Created on 21 Feb 2013
@author: jmht
RosettaModel
(optd=None, rosetta_dir=None)[source]¶Bases: object
Class to run Rosetta modelling
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 |
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Returns: | The list of created ab initio pdb models |
Return type: | list |
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, start=1000000, end=4000000)[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
model_from_flagsfile
(flagsfile, rosetta_executable=None, job_time=43200, consolidate_pdbs=True)[source]¶Run ROSETTA modelling from a flagsfile
setup_domain_restraints
()[source]¶Create the file for restricting the domain termini and return the path to the file.