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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
serialPeptideDocker.py
1 import time
2 import sys
3 import peptideDocker
4 import atomicDomino
5 
6 parameterFileName = sys.argv[1]
7 
8 startTime = time.time()
9 
10 p = peptideDocker.PeptideDocker(parameterFileName)
11 
12 p.createModel()
13 
14 p.loadHelpers()
15 
16 p.initDof()
17 
18 p.addForceFieldRestraints()
19 p.setInitialPositions()
20 p.addClosePairNonBondedRestraints()
21 
22 d = atomicDomino.AtomicDomino(p.getModel(), p.getProtein(), parameterFileName)
23 
24 d.loadDominoHelpers()
25 
26 d.createSubsets()
27 d.writeVisualization()
28 p.logTime("Created subsets")
29 p.addCompleteNonBondedRestraints()
30 
31 p.logTime("Added complete nonbonded restraints")
32 
33 
34 # p.addExcludedVolume()
35 p.logTime("Setup")
36 
37 p.runMolecularDynamics()
38 
39 p.logTime("Run MD")
40 
41 p.runAllCg()
42 
43 p.logTime("Run CG")
44 
45 d.createGrid()
46 
47 d.discretizeNativeProtein()
48 
49 particleNameList = d.getDominoParticleNames()
50 
51 flexibleAtoms = p.getFlexibleAtoms()
52 
53 d.readMdTrajectory(particleNameList, flexibleAtoms)
54 
55 d.readCgTrajectories(particleNameList, flexibleAtoms)
56 
57 p.logTime("Read Trajectory")
58 
59 d.createParticleStatesTable()
60 
61 p.logTime("create particle states table")
62 
63 d.createAllSubsetAssignments()
64 
65 p.logTime("Create Leaf assignments")
66 
67 d.createSampler()
68 
69 d.runDomino()
70 
71 p.logTime("Ran Domino")
72 
73 p.writeOutput()
74 
75 p.outputTimes()
76 
77 d.writeOutput(flexibleAtoms, startTime)