def PlotPanel(DataDir, NativeDir = None, Prefix = None):
print 'PLOTTING PANELS'
print '---------------'
import matplotlib ; matplotlib.use('Agg')
import vis
pset_type = sys.argv[2]
OutDir = os.path.abspath(sys.argv[3])
layout = utils.getPanelLayout(pset_type)
pset = layout['pset']
NativePdbs = []
ClustPdbs = []
Labels = []
for i, p in enumerate(pset):
print 'Aligning ', p
# extract native pdb
nativepdb = utils.parseNative(p, MasterDir = NativeDir)
NativePdbs.append(nativepdb)
# see if cluster pdb is present
hasclustpdb, clustpdb = utils.hasCGData(Prefix = 'prot_'+p, OutDir = os.path.join(OutDir, p, DataDir), Key = 'clustpdb')
ClustPdbs.append(clustpdb)
# extract rmsds for labels
if not hasclustpdb: Labels.append(None)
else:
hasrmsdhist, rmsdhist = utils.hasCGData(Prefix = 'prot_'+p, OutDir = os.path.join(OutDir, p, DataDir), Key = 'rmsd')
if hasrmsdhist:
rmsdavg = np.sum(rmsdhist[0] * rmsdhist[1]) / np.sum(rmsdhist[1])
label = p + ' ' + r'$RMSD = %1.1f \AA$' % rmsdavg
Labels.append(label)
else: Labels.append(None)
# plot panel
print 'Rendering...'
vis.Panel(NativePdbs, ClustPdbs, layout['NRows'], layout['NCols'], Labels, OutDir = OutDir, PanelPrefix = Prefix)
return
# parse paths etc
OutDir = os.path.join(OutDir, PdbName)
if not os.path.isdir(OutDir): os.system('mkdir -p %s' % OutDir)
if hasPseudoGLY:
MasterDir_Native = os.path.expanduser(
'~/protein_model/native_struct/mapped_pseudoGLY')
MasterDir_AATopClust = os.path.expanduser(
'~/protein_model/native_struct/ff96_igb5_glghs_topclust_mapped_pseudoGLY'
)
else:
MasterDir_Native = os.path.expanduser(
'~/protein_model/native_struct/mapped')
MasterDir_AATopClust = os.path.expanduser(
'~/protein_model/native_struct/ff96_igb5_glghs_topclust_mapped')
NativePdb = utils.parseNative(PdbName, MasterDir=MasterDir_Native)
try:
AATopClustPdb = utils.parseNative(PdbName, MasterDir=MasterDir_AATopClust)
except IOError:
print 'Utils Error: Requested Top clust pdb does not exist'
AATopClustPdb = None
FF_File, FFMetadata = utils.parseBBFF(BBType)
Prefix = 'prot_' + PdbName
# backbone forcefield parameters
MinBondOrd = FFMetadata['MinBondOrd']
NKnot = FFMetadata['NKnot']
SPCut = FFMetadata['Cut']
Bonded_NCOSType = FFMetadata['Bonded_NCOSType']
NCOSType = FFMetadata['NCOSType']
def runExperiment():
import Go
PdbName = sys.argv[2]
FFType = sys.argv[3]
OutDir = os.path.abspath(sys.argv[4])
NReplica = int(sys.argv[5]) if len(sys.argv) > 5 else 8
# parse paths etc
OutDir = os.path.join(OutDir, PdbName)
if not os.path.isdir(OutDir): os.system('mkdir -p %s' % OutDir)
NativePdb = utils.parseNative(PdbName, MasterDir = os.path.expanduser('~/Go/native_struct/mapped'))
