pwem.protocols.protocol_export.protocol_export_DB module

class pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases(**kwargs)[source]

Bases: EMProtocol

generates files for elements to submit structures to EMDB/PDB. Since mmcif/pdb is only partially supported by some software the protocol creates 4 versions of the atomic struct file with the hope that at least one of them will work.

ADDITIONALVOLUMEDIR = 'addMaps'

ADDITIONALVOLUMENAME = 'map_%02d.mrc'

COORDINATEFILENAME = 'coordinates.cif'

HALFVOLUMENAME = 'half_map_%d.mrc'

MASKDIR = 'masks'

MASKNAME = 'mask_%02d.mrc'

SYMNAME = 'symmetry_%s.txt'

SYMNAMEORDER = 'symmetry_%s_%d.txt'

SYMPLIFIED_STRUCT = 'symplified_atom_structure.cif'

SYM_CHOICES = {0: 'Cn', 1: 'Dxn', 2: 'Dyn', 3: 'T222', 4: 'Tz3', 5: 'Tz3r', 6: 'O', 7: 'I222', 8: 'I222r', 9: 'In25', 10: 'In25r', 11: 'I2n3', 12: 'I2n3r', 13: 'I2n5', 14: 'I2n5r'}

VOLUMENAME = 'main_map.mrc'

createDirectoryStep(dirPath)[source]

exportAdditionalVolumeStep()[source]

exportAtomStructStep()[source]

exportFSCStep()[source]

exportImageStep()[source]

exportMasksStep()[source]

exportSymmetryStep()[source]: Export symmetry information in a file

exportVolumeStep()[source]

getFnPath(label='volume')[source]