def prepareNative(self, nativePdbInfo=None, resSeqMap=None):
"""do stuff"""
# Find out how many chains and extract the first if > 1
if len(nativePdbInfo.models) > 1:
raise RuntimeError, "More than 1 model."
# Check if > 1 chain
chainID = None
if len(nativePdbInfo.models[0].chains) > 1:
chainID = nativePdbInfo.models[0].chains[0]
# Assume native is standardised
# Extract the chain if > 1
nativePdbChain = ample_util.filename_append(
filename=nativePdbInfo.pdb, astr="chain{0}".format(chainID))
pdb_edit.extract_chain(nativePdbInfo.pdb, nativePdbChain, chainID)
nativePdb = nativePdbChain
else:
nativePdb = nativePdbInfo.pdb
if not resSeqMap.resSeqMatch():
# We need to create a copy of the native with numbering matching the model
nativeRenumber = ample_util.filename_append(filename=nativePdb,
astr="ren")
pdb_edit.match_resseq(targetPdb=nativePdb,
outPdb=nativeRenumber,
resMap=resSeqMap)
nativePdb = nativeRenumber
return nativePdb
def scoreOrigin(self,
origin=None,
mrPdbInfo=None,
nativePdbInfo=None,
resSeqMap=None,
workdir=os.getcwd()
):
self.workdir = workdir
if not resSeqMap.resSeqMatch():
# We need to create a copy of the placed pdb with numbering matching the native
mrPdbRes = ample_util.filename_append( filename=mrPdbInfo.pdb, astr="reseq", directory=self.workdir )
pdb_edit.match_resseq( targetPdb=mrPdbInfo.pdb, sourcePdb=None, outPdb=mrPdbRes, resMap=resSeqMap )
mrPdb = mrPdbRes
else:
mrPdb = mrPdbInfo.pdb
# Make a copy of mrPdb with chains renamed to lower case
ucChains = mrPdbInfo.models[0].chains
toChains = [ c.lower() for c in ucChains ]
mrAaPdb = ample_util.filename_append( filename=mrPdb, astr="ren", directory=self.workdir )
pdb_edit.rename_chains( inpdb=mrPdb, outpdb=mrAaPdb, fromChain=ucChains, toChain=toChains )
# The list of chains in the native that we will be checking contacts from
fromChains = nativePdbInfo.models[0].chains
mrOriginPdb = mrAaPdb
if origin != [ 0.0, 0.0, 0.0 ]:
# Move pdb to new origin
#ostr="origin{0}".format(i)
ostr="o{0}".format( origin ).replace(" ","" )
mrOriginPdb = ample_util.filename_append( filename=mrAaPdb, astr=ostr, directory=self.workdir )
pdb_edit.translate( inpdb=mrAaPdb, outpdb=mrOriginPdb, ftranslate=origin )
# Concatenate into one file
joinedPdb = ample_util.filename_append( filename=mrOriginPdb, astr="joined", directory=self.workdir )
pdb_edit.merge( pdb1=nativePdbInfo.pdb, pdb2=mrOriginPdb, pdbout=joinedPdb )
# Run ncont
data = RioData()
data.origin = origin
data.originPdb = mrOriginPdb
data.joinedPdb = joinedPdb
data.fromChains = fromChains
data.toChains = toChains
# First get AllAtom score
self.calcAllAtom( data )
# Then score RIO
self.calcRio( data )
#data.numGood = data.inregister + data.ooregister
# clean up
os.unlink(mrOriginPdb)
os.unlink(joinedPdb)
if os.path.isfile(mrAaPdb): os.unlink(mrAaPdb)
return data
def scoreOrigin(self,
origin=None,
mrPdbInfo=None,
nativePdbInfo=None,
resSeqMap=None,
workdir=os.getcwd()):
self.workdir = workdir
if not resSeqMap.resSeqMatch():
# We need to create a copy of the placed pdb with numbering matching the native
mrPdbRes = ample_util.filename_append(filename=mrPdbInfo.pdb,
astr="reseq",
directory=self.workdir)
pdb_edit.match_resseq(targetPdb=mrPdbInfo.pdb,
sourcePdb=None,
outPdb=mrPdbRes,
resMap=resSeqMap)
mrPdb = mrPdbRes
else:
mrPdb = mrPdbInfo.pdb
# Make a copy of mrPdb with chains renamed to lower case
ucChains = mrPdbInfo.models[0].chains