try:
AATopClustPdb = utils.parseNative(PdbName, MasterDir = os.path.expanduser('~/Go/native_struct/ff96_igb5_glghs_topclust_mapped'))
except IOError:
print 'Utils Error: Requested Top clust pdb does not exist'
AATopClustPdb = None
Prefix = 'prot_' + PdbName
# parse forcefield parameters
GoFF_File, FFMetadata = utils.parseGoFF(FFType)
# backbone
BBType = FFMetadata['BBType']
BBFF_File = utils.parseBBFF(BBType)[0]
MinBondOrd = FFMetadata['MinBondOrd']
NKnot = FFMetadata['NKnot']
Cut = FFMetadata['Cut']
# sidechain
NCOSType = FFMetadata['NCOSType']
GoType = FFMetadata['GoType']
NonNativeType = FFMetadata['NonNativeType']
# get LJ / spline params
# Note: NonNative params are recorded from the given
# forcefield file but not used currently, as these vary
# depending on the sequence
if not os.path.isfile(GoFF_File):
print 'I/O Error: forcefield file does not exist'
exit()
# single LJ/Sigma for all native interactions
if GoType == 1:
NativeSigma = FFMetadata['NativeSigma']
NativeEpsilon = FFMetadata['NativeEpsilon']
NativeCut = FFMetadata['NativeCut']
# LJ matrix for native interactions
if GoType == 2:
print 'Error: Not implemented yet'
exit()
# splined potential for all native interactions
if GoType == 3:
NativeKnots = FFMetadata['NativeKnots']
NativeNKnot = len(NativeKnots)
NativeCut = FFMetadata['NativeCut']
if NonNativeType == 0:
print 'Error: Will generate too much repulsion'
exit()
if NonNativeType == 1:
NonNativeSigma = FFMetadata['NonNativeSigma']
NonNativeEpsilon = FFMetadata['NonNativeEpsilon']
NonNativeCut = FFMetadata['NonNativeCut']
if NonNativeType == 2:
NonNativeKnots = FFMetadata['NonNativeKnots']
NonNativeNKnot = len(NonNativeKnots)
NonNativeCut = FFMetadata['NonNativeCut']
# temp schedule
TLow = 270.
THigh = 500.
Temps = np.logspace(np.log10(TLow), np.log10(THigh), NReplica)
TempInd = np.argmin(abs(Temps - RoomTemp))
TempSet = Temps[TempInd]
# time-step
Delta_T = FFMetadata['TimeStep'] # femto-seconds
# MD iterations
NStepsMin = int(10000 / Delta_T) # 10 ps
NStepsEquil = int(50000000 / Delta_T) # 50 ns
NStepsProd = int(20000000 / Delta_T) # 20 ns
NStepsSwap = int(1000 / Delta_T) # 1 ps
StepFreq = int(NStepsProd / 10000) # need 10000 frames, 2 ps
# REMD setup template
mdstr_setup = '''
#!/usr/bin/env python
import os, sys, numpy as np, time
import Go, utils
# check if only analysis needs to be done
FullPrefix = os.path.join(os.getcwd(), "%(PREFIX)s")
isDone = utils.checkGoREMD(FullPrefix, [%(TEMPSET)3.2f])
if isDone: exit()
#### REMD ####
# basic settings
Go.Prefix = "%(PREFIX)s"
Go.InPdb ="%(NATIVEPDB)s"
