def makePolymerMultiSys(Seq, cfg, NSys=None, MasterPrefix=None, TempSet=None):
print Preamble()
# parse all lists
if NSys is None: NSys = len(Seq)
else:
if not isinstance(Seq, list):
Seq = [Seq] * NSys
if not isinstance(cfg, list): cfg = [cfg] * NSys
if not isinstance(TempSet, list):
if TempSet is None: TempSet = [RoomTemp] * NSys
else: TempSet = [TempSet] * NSys
# ensure that sidechains are referenced according to residue name
for i in range(NSys):
cfg[i].SSRefType = 'name'
print 'Creating %d-system polymer ensemble...' % NSys
# create the systems
pList = []
SysList = []
for i in range(NSys):
print '\nENSEMBLE SYSTEM: %d' % i
print '==================='
# set Prefix
Prefix = MasterPrefix + '_%d' % i
# create system topology
p = topo.ProteinNCOS(Seq=Seq[i], cfg=cfg[i], Prefix=Prefix)
pList.append(p)
# create Sys object
Sys = topo.MakeSys(p=p, cfg=cfg[i])
ff = []
# create backbone potentials
BB = bb.P_Backbone(p, Sys, cfg=cfg[i])
ff.extend(BB.BB_0())
# create backbone-sidechain potentials
BB_S = bb_s.P_Backbone_Sidechain(p, Sys, cfg=cfg[i])
# 1-alphabet bonded potentials
if cfg[i].Bonded_NCOSType == 0:
print 'ERROR: Multi-alphabet models not implemented yet'
exit()
if cfg[i].Bonded_NCOSType == 1: ff.extend(BB_S.BB_S_Bonded_1())
# 1-alphabet or constant repulsive nonbonded potentials
if cfg[i].NCOSType == 0:
print 'ERROR: Multi-alphabet models not implemented yet'
exit()
if cfg[i].NCOSType == 1: ff.extend(BB_S.BB_S_1())
if cfg[i].NCOSType == 2: ff.extend(BB_S.BB_S_2())
# create sidechain-sidechain potentials (1-alphabet)
SS = ss.P_Sidechain(p, Sys, cfg[i])
ff.extend(SS.SS_1())
# populate forcefield
Sys.ForceField.extend(ff)
# set up other system properties
PrepSys(Sys, TempSet=TempSet[i])
SysList.append(Sys)
# compile
if Verbose: print '\nCompiling extended ensemble model...'
for i, Sys in enumerate(SysList):
print '\nSystem: %d' % i
Sys.Load()
return pList, SysList
def makeMJGoSys(NativePdb, cfg, Prefix=None, TempSet=RoomTemp, Sigma=None):
print Preamble()
# ensure that sidechains are referenced according to residue number
cfg.SSRefType = 'number'
# create system topology
p = topo.ProteinNCOS(Pdb=NativePdb, cfg=cfg, Prefix=Prefix)
# parse native struct for native contacts in given pdb
print '\n'
ContactDict = ps.ParsePdb(p)
# create Sys object
print '\n'
Sys = topo.MakeSys(p=p, cfg=cfg)
ff = []
# create backbone potentials
BB = bb.P_Backbone(p, Sys, cfg=cfg)
print '\n'
ff.extend(BB.BB_0())
# create backbone-sidechain potentials
BB_S = bb_s.P_Backbone_Sidechain(p, Sys, cfg=cfg)
# 1-alphabet bonded potentials
print '\n'
if cfg.Bonded_NCOSType == 0:
print 'Multi-alphabet models not implemented yet'
exit()
if cfg.Bonded_NCOSType == 1: ff.extend(BB_S.BB_S_Bonded_1())
# 1-alphabet or constant repulsive nonbonded potentials
print '\n'
if cfg.NCOSType == 0:
print 'Multi-alphabet models not implemented yet'
exit()
if cfg.NCOSType == 1: ff.extend(BB_S.BB_S_1())
if cfg.NCOSType == 2: ff.extend(BB_S.BB_S_2())
# create sidechain-sidechain potentials
print '\n'
SS = ss.P_Sidechain(p, Sys, cfg=cfg, ContactDict=ContactDict)
# native contacts
print '\n'
ff.extend(SS.Go_native_MJ(Cut=cfg.NativeCut, Sigma=Sigma))
# non-native contacts
# Note: the non-native cutoff needs to be supplied carefully to be compatible
# as a WCA with the supplied sigma
print '\n'
if not cfg.NonNativeType == -1:
cfg.NonNativeType = 0
ff.extend(SS.Go_nonnative_0())
# populate forcefield
Sys.ForceField.extend(ff)
# set up other system properties
PrepSys(Sys, TempSet=TempSet)
# compile
if Verbose: print '\nCompiling model...'