toChains = [c.lower() for c in ucChains]
mrAaPdb = ample_util.filename_append(filename=mrPdb,
astr="ren",
directory=self.workdir)
pdb_edit.rename_chains(inpdb=mrPdb,
outpdb=mrAaPdb,
fromChain=ucChains,
toChain=toChains)
# The list of chains in the native that we will be checking contacts from
fromChains = nativePdbInfo.models[0].chains
mrOriginPdb = mrAaPdb
if origin != [0.0, 0.0, 0.0]:
# Move pdb to new origin
#ostr="origin{0}".format(i)
ostr = "o{0}".format(origin).replace(" ", "")
mrOriginPdb = ample_util.filename_append(filename=mrAaPdb,
astr=ostr,
directory=self.workdir)
pdb_edit.translate(inpdb=mrAaPdb,
outpdb=mrOriginPdb,
ftranslate=origin)
# Concatenate into one file
joinedPdb = ample_util.filename_append(filename=mrOriginPdb,
astr="joined",
directory=self.workdir)
pdb_edit.merge(pdb1=nativePdbInfo.pdb,
pdb2=mrOriginPdb,
pdbout=joinedPdb)
# Run ncont
data = RioData()
data.origin = origin
data.originPdb = mrOriginPdb
data.joinedPdb = joinedPdb
data.fromChains = fromChains
data.toChains = toChains
# First get AllAtom score
self.calcAllAtom(data)
# Then score RIO
self.calcRio(data)
#data.numGood = data.inregister + data.ooregister
# clean up
os.unlink(mrOriginPdb)
os.unlink(joinedPdb)
if os.path.isfile(mrAaPdb): os.unlink(mrAaPdb)
return data
def findOrigin(self,
nativePdbInfo=None,
mrPdbInfo=None,
resSeqMap=None,
origins=None,
allAtom=False,
workdir=os.getcwd()):
"""Find the origin using the maximum number of contacts as metric"""
self.workdir = workdir
if not resSeqMap.resSeqMatch():
# We need to create a copy of the placed pdb with numbering matching the native
mrPdbRes = ample_util.filename_append(filename=mrPdbInfo.pdb,
astr="reseq",
directory=self.workdir)
pdb_edit.match_resseq(targetPdb=mrPdbInfo.pdb,
sourcePdb=None,
outPdb=mrPdbRes,
resMap=resSeqMap)
mrPdb = mrPdbRes
else:
mrPdb = mrPdbInfo.pdb
# Make a copy of mrPdb with chains renamed to lower case
ucChains = mrPdbInfo.models[0].chains
toChains = [c.lower() for c in ucChains]
placedAaPdb = ample_util.filename_append(filename=mrPdb,
astr="ren",
directory=self.workdir)
pdb_edit.rename_chains(inpdb=mrPdb,
outpdb=placedAaPdb,
fromChain=ucChains,
toChain=toChains)
# The list of chains in the native that we will be checking contacts from
fromChains = nativePdbInfo.models[0].chains
# Loop over origins, move the placed pdb to the new origin and then run ncont
# Object to hold data on best origin
self.data = None
for origin in origins:
placedOriginPdb = placedAaPdb
if origin != [0.0, 0.0, 0.0]:
# Move pdb to new origin
#ostr="origin{0}".format(i)
ostr = "o{0}".format(origin).replace(" ", "")
placedOriginPdb = ample_util.filename_append(
filename=placedAaPdb, astr=ostr, directory=self.workdir)
pdb_edit.translate(inpdb=placedAaPdb,
outpdb=placedOriginPdb,
ftranslate=origin)
# Concatenate into one file
joinedPdb = ample_util.filename_append(filename=placedOriginPdb,
astr="joined",
directory=self.workdir)
pdb_edit.merge(pdb1=nativePdbInfo.pdb,
pdb2=placedOriginPdb,
pdbout=joinedPdb)
# Set up object to hold data
data = RioData()
data.origin = origin
data.originPdb = placedOriginPdb
data.joinedPdb = joinedPdb
data.fromChains = fromChains
data.toChains = toChains
data.numGood = 0 # For holding the metric
# Run ncont
if allAtom:
self.calcAllAtom(data)
data.numGood = data.aaNumContacts
else:
self.calcRio(data)
data.numGood = data.rioInRegister + data.rioOoRegister