Go.Temps = np.logspace(np.log10(%(TLOW)3.2f), np.log10(%(THIGH)3.2f), %(NREPLICA)d)
Go.TempSet = %(TEMPSET)3.2f
# backbone settings
Go.MinBondOrd = %(MINBONDORD)d
Go.NKnot = %(NKNOT)d
Go.SPCut = %(CUT)g
Go.BB_forcefield_file = "%(BBFF_FILE)s"
Go.NCOSType = %(NCOSTYPE)d
# md iterations
Go.NStepsMin = %(NSTEPSMIN)d
Go.NStepsEquil = %(NSTEPSEQUIL)d
Go.NStepsProd = %(NSTEPSPROD)d
Go.NStepsSwap = %(NSTEPSSWAP)d
Go.StepFreq = %(STEPFREQ)d
'''
# side-chain interactions template
mdstr_sidechain = {
'native_LJ': '''
# native contacts
Go.GoType = 1
Go.NativeSigma = None if %(AUTOSIGMA)d else %(NATIVESIGMA)g
Go.NativeEpsilon = %(NATIVEEPSILON)g
Go.NativeCut = %(NATIVECUT)g
''',
'native_Spline': '''
# native contacts
Go.GoType = 3
Go.NativeNKnot = %(NATIVENKNOT)d
Go.NativeKnots = %(NATIVEKNOTS)s
Go.NativeCut = %(NATIVECUT)g
''',
'nonnative_LJ': '''
# non-native contacts
Go.NonNativeType = 1
Go.NonNativeSigma = %(NONNATIVESIGMA)g
Go.NonNativeEpsilon = %(NONNATIVEEPSILON)g
Go.NonNativeCut = %(NONNATIVECUT)g
''',
'nonnative_Spline': '''
# non-native contacts
Go.NonNativeType = 2
Go.NonNativeNKnot = %(NONNATIVENKNOT)d
Go.NonNativeKnots = %(NONNATIVEKNOTS)s
Go.NonNativeCut = %(NONNATIVECUT)g
'''}
# run template
mdstr_run = '''
# compile Sys object
Sys = Go.makeGoSys()
for m in Sys.Int.Methods: m.TimeStep *= %(TIMESTEP)g
# run REMD
t1 = time.time()
TrajFile, LogFile = Go.runREMD(Sys)
t2 = time.time()
# reorder by temperature only at room temp
Go.reorderTraj(ReorderTemps = [%(TEMPSET)3.2f] )
t3 = time.time()
# print stats
print "REMD time: ", (t2-t1), " seconds"
print "Reordering time: ", (t3-t2), " seconds"
'''
# job script template
jobstr = '''
#!/bin/bash
#
#$ -V
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -N %(JOBNAME)s
export PYTHONPATH=$PYTHONPATH:~/Go
date
python remd.py
mkdir -p ./NativeAnalysis
mkdir -p ./AATopClustAnalysis
python ~/Go/analyze_go.py %(NATIVEPDB)s %(PREFIX)s ./ ./NativeAnalysis
python ~/Go/analyze_go.py %(AATOPCLUSTPDB)s %(PREFIX)s ./ ./AATopClustAnalysis
date
'''
# dict for filling md script template
d_setup_run = {
'PREFIX' : Prefix,
'NATIVEPDB' : NativePdb,
'TLOW' : TLow,
'THIGH' : THigh,
'NREPLICA' : NReplica,
'TEMPSET' : TempSet,
'TEMPIND' : TempInd,
'BBFF_FILE' : BBFF_File,
'MINBONDORD' : MinBondOrd,
'NKNOT' : NKnot,
'CUT' : Cut,
'NCOSTYPE' : NCOSType,
'TIMESTEP' : Delta_T,
'NSTEPSMIN' : NStepsMin,
'NSTEPSEQUIL' : NStepsEquil,
'NSTEPSPROD' : NStepsProd,
'NSTEPSSWAP' : NStepsSwap,
'STEPFREQ' : StepFreq
}
if GoType == 1:
d_native = {
'AUTOSIGMA' : int(AutoSigma),
'NATIVESIGMA' : NativeSigma,
'NATIVEEPSILON' : NativeEpsilon,
'NATIVECUT' : NativeCut,
}
if GoType == 2:
