18 parameterFileName = sys.argv[1]
20 startTime = time.time()
22 p = peptideDocker.PeptideDocker(parameterFileName)
30 p.addForceFieldRestraints()
31 p.setInitialPositions()
32 p.addClosePairNonBondedRestraints()
34 d = atomicDomino.AtomicDomino(p.getModel(), p.getProtein(), parameterFileName)
39 d.writeVisualization()
40 p.logTime(
"Created subsets")
41 p.addCompleteNonBondedRestraints()
43 p.logTime(
"Added complete nonbonded restraints")
51 p.runMolecularDynamics()
61 d.discretizeNativeProtein()
63 particleNameList = d.getDominoParticleNames()
65 flexibleAtoms = p.getFlexibleAtoms()
67 d.readMdTrajectory(particleNameList, flexibleAtoms)
69 d.readCgTrajectories(particleNameList, flexibleAtoms)
71 p.logTime(
"Read Trajectory")
73 d.createParticleStatesTable()
75 p.logTime(
"create particle states table")
77 d.createAllSubsetAssignments()
79 p.logTime(
"Create Leaf assignments")
85 p.logTime(
"Ran Domino")
91 d.writeOutput(flexibleAtoms, startTime)