# Save the first origin and only update if we get a better score
if not self.data or data.numGood > self.data.numGood:
self.data = data
# End loop over origins
# Now need to calculate data for whichever one we didn't calculate
if allAtom:
self.calcRio(self.data)
else:
self.calcAllAtom(self.data)
if self.data.numGood > 0:
# If we got a match run csymmatch so we can see the result
csym = csymmatch.Csymmatch()
csymmatchPdb = ample_util.filename_append(
filename=self.data.originPdb,
astr="csymmatch_best",
directory=self.workdir)
csym.run(refPdb=nativePdbInfo.pdb,
inPdb=self.data.originPdb,
outPdb=csymmatchPdb,
originHand=False)
return self.data
def findOrigin(self,
nativePdbInfo=None,
mrPdbInfo=None,
resSeqMap=None,
origins=None,
allAtom=False,
workdir=os.getcwd() ):
"""Find the origin using the maximum number of contacts as metric"""
self.workdir = workdir
if not resSeqMap.resSeqMatch():
# We need to create a copy of the placed pdb with numbering matching the native
mrPdbRes = ample_util.filename_append( filename=mrPdbInfo.pdb, astr="reseq", directory=self.workdir )
pdb_edit.match_resseq( targetPdb=mrPdbInfo.pdb, sourcePdb=None, outPdb=mrPdbRes, resMap=resSeqMap )
mrPdb = mrPdbRes
else:
mrPdb = mrPdbInfo.pdb
# Make a copy of mrPdb with chains renamed to lower case
ucChains = mrPdbInfo.models[0].chains
toChains = [ c.lower() for c in ucChains ]
placedAaPdb = ample_util.filename_append( filename=mrPdb, astr="ren", directory=self.workdir )
pdb_edit.rename_chains( inpdb=mrPdb, outpdb=placedAaPdb, fromChain=ucChains, toChain=toChains )
# The list of chains in the native that we will be checking contacts from
fromChains = nativePdbInfo.models[0].chains
# Loop over origins, move the placed pdb to the new origin and then run ncont
# Object to hold data on best origin
self.data = None
for origin in origins:
placedOriginPdb = placedAaPdb
if origin != [ 0.0, 0.0, 0.0 ]:
# Move pdb to new origin
#ostr="origin{0}".format(i)
ostr="o{0}".format( origin ).replace(" ","" )
placedOriginPdb = ample_util.filename_append( filename=placedAaPdb, astr=ostr, directory=self.workdir )
pdb_edit.translate( inpdb=placedAaPdb, outpdb=placedOriginPdb, ftranslate=origin )
# Concatenate into one file
joinedPdb = ample_util.filename_append( filename=placedOriginPdb, astr="joined", directory=self.workdir )
pdb_edit.merge( pdb1=nativePdbInfo.pdb, pdb2=placedOriginPdb, pdbout=joinedPdb )
# Set up object to hold data
data = RioData()
data.origin = origin
data.originPdb = placedOriginPdb
data.joinedPdb = joinedPdb
data.fromChains = fromChains
data.toChains = toChains
data.numGood = 0 # For holding the metric
# Run ncont
if allAtom:
self.calcAllAtom( data )
data.numGood = data.aaNumContacts
else:
self.calcRio( data )
data.numGood = data.rioInRegister + data.rioOoRegister
# Save the first origin and only update if we get a better score
if not self.data or data.numGood > self.data.numGood:
self.data = data
# End loop over origins
# Now need to calculate data for whichever one we didn't calculate
if allAtom:
self.calcRio( self.data )
else:
self.calcAllAtom( self.data )
if self.data.numGood > 0:
# If we got a match run csymmatch so we can see the result
csym = csymmatch.Csymmatch()
csymmatchPdb = ample_util.filename_append( filename=self.data.originPdb,
astr="csymmatch_best",
directory=self.workdir )
csym.run( refPdb=nativePdbInfo.pdb,
inPdb=self.data.originPdb,
outPdb=csymmatchPdb,
originHand=False )
return self.data