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")
49 p.runMolecularDynamics()
59 d.discretizeNativeProtein()
61 particleNameList = d.getDominoParticleNames()
63 flexibleAtoms = p.getFlexibleAtoms()
65 d.readMdTrajectory(particleNameList, flexibleAtoms)
67 d.readCgTrajectories(particleNameList, flexibleAtoms)
69 p.logTime(
"Read Trajectory")
71 d.createParticleStatesTable()
73 p.logTime(
"create particle states table")
75 d.createAllSubsetAssignments()
77 p.logTime(
"Create Leaf assignments")
83 p.logTime(
"Ran Domino")
89 d.writeOutput(flexibleAtoms, startTime)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.