pwem.protocols.protocol_import.volumes module

class pwem.protocols.protocol_import.volumes.ImportVolumeOutputs(value)[source]

Bases: Enum

An enumeration.

outputVolume = <class 'pwem.objects.data.Volume'>
outputVolumes = <class 'pwem.objects.data.SetOfVolumes'>
class pwem.protocols.protocol_import.volumes.ProtImportPdb(**args)[source]

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)[source]

Copy the PDB structure and register the output object.

pdbDownloadStep()[source]

Download all pdb files in file_list and unzip them.

class pwem.protocols.protocol_import.volumes.ProtImportSetOfAtomStructs(**args)[source]

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)[source]

Copy the PDB structures and register the output object.

pdbDownloadStep()[source]

Download all pdb files in file_list and unzip them.

class pwem.protocols.protocol_import.volumes.ProtImportVolumes(**args)[source]

Bases: ProtImportImages

Protocol to import a set of volumes to the project

IMPORT_FROM_EMDB = 1
importFromEMDBStep()[source]

Copy images matching the filename pattern Register other parameters.

importFromFileStep(pattern, samplingRate, setOrigCoord=False)[source]

Copy images matching the filename pattern Register other parameters.

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

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='')[source]

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)[source]