6 parameterFileName = sys.argv[1]
8 startTime = time.time()
10 p = peptideDocker.PeptideDocker(parameterFileName)
18 p.addForceFieldRestraints()
19 p.setInitialPositions()
20 p.addClosePairNonBondedRestraints()
22 d = atomicDomino.AtomicDomino(p.getModel(), p.getProtein(), parameterFileName)
27 d.writeVisualization()
28 p.logTime(
"Created subsets")
29 p.addCompleteNonBondedRestraints()
31 p.logTime(
"Added complete nonbonded restraints")
37 p.runMolecularDynamics()
47 d.discretizeNativeProtein()
49 particleNameList = d.getDominoParticleNames()
51 flexibleAtoms = p.getFlexibleAtoms()
53 d.readMdTrajectory(particleNameList, flexibleAtoms)
55 d.readCgTrajectories(particleNameList, flexibleAtoms)
57 p.logTime(
"Read Trajectory")
59 d.createParticleStatesTable()
61 p.logTime(
"create particle states table")
63 d.createAllSubsetAssignments()
65 p.logTime(
"Create Leaf assignments")
71 p.logTime(
"Ran Domino")
77 d.writeOutput(flexibleAtoms, startTime)