annotate spring_model.py @ 24:802daf2993b0 draft

"planemo upload commit 37a4c6844fd7ab1071ddf90f51915ec1a13c26b3-dirty"

#! /usr/bin/env python3
import argparse
import os

from spring_package.Alignment import Alignment
from spring_package.Energy import Energy
from spring_package.Molecule import Molecule

def buildModel(resultFile, templateFile, chainName, outputName):
	template = Molecule(templateFile)
	if chainName not in template.calpha:
		raise Exception("Chain not found in template [%s]" % chainName)
	chain = template.calpha[chainName]
	alignment = Alignment(resultFile)
	alignment.createModel(chain)
	template.saveChain(chainName, outputName)
	os.system("./build/pulchra %s" % outputName)

def TMalign(fileA, fileB):
	baseA = os.path.basename(fileA)
	baseB = os.path.basename(fileB)
	baseA = os.path.splitext(baseA)[0]
	baseB = os.path.splitext(baseB)[0]
	tmName = "temp/tmalign.%s.%s" % (baseA, baseB)
	os.system("build/TMalign %s %s -m %s.mat > %s.out" % (fileA, fileB, tmName, tmName))
	rotmat = list()
	with open("%s.mat" % tmName) as file:
		line = next(file)
		line = next(file)
		for i in range(3):
			line = next(file)
			rotmatLine = line[1:].split()
			rotmatLine = list(map(lambda x: float(x), rotmatLine))
			rotmatLine = [rotmatLine[1], rotmatLine[2], rotmatLine[3], rotmatLine[0]]
			rotmat.append(rotmatLine)
	with open("%s.out" % tmName) as file:
		for i in range(14):
			line = next(file)
		try:
			tmscore = float(line[9:17])
			line = next(file)
			tmscore = max(tmscore, float(line[9:17]))
		except:
			raise Exception("TMalign::Failed to retrieve TMscore.")
	molecule = Molecule(fileA)
	for atom in molecule.atoms:
		molecule.applyMatrix(atom, rotmat)
	return tmscore, molecule

def main(args):
	os.system("mkdir -p temp")
	os.system("rm -f temp/*.*")
	buildModel(args.a_result, args.a_template, args.a_chain, "temp/monomerA.pdb")
	buildModel(args.b_result, args.b_template, args.b_chain, "temp/monomerB.pdb")
	interfaceEnergy = Energy()
	templateMolecule = Molecule(args.template)
	modelCount = 0
	for biomolNumber in range(len(templateMolecule.rotmat.keys())):
		os.system("rm -f temp/template*.pdb")
		if biomolNumber == 0:
			bioMolecule = templateMolecule
		else:
			bioMolecule = templateMolecule.createUnit(biomolNumber)
		if len(bioMolecule.calpha.keys()) > 1 and args.template_core in bioMolecule.calpha:
			for chainName in bioMolecule.calpha.keys():
				bioMolecule.saveChain(chainName, "temp/template%s.pdb" % chainName)
			coreTMscore, coreMolecule = TMalign("temp/monomerA.rebuilt.pdb", "temp/template%s.pdb" % args.template_core)
			maxScore = -9999
			maxMolecule = None
			for chainName in bioMolecule.calpha.keys():
				if chainName != args.template_core and len(bioMolecule.calpha[chainName]) > 0:
					print("Evaluating chain %s..." % chainName)
					try:
						partnerTMscore, partnerMolecule = TMalign("temp/monomerB.rebuilt.pdb", "temp/template%s.pdb" % chainName)
					except:
						continue
					minTM = min(coreTMscore, partnerTMscore)
					print("min-TMscore: %5.5f" % minTM)
					energy = interfaceEnergy.get(coreMolecule, partnerMolecule)
					print("Interaction: %5.5f" % energy)
					springScore = minTM * args.wtm - energy * args.wenergy
					print("SpringScore: %5.5f" % springScore)
					if springScore > maxScore:
						maxMolecule = partnerMolecule
					modelName = "temp/model%s_%s.pdb" % (modelCount, chainName)
					coreMolecule.save(modelName, chainName="A")
					maxMolecule.save(modelName, chainName="B", append=True)
					modelCount = modelCount + 1

if __name__ == "__main__":
	parser = argparse.ArgumentParser(description='Create a 3D model from HH-search results.')
	parser.add_argument('-ar', '--a_result', help='First HHR target file result', required=True)
	parser.add_argument('-ac', '--a_chain', help='First template chain name', required=True)
	parser.add_argument('-at', '--a_template', help='First template PDB', required=True)
	parser.add_argument('-br', '--b_result', help='Second HHR target file result', required=True)
	parser.add_argument('-bc', '--b_chain', help='Second structure chain name', required=True)
	parser.add_argument('-bt', '--b_template', help='Second template PDB', required=True)
	parser.add_argument('-ts', '--template', help='Structure template', required=True)
	parser.add_argument('-tc', '--template_core', help='Core template chain name', required=True)
	parser.add_argument('-o', '--output', help='Output PDB file', required=False)
	parser.add_argument('-wt', '--wtm', help='Weight TM-score', type=float, default=12.4, required=False)
	parser.add_argument('-we', '--wenergy', help='Weight Energy term', type=float, default=-0.2, required=False)
	args = parser.parse_args()
	main(args)