# 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()
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()
# 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()
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()
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()
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()