print 'Error: Not yet implemented'
exit()
if GoType == 3:
d_native = {
'NATIVENKNOT' : NativeNKnot,
'NATIVEKNOTS' : str(NativeKnots),
'NATIVECUT' : NativeCut
}
if NonNativeType == 0:
# verified this with simulations of protein-G
print 'Error: Will generate too much non-native repulsion'
exit()
if NonNativeType == 1:
d_nonnative = {
'NONNATIVESIGMA' : NativeSigma,
'NONNATIVEEPSILON' : NativeEpsilon,
'NONNATIVECUT' : NonNativeCut,
}
if NonNativeType == 2:
d_nonnative = {
'NONNATIVENKNOT' : NonNativeNKnot,
'NONNATIVEKNOTS' : NonNativeKnots,
'NONNATIVECUT' : NonNativeCut
}
# extract complete dic
d1 = {}
for x in [d_setup_run, d_native, d_nonnative]:
for k, v in x.iteritems(): d1[k] = v
# dict for filling job script template
d2 = {'JOBNAME': Prefix, 'NATIVEPDB': NativePdb, 'AATOPCLUSTPDB': AATopClustPdb, 'PREFIX': Prefix}
# extract complete template
s = mdstr_setup
if GoType == 1:
s += mdstr_sidechain['native_LJ']
if GoType == 2:
print 'Error: Not implemented yet'
exit()
if GoType == 3:
s += mdstr_sidechain['native_Spline']
if NonNativeType == 0:
print 'Error: Will generate too much non-native repulsion'
exit()
if NonNativeType == 1:
s += mdstr_sidechain['nonnative_LJ']
if NonNativeType == 2:
s += mdstr_sidechain['nonnative_Spline']
s += mdstr_run
# fill template and submit job
print 'Using backbone type:' , BBType
print 'Using GoType: ', GoType
print 'Using Non-Native Type: ', NonNativeType
mdscript = os.path.join(OutDir, 'remd.py')
jobscript = os.path.join(OutDir, 'remdjob.sh')
if not os.path.isfile(mdscript): file(mdscript, 'w').write(s % d1)
file(jobscript, 'w').write(jobstr % d2)
os.chdir(OutDir)
os.system('qsub remdjob.sh')
os.chdir(CURRDIR)
return
def runExperiment():
import Go
PdbName = sys.argv[2]
BBType = sys.argv[3]
OutDir = os.path.abspath(sys.argv[4])
NReplica = int(sys.argv[5]) if len(sys.argv) > 5 else 8
# parse paths etc
OutDir = os.path.join(OutDir, PdbName)
if not os.path.isdir(OutDir): os.system('mkdir -p %s' % OutDir)
NativePdb = utils.parseNative(PdbName, MasterDir = os.path.expanduser('~/Go/native_struct/mapped'))
try:
AATopClustPdb = utils.parseNative(PdbName, MasterDir = os.path.expanduser('~/Go/native_struct/ff96_igb5_glghs_topclust_mapped'))
except IOError:
print 'Utils Error: Requested Top clust pdb does not exist'
AATopClustPdb = None
FF_File, FFMetadata = utils.parseBBFF(BBType)
Prefix = 'prot_' + PdbName
# parse forcefield parameters
MinBondOrd = FFMetadata['MinBondOrd']
NKnot = FFMetadata['NKnot']
Cut = FFMetadata['Cut']
# Go parameters
HarmonicFluct = np.sqrt(2.) # used to tune the force constant in s-s bias
# temp schedule
TLow = 270.
THigh = 500.
