def extractChainStep(self, structFileName):
import json
outFileName = self._getExtraPath("atomStruct_extractChain.cif")
aStruct1 = AtomicStructHandler(structFileName)
chainIdDict = json.loads(self.inputStructureChain.get())
end = self.end.get()
if end == -1:
end = sys.maxsize
aStruct1.extractChain(chainID=chainIdDict['chain'],
start=self.start.get(),
end=end,
modelID=chainIdDict['model'],
filename=outFileName)
self.createOutputStep(outFileName)
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)