# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(1603) #set random seed - by time
command = xplor.command
# generate PSF data from sequence and initialize the correct parameters.
#
from psfGen import seqToPSF
seqToPSF('protG.seq') ## modify ##
# generate random extended initial structure with correct covalent geometry
#
protocol.genExtendedStructure()
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
from potList import PotList
potList = PotList()
# parameters to ramp up during the simulated annealing protocol
#
from simulationTools import MultRamp, StaticRamp, InitialParams, IVMAction
rampedParams = []
highTempParams = []
)
elif os.path.exists(pdbFilename):
psfGen.pdbToPSF(pdbFilename)
# protocol.initCoords(pdbFilename)
elif os.path.exists(psfFilename):
# read in the PSF file and initial structure
command("structure @%s end" % psfFilename)
protocol.initParams("protein.par", weak_omega=1)
# command("coor @gb3_xray.pdb")
else:
print "ERROR: failed to find seq or psf file in %s" % os.getcwd()
sys.exit(1)
# end if
# generate a random extended structure with correct covalent geometry
protocol.genExtendedStructure(extFilename)
#
# a PotList conatins a list of potential terms. This is used to specify which
# terms are active during refinement.
#
potList = PotList()
# set up NOE potential
noe = create_NOEPot("noe", file=noeFilename)
noe.setPotType("soft")
noe.setRSwitch(0.5)
noe.setAsympSlope(1.)
noe.setSoftExp(1.)
noe.setThreshold(0.5)
print noe.info()
# protocol module has many high-level helper functions.
#
protocol.initRandomSeed() #set random seed - by time
command = xplor.command
# generate PSF data from sequence and initialize the correct parameters.
#
#seqToPSF('%s.seq'% pname)
#Simply read the psf already generated.
xplor.command("""struct @%s.psf end""" % pname)
# generate random extended initial structure with correct covalent geometry
#
protocol.genExtendedStructure()
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
potList = PotList()
# parameters to ramp up during the simulated annealing protocol
#
rampedParams=[]
highTempParams=[]
## compare atomic Cartesian rmsd with a reference structure
## backbone and heavy atom RMSDs will be printed in the output
)
elif os.path.exists( pdbFilename ):
psfGen.pdbToPSF(pdbFilename)
# protocol.initCoords(pdbFilename)
elif os.path.exists( psfFilename ):
# read in the PSF file and initial structure
command("structure @%s end" % psfFilename)
protocol.initParams("protein.par", weak_omega=1)
# command("coor @gb3_xray.pdb")
else:
print "ERROR: failed to find seq or psf file in %s" % os.getcwd()
sys.exit(1)
# end if
# generate a random extended structure with correct covalent geometry
protocol.genExtendedStructure(extFilename)
#
# a PotList conatins a list of potential terms. This is used to specify which
# terms are active during refinement.
#
potList = PotList()
# set up NOE potential
noe = create_NOEPot("noe",file=noeFilename)
noe.setPotType( "soft" )
noe.setRSwitch( 0.5 )
noe.setAsympSlope( 1. )
noe.setSoftExp(1.)
noe.setThreshold(0.5)
print noe.info()
