pwem.protocols.protocol_import.volumes module

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

Bases: pwem.protocols.protocol_import.base.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.ProtImportVolumes(**args)[source]

Bases: pwem.protocols.protocol_import.images.ProtImportImages

Protocol to import a set of volumes to the project

IMPORT_FROM_EMDB = 1
importVolumesStep(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]