def __init__(self, model, protein, parameterFileName):
self.model = model
self.protein = protein
self.namesToParticles = atomicDominoUtilities.makeNamesToParticles(protein)
self.readParameters(parameterFileName)
self.wroteNativeProtein = 0
self.maxMem = 0
def loadDockingHelpers(self):
outputDir = self.getParam("output_directory")
mkdirProcess = subprocess.Popen(['mkdir', '-p', self.getParam('output_directory')], shell=False, stderr=subprocess.PIPE)
output = mkdirProcess.communicate()
self.namesToParticles = atomicDominoUtilities.makeNamesToParticles(self.protein)
self.times = []
self.rawTimes = []
def calculateRmsd(self, otherProtein, flexibleAtoms):
otherNamesToParticles = atomicDominoUtilities.makeNamesToParticles(otherProtein)
otherVector = []
modelVector = []
for pName in otherNamesToParticles.keys():
if (flexibleAtoms.has_key(pName) == 0):
continue
otherParticle = otherNamesToParticles[pName]
modelParticle = self.namesToParticles[pName]
otherVector.append(IMP.core.XYZ.decorate_particle(otherParticle).get_coordinates())
modelVector.append(IMP.core.XYZ.decorate_particle(modelParticle).get_coordinates())
rmsd = IMP.atom.get_rmsd(otherVector, modelVector)
return rmsd