annotate spring_package/Molecule.py @ 21:5feab7f00f02 draft

"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"

class Molecule:
	def __init__(self, fileName = None):
		self.calpha = dict()
		self.biomol = dict()
		self.rotmat = dict()
		self.atoms = list()
		if fileName is not None:
			self.fromFile(fileName)

	def fromFile(self, fileName):
		biomolNumber = 0
		biomolChains = list()
		with open(fileName) as file:
			for index, line in enumerate(file):
				key = line[0:6].strip()
				if key == "ATOM":
					atom = line[12:16]
					atomNumber = line[6:11]
					chainName = line[21:22]
					if chainName not in self.calpha:
						self.calpha[chainName] = dict()
					x = self.toFloat(line[30:38])
					y = self.toFloat(line[38:46])
					z = self.toFloat(line[46:54])
					occupancy = self.toFloat(line[54:60], optional=True)
					temperature = self.toFloat(line[54:60], optional=True)
					residue = line[17:20]
					residueNumber = self.toInt(line[22:26])
					atomNumber = self.toInt(line[6:11])
					atomName = line[12:16]
					atomDict = dict(x=x, y=y, z=z,
									residue=residue,
									occupancy=occupancy,
									temperature=temperature,
									atomNumber=atomNumber,
									atomName=atomName,
									residueNumber=residueNumber,
									chainName=chainName)
					if atom.strip() == "CA":
						self.calpha[chainName][residueNumber] = atomDict
					self.atoms.append(atomDict)
				biokey = "REMARK 350 BIOMOLECULE:"
				if line[0:len(biokey)] == biokey:
					biomolNumber = self.toInt(line[len(biokey):])
					biokey = "REMARK 350 APPLY THE FOLLOWING TO CHAINS:"
					nextLine = next(file)
					while nextLine[:len(biokey)] != biokey:
						nextLine = next(file)
					biomolChains = nextLine[len(biokey):].split(",")
					biomolChains = list(map(lambda x: x.strip(), biomolChains))
					biokey = "REMARK 350                    AND CHAINS:"
					nextLine = next(file)
					while nextLine[:len(biokey)] == biokey:
						moreChains = nextLine[len(biokey):].split(",")
						moreChains = list(map(lambda x: x.strip(), moreChains))
						biomolChains = biomolChains + moreChains
						nextLine = next(file)
					biokey = "REMARK 350   BIOMT"
					if nextLine[:len(biokey)] == biokey:
						biomolMatId1, biomolMat1 = self.getFloats(nextLine)
						nextLine = next(file)
						biomolMatId2, biomolMat2 = self.getFloats(nextLine)
						nextLine = next(file)
						biomolMatId3, biomolMat3 = self.getFloats(nextLine)
						if biomolMatId1 != biomolMatId2 or biomolMatId1 != biomolMatId3:
							raise Exception("Invalid rotation matrix format [%s]." % biomolMatId1)
						matrix = [biomolMat1, biomolMat2, biomolMat3]
						biomolChains = [c for c in biomolChains if c]
						if biomolNumber not in self.rotmat:
							self.rotmat[biomolNumber] = list()
						self.rotmat[biomolNumber].append(dict(chains=biomolChains, matrix=matrix))
		removeChains = []
		for chainName in self.calpha:
			if len(self.calpha[chainName]) == 0:
				removeChains.append(chainName)
		for chainName in removeChains:
			del self.calpha[chainName]
		if not self.calpha:
			raise Exception("Molecule has no atoms.")

	def getFloats(self, nextLine):
		matId = self.toInt(nextLine[20:23])
		matLine = nextLine[23:].split()
		matLine = list(map(lambda x: self.toFloat(x), matLine))
		return matId, matLine

	def createUnit(self, biomolNumber = 1):
		molecule = Molecule()
		chainCount = 0
		for matrixDict in self.rotmat[biomolNumber]:
			for chain in matrixDict["chains"]:
				if chain in self.calpha:
					chainCopy = dict()
					for residue in self.calpha[chain]:
						chainCopy[residue] = self.calpha[chain][residue].copy()
					for atomNumber in chainCopy:
						atom = chainCopy[atomNumber]
						rotmat = matrixDict["matrix"]
						self.applyMatrix(atom, rotmat)
					if chain in molecule.calpha:
						chainName = chainCount
					else:
						chainName = chain
					molecule.calpha[chainName] = chainCopy
					chainCount = chainCount + 1
		return molecule

	def applyMatrix(self, atom, rotmat):
		newx = atom["x"] * rotmat[0][0] + atom["y"] * rotmat[0][1] + atom["z"] * rotmat[0][2] + rotmat[0][3]
		newy = atom["x"] * rotmat[1][0] + atom["y"] * rotmat[1][1] + atom["z"] * rotmat[1][2] + rotmat[1][3]
		newz = atom["x"] * rotmat[2][0] + atom["y"] * rotmat[2][1] + atom["z"] * rotmat[2][2] + rotmat[2][3]
		atom["x"] = newx
		atom["y"] = newy
		atom["z"] = newz
		return atom

	def toFloat(self, x, optional=False):
		try:
			return float(x)
		except:
			if not optional:
				raise Exception("Invalid float conversion [%s]." % x)
			return 0.0

	def toInt(self, x):
		try:
			return int(x)
		except:
			raise Exception("Invalid integer conversion [%s]." % x)

	def saveChain(self, chainName, outputName):
		print ("Writing PDB file to %s." % outputName)
		f = open(outputName, "w")
		for residueNumber in sorted(self.calpha[chainName].keys()):  
			ca = self.calpha[chainName][residueNumber]
			if ca["residue"] is not None:
				f.write(self.atomString(ca))
		f.close()

	def save(self, outputName, append=False, chainName=None):
		print ("Writing atoms to PDB file to %s." % outputName)
		fileFlag = "+a" if append else "w"
		f = open(outputName, fileFlag)
		for atom in self.atoms:
			atom["chainName"] = chainName if chainName else atom["chainName"]
			f.write(self.atomString(atom))
		f.write("TER\n")
		f.close()

	def atomString(self, atom):
		return "ATOM  %5d %s %s %s%4d    %8.3f%8.3f%8.3f%6.2f%6.2f\n" % (atom["atomNumber"], atom["atomName"], atom["residue"], atom["chainName"], atom["residueNumber"], atom["x"], atom["y"], atom["z"], atom["occupancy"], atom["temperature"])