Sys.Load()
return p, Sys
def makePolymerSys(Seq, cfg, Prefix=None, TempSet=RoomTemp, NChains=1):
print Preamble()
# create system topology
print '\n'
p = topo.ProteinNCOS(Seq=Seq, cfg=cfg, Prefix=Prefix)
# ensure that siechains are referenced according to residue name
cfg.SSRefType = 'name'
print '\n'
Sys = topo.MakeSys(p=p, cfg=cfg, NChains=NChains)
ff = []
# create backbone potentials
BB = bb.P_Backbone(p, Sys, cfg)
print '\n'
ff.extend(BB.BB_0())
# create backbone-sidechain potentials
BB_S = bb_s.P_Backbone_Sidechain(p, Sys, cfg)
# 1-alphabet bonded potentials
print '\n'
if cfg.Bonded_NCOSType == 0:
print 'Error: Multi-alphabet models not implemented yet'
exit()
if cfg.Bonded_NCOSType == 1: ff.extend(BB_S.BB_S_Bonded_1())
# 1-alphabet or constant repulsive nonbonded potentials
print '\n'
if cfg.NCOSType == 0:
print 'Error: Multi-alphabet models not implemented yet'
exit()
if cfg.NCOSType == 1: ff.extend(BB_S.BB_S_1())
if cfg.NCOSType == 2: ff.extend(BB_S.BB_S_2())
# create sidechain-sidechain potentials (1-alphabet)
SS = ss.P_Sidechain(p, Sys, cfg)
print '\n'
ff.extend(SS.SS_1())
# populate forcefield
Sys.ForceField.extend(ff)
# set up other system properties
PrepSys(Sys, TempSet=TempSet)
# compile
if Verbose: print '\nCompiling model...'
Sys.Load()
return p, Sys
def makeSplineGoMultiSys(NativePdb,
cfg,
NSys=None,
MasterPrefix=None,
TempSet=None):
print Preamble()
# parse all lists
if NSys is None: NSys = len(NativePdb)
else:
if not isinstance(NativePdb, list):
NativePdb = [NativePdb] * NSys
if not isinstance(cfg, list): cfg = [cfg] * NSys
if not isinstance(TempSet, list):
if TempSet is None: TempSet = [RoomTemp] * NSys
else: TempSet = [TempSet] * NSys
# ensure that sidechains are referenced according to residue number
for i in range(NSys):
cfg[i].SSRefType = 'number'
print 'Creating %d-system Go model ensemble...' % NSys
# create the systems
pList = []
SysList = []
for i in range(NSys):
print '\nENSEMBLE SYSTEM: %d' % i
print '==================='
# set Prefix
Prefix = MasterPrefix + '_%d' % i
# create system topology
p = topo.ProteinNCOS(Pdb=NativePdb[i], cfg=cfg[i], Prefix=Prefix)
pList.append(p)
# parse native struct for native contacts in given pdb
ps.Verbose = False
ContactDict = ps.ParsePdb(p)
# create Sys object
Sys = topo.MakeSys(p=p, cfg=cfg[i])
ff = []
# create backbone potentials
BB = bb.P_Backbone(p, Sys, cfg=cfg[i])
ff.extend(BB.BB_0())
# create backbone-sidechain potentials
BB_S = bb_s.P_Backbone_Sidechain(p, Sys, cfg=cfg[i])
# 1-alphabet bonded potentials
if cfg[i].Bonded_NCOSType == 0:
print 'ERROR: Multi-alphabet models not implemented yet'
exit()
if cfg[i].Bonded_NCOSType == 1: ff.extend(BB_S.BB_S_Bonded_1())
# 1-alphabet or constant repulsive nonbonded potentials
if cfg[i].NCOSType == 0:
print 'ERROR: Multi-alphabet models not implemented yet'
exit()
if cfg[i].NCOSType == 1: ff.extend(BB_S.BB_S_1())
if cfg[i].NCOSType == 2: ff.extend(BB_S.BB_S_2())
# create sidechain-sidechain potentials
SS = ss.P_Sidechain(p, Sys, cfg=cfg[i], ContactDict=ContactDict)
# native contacts
cfg[i].NativeType = 1
ff.extend(SS.Go_native_1(Cut=cfg[i].NativeCut))
# non-native contacts
# Note: the non-native cutoff needs to be supplied carefully to be compatible
# as a WCA with the supplied sigma
if not cfg[i].NonNativeType == -1:
cfg[i].NonNativeType = 0
ff.extend(SS.Go_nonnative_0())
# populate forcefield
Sys.ForceField.extend(ff)
# set up other system properties
PrepSys(Sys, TempSet=TempSet[i])
SysList.append(Sys)
# compile
if Verbose: print '\nCompiling extended ensemble model...'
