def testRenameChain(self):
pdb1 = self._importStructurePDB('5NI1') # A, B, C
_dictOperations = ProtAtomStrucOperate.operationsDictInv
args = {
'pdbFileToBeRefined': pdb1,
'Operation': _dictOperations['reNameChain'],
'inputStructureChain':
'{"model": 0, "chain": "B", "residues": 146}',
'chainName': 'AA'
}
protAtomStrucExtractChain = self.newProtocol(ProtAtomStrucOperate,
**args)
self.launchProtocol(protAtomStrucExtractChain)
aSH2 = AtomicStructHandler()
outFileName = protAtomStrucExtractChain.outputPdb.getFileName()
aSH2.read(outFileName)
atomsNumT = len([atom.id for atom in aSH2.getStructure().get_atoms()])
# check size
self.assertEqual(4579, atomsNumT)
# check chain names
d1, d2 = aSH2.getModelsChains()
chains = d1[0].keys()
self.assertTrue('A' in chains)
self.assertTrue('AA' in chains)
self.assertTrue('C' in chains)
self.assertTrue('D' in chains)
self.assertFalse('B' in chains)
def extractAllChainsStep(self, structFileName):
import json
outFileName = self._getExtraPath("atomStruct_extractChain_%s.cif")
aStruct1 = AtomicStructHandler(structFileName)
listOfChains, _ = aStruct1.getModelsChains()
for model, chainDic in listOfChains.items():
for chainID, lenResidues in chainDic.items():
chainIdDict = json.loads(
'{"model": %d, "chain": "%s", "residues": %d}' %
(model, str(chainID), lenResidues))
chainIDStr = chainIdDict['chain']
aStruct1.extractChain(modelID=chainIdDict['model'],
chainID=chainIDStr,
start=-1,
end=sys.maxsize,
filename=outFileName % chainIDStr)
self.createOutputStep(outFileName % chainIDStr,
suffix=chainIDStr)