示例#1
0
 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
示例#2
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 = []
示例#3
0
 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