pwem.protocols.protocol_import.volumes module

class pwem.protocols.protocol_import.volumes.ImportVolumeOutputs(value)

Bases: Enum

An enumeration.

outputVolume = <class 'pwem.objects.data.Volume'>

outputVolumes = <class 'pwem.objects.data.SetOfVolumes'>

class pwem.protocols.protocol_import.volumes.ProtImportPdb(**args)

Bases: ProtImportFiles

Protocol to import an atomic structure to the project. Format may be PDB or MMCIF

IMPORT_FROM_FILES = 1

IMPORT_FROM_ID = 0

SYMPLIFIED_STRUCT = 'symplified_atom_structure.cif'

createOutputStep(atomStructPath)

Copy the PDB structure and register the output object.

pdbDownloadStep()

Download all pdb files in file_list and unzip them.

class pwem.protocols.protocol_import.volumes.ProtImportSetOfAtomStructs(**args)

Bases: ProtImportFiles

Protocol to import a set of atomic structure to the project. Format may be PDB or MMCIF

IMPORT_FROM_FILES = 1

IMPORT_FROM_ID = 0

createOutputStep(atomStructPaths)

Copy the PDB structures and register the output object.

pdbDownloadStep()

Download all pdb files in file_list and unzip them.

class pwem.protocols.protocol_import.volumes.ProtImportVolumes(**args)

Bases: ProtImportImages

Protocol to import a set of volumes to the project

IMPORT_FROM_EMDB = 1

importFromEMDBStep()

Copy images matching the filename pattern Register other parameters.

importFromFileStep(pattern, samplingRate, setOrigCoord=False)

Copy images matching the filename pattern Register other parameters.

pwem.protocols.protocol_import.volumes.fetch_emdb_map(id, directory, tmpDirectory)

get map from emd :param id: 3D MAP ID in EMDB :return: local 3Dmap filename

pwem.protocols.protocol_import.volumes.fetch_file(url, url_rest_api, name, minimum_file_size=8192, save_dir='', tmp_dir='', save_name='')

Download 3DMAPfile from EMDB

Parameters

• name – EMB name id, format -> EMD-id

• url_rest_api – EMDB rest api, here we ay ask for 3D map properties

• tmp_dir – directory in which the compressed file will be saved temporarily

• url – 3D map url

• minimum_file_size –

• save_dir – save file in this directory

• save_name – local filename

Returns

local file name

pwem.protocols.protocol_import.volumes.gunzip(gzpath, path)