for i, Sys in enumerate(SysList):
print '\nSystem: %d' % i
Sys.Load()
return pList, SysList
def makeHarmonicGoSys(NativePdb, cfg, Prefix=None, TempSet=RoomTemp):
print Preamble()
# map NativePdb to polymer
if cfg.Map2Polymer:
print '\n'
PdbName = NativePdb.split('/')[-1].split('.pdb')[0]
AAPdb = os.path.join(NATIVEPATH['Unmapped'], PdbName + '.pdb')
MappedPdb = mapNCOS.Map2Polymer(Pdb=NativePdb,
PolyName=cfg.PolyName,
AAPdb=AAPdb,
hasPseudoGLY=cfg.hasPseudoGLY())
# ensure that sidechains are referenced according to residue number
cfg.SSRefType = 'number'
# create system topology
print '\n'
p = topo.ProteinNCOS(Pdb=NativePdb, cfg=cfg, Prefix=Prefix)
# parse native struct for native contacts in given pdb
print '\n'
ContactDict = ps.ParsePdb(p)
# using these native contacts get distances between contact sidechains in the polymer-mapped Pdb
if cfg.Map2Polymer:
print '\n'
print 'Repopulating native contact database with intra-sidechain distances from %s mapped sequence' % cfg.PolyName.upper(
)
p_Mapped = topo.ProteinNCOS(Pdb=MappedPdb,
cfg=cfg,
Prefix=Prefix +
'_map2%s' % cfg.PolyName.lower())
MappedContactDict = ps.ParsePdb(
p_Mapped, ResContactList=ContactDict['ResContactList'])
ContactDict = MappedContactDict
# bond sidechains of native contacts for harmonic restraints
# must be done prior to creating the Sys object
print '\n'
p.BondNativeContacts(ContactDict)
# create Sys object
print '\n'
Sys = topo.MakeSys(p=p, cfg=cfg)
ff = []
# create backbone potentials
BB = bb.P_Backbone(p, Sys, cfg=cfg)
print '\n'
ff.extend(BB.BB_0())
# create backbone-sidechain potentials
BB_S = bb_s.P_Backbone_Sidechain(p, Sys, cfg=cfg)
# 1-alphabet bonded potentials
print '\n'
if cfg.Bonded_NCOSType == 0:
print 'Error: Multi-alphabet models not implemented yet'
exit()
if cfg.Bonded_NCOSType == 1: ff.extend(BB_S.BB_S_Bonded_1())
# constant repulsive nonbonded potentials
print '\n'
if cfg.NCOSType == 0:
print 'Error: Multi-alphabet models not implemented yet'
exit()
if cfg.NCOSType == 1: ff.extend(BB_S.BB_S_1())
if cfg.NCOSType == 2: ff.extend(BB_S.BB_S_2())
# create sidechain-sidechain potentials
print '\n'
SS = ss.P_Sidechain(p, Sys, cfg=cfg, ContactDict=ContactDict)
# harmonic restraints between native contacts
print '\n'
cfg.NativeType = 2
ff.extend(
SS.Go_native_2(FConst=cfg.NativeFConst,
HarmonicFluct=cfg.NativeHarmonicFluct))
# populate forcefield
Sys.ForceField.extend(ff)
# set up other system properties
PrepSys(Sys, TempSet=TempSet)
# compile
if Verbose: print '\nCompiling model...'
Sys.Load()
return p, Sys