def test_resSeqMap3(self):
# See if we can sort out the indexing between the native and model
nativePdb = os.path.join(self.testfiles_dir,"2UUI.pdb")
modelPdb = os.path.join(self.testfiles_dir,"2UUI_S_00000001.pdb")
chainA = "2UUI_A.pdb"
pdb_edit.extract_chain( nativePdb, chainA, chainID='A' )
chainAstd = "2UUI_A_std.pdb"
pdb_edit.standardise(chainA, chainAstd)
resSeqMap = residue_map.residueSequenceMap( chainA, modelPdb )
self.assertEqual( 156, resSeqMap._lenMatch() )
nativeMask = [ False ] * 155 + [ True ]
self.assertEqual( resSeqMap.refCAlphaMask, nativeMask)
self.assertEqual( resSeqMap.ref2target(10), 16 )
self.assertEqual( resSeqMap.target2ref(155), 149 )
# Check ends match up
m1 = resSeqMap.targetResSeq[ resSeqMap.targetOffset ]
n1 = resSeqMap.target2ref( m1 )
self.assertEqual( m1, resSeqMap.ref2target(n1) )
re = resSeqMap.refResSeq[ resSeqMap.refOffset + resSeqMap.lenMatch - 1 ]
self.assertEqual( resSeqMap.ref2target( re ), resSeqMap.targetResSeq[ resSeqMap.targetOffset + resSeqMap.lenMatch - 1 ] )
os.unlink( chainA )
os.unlink( chainAstd )
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 test_resSeqMap3(self):
# See if we can sort out the indexing between the native and model
nativePdb = os.path.join(self.testfiles_dir, "2UUI.pdb")
modelPdb = os.path.join(self.testfiles_dir, "2UUI_S_00000001.pdb")
chainA = "2UUI_A.pdb"
pdb_edit.extract_chain(nativePdb, chainA, chainID='A')
chainAstd = "2UUI_A_std.pdb"
pdb_edit.standardise(chainA, chainAstd)
resSeqMap = residue_map.residueSequenceMap(chainA, modelPdb)
self.assertEqual(156, resSeqMap._lenMatch())
nativeMask = [False] * 155 + [True]
self.assertEqual(resSeqMap.refCAlphaMask, nativeMask)
self.assertEqual(resSeqMap.ref2target(10), 16)
self.assertEqual(resSeqMap.target2ref(155), 149)
# Check ends match up
m1 = resSeqMap.targetResSeq[resSeqMap.targetOffset]
n1 = resSeqMap.target2ref(m1)
self.assertEqual(m1, resSeqMap.ref2target(n1))
re = resSeqMap.refResSeq[resSeqMap.refOffset + resSeqMap.lenMatch - 1]
self.assertEqual(
resSeqMap.ref2target(re), resSeqMap.targetResSeq[resSeqMap.targetOffset + resSeqMap.lenMatch - 1]
)
os.unlink(chainA)
os.unlink(chainAstd)
def getRmsd(self,
nativePdbInfo=None,
placedPdbInfo=None,
refModelPdbInfo=None,
workdir=None,
cAlphaOnly=True):
"""For now just save lowest rmsd - can look at collecting more nativeInfo later
Currently we assume we are only given one model and that it has already been standardised.
"""
if workdir:
self.workdir = workdir
if not self.workdir:
self.workdir = os.getcwd()
self.cAlphaOnly = cAlphaOnly # Whether to only compare c-alpha atoms
# Run a pass to find the # chains
native_chains = nativePdbInfo.models[0].chains
placed_chains = placedPdbInfo.models[0].chains
rmsds = {
} # dict of rmsd -> ( chainIDnative, chainIDrefined, reforiginLogfile )
# Match each chain in native against refined and pick the best
for nativeChainID in native_chains:
if len(native_chains) == 1:
# Don't need to do owt as we are just using the native as is
nativeChainPdb = nativePdbInfo.pdb
else:
# Extract the chain from the pdb
astr = "chain{0}".format(nativeChainID)
nativeChainPdb = ample_util.filename_append(
filename=nativePdbInfo.pdb,
astr=astr,
directory=self.workdir)
pdb_edit.extract_chain(nativePdbInfo.pdb,
nativeChainPdb,
chainID=nativeChainID)
# Calculate the RefSeqMap - need to do this before we reduce to c-alphas
# The second chain may be a different composition to the first, so we only generate a traceback if we fail
# on the first chain. The model only has one chain, so the residueMap has to be the same for all the chains
try:
resSeqMap = residue_map.residueSequenceMap()
resSeqMap.fromInfo(
refInfo=nativePdbInfo,
refChainID=nativeChainID,
targetInfo=refModelPdbInfo,
targetChainID='A' # Model only has one chain
)
except RuntimeError:
if nativeChainID == native_chains[0]:
raise Exception
else:
# Only compare the first chain
break
for placedChainID in placed_chains:
# Prepare the placed PDB
placedChainPdb = self.preparePlacedPdb(
placedPdb=placedPdbInfo.pdb,
placedChainID=placedChainID,
nativeChainID=nativeChainID,
resSeqMap=resSeqMap)
# Now create a PDB with the matching atoms from native that are in refined
nativePdbMatch = ample_util.filename_append(
filename=nativeChainPdb,
astr="matched",
directory=self.workdir)
pdb_edit.keep_matching(refpdb=placedChainPdb,
targetpdb=nativeChainPdb,
outpdb=nativePdbMatch,
resSeqMap=resSeqMap)
# Now get the rmsd
astr = "chain{0}_reforigin".format(nativeChainID)
reforiginOut = ample_util.filename_append(
filename=placedChainPdb, astr=astr, directory=self.workdir)
try:
rms = self.calculate(refpdb=nativePdbMatch,
targetpdb=placedChainPdb,
outpdb=reforiginOut)
except RuntimeError as e:
logger.critical(
"GOT REFORIGIN ERROR for {0},{1},{2}\n{3}".format(
placedChainPdb, nativeChainPdb, nativeChainID, e))
rms = 99999
rmsds[rms] = (nativeChainID, placedChainID, reforiginOut)
# Clean up
os.unlink(placedChainPdb)
os.unlink(nativePdbMatch)
# Now pick the best...
rmsd = sorted(rmsds.keys())[0]
self.rmsd = rmsd
self.bestNativeChain = rmsds[rmsd][0]
self.bestPlacedChain = rmsds[rmsd][1]
self.bestReforiginPdb = rmsds[rmsd][2]
for k in rmsds.keys():
if k != rmsd:
try:
os.unlink(rmsds[k][2])
except Exception:
pass