(pdbin, directory=None)[source]¶Return the path to the pdb generated by idealize for pdbin
setup_domain_restraints
()[source]¶Create the file for restricting the domain termini and return the path to the file