def getAtomTypeCounts(self, atomNames): atomNames = atomNames.lstrip('[') atomNames = atomNames.rstrip(']') atomNames = atomNames.rstrip() atomList = atomNames.split(" ") #atom names peptideAtomCount = 0 proteinAtomCount = 0 for atom in atomList: [chain, residue, atom] = atomicDominoUtilities.getAtomInfoFromName(atom) if (chain == self.getParam("peptide_chain")): peptideAtomCount += 1 else: proteinAtomCount += 1 return [peptideAtomCount, proteinAtomCount]
def writeCytoscapeIgInput(self): outputDir = self.getParam("output_directory") igOutputFile = self.getParam("ig_output_file") [nodesToNames, nodesToNodes] = self.getGraphStructure(self.ig, os.path.join(outputDir, igOutputFile), "-") self.writeEdgeFile(nodesToNodes, self.getParam("ig_cytoscape_input_file")) #write residue numbers for each node igResiduesFile = self.getParam("ig_cytoscape_residues_file") peptideChain = self.getParam("peptide_chain") subsetResidueFile = open(os.path.join(outputDir, igResiduesFile), 'w') subsetResidueFile.write("ResidueNumber\n") for nodeNumber in nodesToNames.keys(): nodeName = nodesToNames[nodeNumber] [nodeChain, residueNumber, nodeAtom] = atomicDominoUtilities.getAtomInfoFromName(nodeName) if (nodeChain == peptideChain): #peptideAtom subsetResidueFile.write("%s = %s\n" % (nodeNumber, residueNumber)) else: subsetResidueFile.write("%s = 100\n" % nodeNumber) #for now just write arbitrary number to designate as protein atom