doc/html/serialPeptideDocker_8py_source.html

import IMP

import subprocess

import random

import IMP.domino

import IMP.core

import IMP.rmf

import RMF

import time

import IMP.algebra

import types

import re

import sys

import operator

import os

import peptideDocker

import atomicDomino


parameterFileName = sys.argv[1]


startTime = time.time()


p = peptideDocker.PeptideDocker(parameterFileName)


p.createModel()


p.loadHelpers()


p.initDof()


p.addForceFieldRestraints()

p.setInitialPositions()

p.addClosePairNonBondedRestraints()


d = atomicDomino.AtomicDomino(p.getModel(), p.getProtein(), parameterFileName)


d.loadDominoHelpers()


d.createSubsets()

d.writeVisualization()

p.logTime("Created subsets")

p.addCompleteNonBondedRestraints()


p.logTime("Added complete nonbonded restraints")


#p.addExcludedVolume()


p.logTime("Setup")


p.runMolecularDynamics()


p.logTime("Run MD")


p.runAllCg()


p.logTime("Run CG")


d.createGrid()


d.discretizeNativeProtein()


particleNameList = d.getDominoParticleNames()


flexibleAtoms = p.getFlexibleAtoms()


d.readMdTrajectory(particleNameList, flexibleAtoms)


d.readCgTrajectories(particleNameList, flexibleAtoms)


p.logTime("Read Trajectory")


d.createParticleStatesTable()


p.logTime("create particle states table")


d.createAllSubsetAssignments()


p.logTime("Create Leaf assignments")


d.createSampler()


d.runDomino()


p.logTime("Ran Domino")


p.writeOutput()


p.outputTimes()


d.writeOutput(flexibleAtoms, startTime)