Python StructureLoop Examples

Example #1

File: 6nbn_Xplor-NIH_refine.py Project: PDNALab/NEF

    # final all- atom minimization
    #
    protocol.initMinimize(minc, potList=potList, dEPred=10)
    minc.run()

    #do analysis and write structure when this function returns
    toIUPAC()
    from simulationTools import analyze
    protocol.writeCIF(loopInfo.filename() + ".cif", remarks=analyze(potList))
    fromIUPAC()

    pass


from simulationTools import StructureLoop, FinalParams
StructureLoop(
    numStructures=100,
    structLoopAction=calcOneStructure,
    pdbTemplate="SCRIPT_STRUCTURE.sa",
    #              calcMissingStructs=True, #calculate only missing structures
    doWriteStructures=True,  #analyze and write coords after calc
    genViolationStats=True,
    averagePotList=potList,
    averageCrossTerms=refRMSD,
    averageTopFraction=0.2,  #report only on best 20% of structs
    #              averageAccept=accept,   #only use structures which pass accept()
    averageContext=FinalParams(rampedParams),
    averageFilename="SCRIPT_ave.pdb",  #generate regularized ave structure
    averageFitSel="ordered and name CA",
    averageCompSel="not resname ANI and not name H*").run()

Example #2

    cool.run()

    # final torsion angle minimization
    #
    protocol.initMinimize(dyn, printInterval=50)
    dyn.run()

    # final all- atomic degrees of freedom minimization
    #
    protocol.initMinimize(minc, potList=potList, dEPred=10)
    minc.run()

    #do analysis and write structure when function returns
    pass


## modify ##
from simulationTools import StructureLoop, FinalParams
StructureLoop(
    numStructures=numberOfStructures,
    doWriteStructures=True,
    pdbTemplate=outFilename,
    structLoopAction=calcOneStructure,
    genViolationStats=True,
    averageTopFraction=0.25,  #report stats on best 25% of structs
    averageSortPots=[potList['torsionDB']],
    averageContext=FinalParams(rampedParams),
    #averageCrossTerms=refRMSD,
    averageFilename="XPLOR_output/SCRIPT_ave.pdb",
    averagePotList=potList).run()

Example #3

File: annealing.py Project: suzannejin/DeepConTree

    # final torsion angle minimization
    #
    protocol.initMinimize(dyn,
                          printInterval=50)
    dyn.run()

    # final all- atomic degrees of freedom minimization
    #
    protocol.initMinimize(minc,
                          potList=potList,
                          dEPred=10)
    minc.run()

    #do analysis and write structure when function returns
    pass



from simulationTools import StructureLoop, FinalParams
StructureLoop(numStructures=numberOfStructures,
              doWriteStructures=True,
              pdbTemplate=outFilename,
              structLoopAction=calcOneStructure,
              genViolationStats=True,
              averageTopFraction=topavg, #report stats on best x% of structs
              averageSortPots=[potList['torsionDB'],potList['noe']], #potential terms used for sorting structures
              averageContext=FinalParams(rampedParams),
              #averageCrossTerms=refRMSD,
              averageFilename=folder+"/SCRIPT_ave.pdb",
              averagePotList=potList).run()

Example #4

File: wrefine.py Project: xubiaopeng/PRASD

    noe.append(pot)
rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )

# Set up dihedral angles
from xplorPot import XplorPot
protocol.initDihedrals("constraints/yourfolder/yourfolder_dihed_g_all.tbl",
                       useDefaults=False)
potList.append( XplorPot('CDIH') )
rampedParams.append( StaticRamp("potList['CDIH'].setScale(200)") )

from simulationTools import StructureLoop


def calcOneStructure( structData ):
    from waterRefineTools import refine
    refine(outFilename=structData.filename(),
           potList=potList,
           coolingParams=rampedParams,
#           keepWaters=True,
           waterResname=waterResname)
    pass


StructureLoop(pdbFilesIn=inputStructures,
              pdbTemplate="WRresult_your_pdbfile",
              structLoopAction=calcOneStructure,
              genViolationStats=True,
              averagePotList=potList,
              averageContext=FinalParams(rampedParams),
              ).run()

Example #5

    protocol.initMinimize(dyn, printInterval=50)
    dyn.run()

    # final all- atom minimization
    #
    protocol.initMinimize(minc, potList=potList, dEPred=10)
    minc.run()

    #do analysis and write structure when this function returns
    pass


from simulationTools import StructureLoop, FinalParams

StructureLoop(
    numStructures=numberOfStructures,
    structLoopAction=calcOneStructure,
    calcMissingStructs=True,  #calculate only missing structures
    doWriteStructures=True,  #analyze and write coords after calc
    pdbTemplate=outFilename,
    genViolationStats=True,
    averagePotList=potList,
    #averageCrossTerms=refRMSD,
    averageTopFraction=0.1,  #report only on best 50% of structs
    averageAccept=accept,  #only use structures which pass accept()
    averageContext=FinalParams(rampedParams),
    averageFilename=
    "contacts55perfect_diheSSpsipred/SCRIPT_ave.pdb",  #generate regularized ave structure
    averageFitSel="name CA",
    averageCompSel="not resname ANI and not name H*").run()

Example #6

                setConstraints(k_ang.value(),
                               k_imp.value())).run()

    #
    # final torsion angle minimization
    #
    protocol.initMinimize(dyn, printInterval=50)
    dyn.run()

    #
    # final all atom minimization
    #
    protocol.initMinimize(minc, potList=potList, printInterval=100)
    minc.run()

    #
    # analyze and write out structure
    #
    print "Starting writeStructure"
    loopInfo.writeStructure(potList)


# end def

print "Starting structure loop"
StructureLoop(numStructures=numberOfStructures,
              pdbTemplate=pdbTemplate,
              structLoopAction=structLoopAction,
              genViolationStats=1,
              averagePotList=potList).run()