atomstructutils.protocols.protocol_operate module

class atomstructutils.protocols.protocol_operate.ProtAtomStrucOperate(**kwargs)

Bases: pwem.protocols.protocol.EMProtocol

Utilities for handling PDB/mmcif atomic structure files. Current plugin utilities: (A) extract a chain from an atom structure (pdb/cif file), (B) perform union of several atomic structures

addChainStep(structFileName, listStructFileName)

createOutputStep(outFileName, twoRelations=False, suffix='')

extractAllChainsStep(structFileName)

extractChainStep(structFileName)

operationsDict = {0: 'addChain', 1: 'extractChain', 2: 'reNumberChain', 3: 'reNameChain', 4: 'extractAllChains'}

operationsDictInv = {'addChain': 0, 'extractAllChains': 4, 'extractChain': 1, 'reNameChain': 3, 'reNumberChain': 2}

reNameChainStep(structFileName)

reNumberChainStep(structFileName)