Temps = np.logspace(np.log10(TLow), np.log10(THigh), NReplica)
TempInd = np.argmin(abs(Temps - RoomTemp))
TempSet = Temps[TempInd]
# time-step
Delta_T = FFMetadata['TimeStep'] # femto-seconds
# MD iterations
NStepsMin = int(10000 / Delta_T) # 10 ps
NStepsEquil = int(50000000 / Delta_T) # 50 ns
NStepsProd = int(20000000 / Delta_T) # 20 ns
NStepsSwap = int(1000 / Delta_T) # 1 ps
StepFreq = int(NStepsProd / 10000) # need 10000 frames, 2 ps
# REMD script template
mdstr = '''
#!/usr/bin/env python
import os, sys, numpy as np, time
import Go, utils
# check if only analysis needs to be done
FullPrefix = os.path.join(os.getcwd(), "%(PREFIX)s")
isDone = utils.checkGoREMD(FullPrefix, [%(TEMPSET)3.2f])
if isDone: exit()
#### REMD ####
# basic settings
Go.Prefix = "%(PREFIX)s"
Go.InPdb ="%(NATIVEPDB)s"
Go.Temps = np.logspace(np.log10(%(TLOW)3.2f), np.log10(%(THIGH)3.2f), %(NREPLICA)d)
Go.TempSet = %(TEMPSET)3.2f
# forcefield settings
Go.MinBondOrd = %(MINBONDORD)d
Go.NKnot = %(NKNOT)d
Go.SPCut = %(CUT)g
Go.BB_forcefield_file = "%(FF_FILE)s"
# native harmonic restraints
Go.GoType = 4
Go.HarmonicFluct = %(HARMONICFLUCT)g
# no non-native interactions
Go.NonNativeType = -1
# md iterations
Go.NStepsMin = %(NSTEPSMIN)d
Go.NStepsEquil = %(NSTEPSEQUIL)d
Go.NStepsProd = %(NSTEPSPROD)d
Go.NStepsSwap = %(NSTEPSSWAP)d
Go.StepFreq = %(STEPFREQ)d
# compile Sys object
Sys = Go.makeGoSys()
for m in Sys.Int.Methods: m.TimeStep *= %(TIMESTEP)g
# run REMD
t1 = time.time()
TrajFile, LogFile = Go.runREMD(Sys)
t2 = time.time()
# reorder by temperature only at room temp
Go.reorderTraj(ReorderTemps = [%(TEMPSET)3.2f] )
t3 = time.time()
# print stats
print "REMD time: ", (t2-t1), " seconds"
print "Reordering time: ", (t3-t2), " seconds"
'''
# job script template
jobstr = '''
#!/bin/bash
#
#$ -V
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -N %(JOBNAME)s
export PYTHONPATH=$PYTHONPATH:~/Go
date
python remd.py
mkdir -p ./NativeAnalysis
mkdir -p ./AATopClustAnalysis
python ~/Go/analyze_go.py %(NATIVEPDB)s %(PREFIX)s ./ ./NativeAnalysis
python ~/Go/analyze_go.py %(AATOPCLUSTPDB)s %(PREFIX)s ./ ./AATopClustAnalysis
date
'''
# dict for filling md script template
d1 = {
'PREFIX': Prefix,
'NATIVEPDB': NativePdb,
'FF_FILE': FF_File,
'MINBONDORD': MinBondOrd,
'NKNOT' : NKnot,
'CUT' : Cut,
'HARMONICFLUCT': HarmonicFluct,
'TLOW' : TLow,
'THIGH' : THigh,
'NREPLICA': NReplica,
'TEMPSET' : TempSet,
'TEMPIND' : TempInd,
'TIMESTEP' : Delta_T,
'NSTEPSMIN': NStepsMin,
'NSTEPSEQUIL': NStepsEquil,
'NSTEPSPROD' : NStepsProd,
'NSTEPSSWAP' : NStepsSwap,
'STEPFREQ': StepFreq
}
# dict for filling job script template
d2 = {'JOBNAME': Prefix, 'NATIVEPDB': NativePdb, 'AATOPCLUSTPDB': AATopClustPdb, 'PREFIX': Prefix}
# run REMD job
print 'Using backbone type:' , BBType
print 'Using harmonic restraints on side chains of native contacts'
mdscript = os.path.join(OutDir, 'remd.py')
jobscript = os.path.join(OutDir, 'remdjob.sh')
if not os.path.isfile(mdscript): file(mdscript, 'w').write(mdstr % d1)
file(jobscript, 'w').write(jobstr % d2)
os.chdir(OutDir)
os.system('qsub remdjob.sh')
os.chdir(CURRDIR)
return