# parameters to ramp up during the simulated annealing protocol
#
from simulationTools import MultRamp, StaticRamp, InitialParams
rampedParams = []
highTempParams = []
# compare atomic Cartesian rmsd with a reference structure
# backbone and heavy atom RMSDs will be printed in the output
# structure files
#
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD", "name CA C N O", selection2="initial")
from noePotTools import create_NOEPot, readNEF
noe = create_NOEPot("noe", nef=nefData)
noe.setAllowOverlap(False)
noe.setShowAllRestraints(True)
potList.append(noe)
rampedParams.append(MultRamp(2, 30, "noe.setScale( VALUE )"))
import nefTools
from potList import PotList
rdcs = PotList('rdcs')
try:
rdcNames = nefTools.getBlockNames(nefData, 'rdc')
except:
rdcNames = []
pass
tensors = []
# structure files
#
# from posDiffPotTools import create_PosDiffPot
# refRMSD = create_PosDiffPot("refRMSD","name CA or name C or name N",
# pdbFile='g_xray.pdb', ## modify ##
# cmpSel="not name H*")
# set up NOE potential
noe = PotList('noe')
potList.append(noe)
from noePotTools import create_NOEPot
for (name, scale, file) in [
('all', 1, "NOE_contacts55rand_perfect.tbl"), ## modify ##
#add entries for additional tables
]:
pot = create_NOEPot(name, file)
## use soft PotType##
# pot.setPotType("soft") # if you think there may be bad NOEs
pot.setAveType(
"shortest"
) ## use shortest distance between atom selections (side chain heavy atoms)
pot.setScale(scale)
noe.append(pot)
rampedParams.append(MultRamp(2, 30, "noe.setScale( VALUE )"))
## no J couplings ##
# set up J coupling - with Karplus coefficients
##from jCoupPotTools import create_JCoupPot
##jCoup = create_JCoupPot("jcoup","jna_coup.tbl",
## A=6.98,B=-1.38,C=1.72,phase=-60.0)
##potList.append(jCoup)
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()
potList.append(noe)
# Set up dihedral angles
protocol.initDihedrals(
dihFilename,
scale=5, #initial force constant
useDefaults=0)
potList.append(XplorPot('CDIH'))
# #3) Da rescaling factor (separate multiplicative factor)
# # scale *= ( 9.9 / rdc.oTensor.Da(0) )**2
# rdc.setScale(scale)
# rdcs.append(rdc)
# pass
#potList.append(rdcs)
#rampedParams.append( MultRamp(0.01,1.0, "rdcs.setScale( VALUE )") )
# set up NOE potential
noe=PotList('noe')
potList.append(noe)
for (name,scale,file) in [('all',1,"%s_dis.tbl"%pname),
#add entries for additional tables
]:
pot = create_NOEPot(name,file)
# pot.setPotType("soft") # if you think there may be bad NOEs
pot.setScale(scale)
noe.append(pot)
rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )
# set up J coupling - with Karplus coefficients
#jCoup = create_JCoupPot("jcoup","jna_coup.tbl",
# A=6.98,B=-1.38,C=1.72,phase=-60.0)
#potList.append(jCoup)
# Set up dihedral angles
protocol.initDihedrals("%s_dih.tbl"%pname,
#useDefaults=False # by default, symmetric sidechain
# restraints are included
)
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()
potList.append(noe)
# Set up dihedral angles
protocol.initDihedrals(dihFilename,
scale=5, #initial force constant
useDefaults=0)
potList.append( XplorPot('CDIH') )