]:
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
)
potList.append(XplorPot('CDIH'))
highTempParams.append(StaticRamp("potList['CDIH'].setScale(10)"))
rampedParams.append(StaticRamp("potList['CDIH'].setScale(200)"))
# set custom values of threshold values for violation calculation
#
potList['CDIH'].setThreshold(5)
# radius of gyration term
#
#protocol.initCollapse("resid -999:999",
# Rtarget=10.16)
#potList.append( XplorPot('COLL') )
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)
# Set up dihedral angles
from xplorPot import XplorPot
dihedralRestraintFilename = "dihe_ss_1pga.tbl" ## modify, and check that if works if dihedral angles are incomplete ##
protocol.initDihedrals(
dihedralRestraintFilename,
#useDefaults=False # by default, symmetric sidechain
# restraints are included
)
potList.append(XplorPot('CDIH'))
highTempParams.append(StaticRamp("potList['CDIH'].setScale(10)"))
rampedParams.append(StaticRamp("potList['CDIH'].setScale(200)"))
# set custom values of threshold values for violation calculation
#
potList['CDIH'].setThreshold(5)
# gyration volume term
#
from gyrPotTools import create_GyrPot
gyr = create_GyrPot("Vgyr",
"resid 1:56") # selection should exclude disordered tails
potList.append(gyr)
# set up NOE potential
noe=PotList('noe')
potList.append(noe)
from noePotTools import create_NOEPot
for (name,scale,file) in [('all',1,"constraints/yourfolder/yourfoldernoe.tbl"),
#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 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
#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
)
potList.append( XplorPot('CDIH') )
highTempParams.append( StaticRamp("potList['CDIH'].setScale(10)") )
rampedParams.append( StaticRamp("potList['CDIH'].setScale(200)") )
# set custom values of threshold values for violation calculation
#
potList['CDIH'].setThreshold( 5 )
# radius of gyration term
#
#protocol.initCollapse("resid -999:999",
# Rtarget=10.16)
#potList.append( XplorPot('COLL') )
pot.setScale(scale)
noe.append(pot)
rampedParams.append(MultRamp(2, 30, "noe.setScale( VALUE )"))
### 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)
# Set up dihedral angles
from xplorPot import XplorPot
protocol.initDihedrals(
"dihe_ss_1pga.tbl",
#useDefaults=False # by default, symmetric sidechain
# restraints are included
)
potList.append(XplorPot('CDIH'))
highTempParams.append(StaticRamp("potList['CDIH'].setScale(10)"))
rampedParams.append(StaticRamp("potList['CDIH'].setScale(200)"))
# gyration volume term
#
# gyration volume term
#
from gyrPotTools import create_GyrPot
gyr = create_GyrPot("Vgyr",
"resid 1:56") # selection should exclude disordered tails
potList.append(gyr)
#
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'))
#
# setup parameters for atom-atom repulsive term. (van der Waals-like term)
#
protocol.initNBond(
nbxmod=4, # Can use 4 here, due to IVM dynamic
repel=0.5) # initial effective atom radius
potList.append(XplorPot('VDW'))
#
# annealing settings
#
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') )
#
# setup parameters for atom-atom repulsive term. (van der Waals-like term)
#
protocol.initNBond(nbxmod=4, # Can use 4 here, due to IVM dynamic
repel=0.5) # initial effective atom radius
potList.append( XplorPot('VDW') )
#
# annealing settings
#
init_t = 3500. # Need high temp and slow annealing to converge
