Source code for promod3.pipeline.run_engine

'''Everything sticked together to build models using ProMod3
'''

import ost

from promod3 import loop

[docs]def BuildFromRawModel(raw_model, structure_db=None, fragment_db=None, torsion_sampler=None): '''Build a model starting with a :class:`RawModel <promod3.rawmodel.RawModelingResult>`. :param raw_model: The prepared template coordinates loaded with the input alignment. :type raw_model: :class:`~promod3.rawmodel.RawModelingResult` :param structure_db: The structural database. Loads the default one shipped with |project| if omitted. :type structure_db: :class:`~promod3.loop.StructureDB` :param fragment_db: A fragment database coupled to the *structure_db*. Loads the default one shipped with |project| if omitted. :type fragment_db: :class:`~promod3.loop.FragDB` :param torsion_sampler: A sampler for torsion angles. Loads the default one shipped with |project| if omitted. :type torsion_sampler: :class:`~promod3.loop.TorsionSampler` EXAMPLE: obtain raw model, build model :return: Delivers the model as an |ost_s| entity. :rtype: :class:`Entity <ost.mol.EntityHandle>` ''' ost.LogVerbose("Starting modelling based on a raw model") # a bit of setup if structure_db == None: structure_db = loop.LoadStructureDB() if fragment_db == None: fragment_db = loop.LoadFragDB() if torsion_sampler == None: torsion_sampler = loop.LoadTorsionSamplerCoil() scorer = loop.SetupBackboneScorer(raw_model) # step 1: close small deletions in the raw model ost.LogVerbose("Trying to close small deletions.") raw_model.CloseSmallDeletions(scorer) return raw_model.model
__all__ = ('BuildProMod3Model') # LocalWords: BuildProMod ProMod sticked ost promod BuildFromRawModel param # LocalWords: RawModel rtype bool LoadStructureDB LogVerbose LoadFragDB # LocalWords: LoadTorsionSamplerCoil SetupBackboneScorer # LocalWords: CloseSmallDeletions