def test_helix5(self):
logfile = os.path.join(self.testfiles_dir, "ncont5.log")
dssplog = os.path.join(self.testfiles_dir, "3RA3.dssp")
c = rio.Rio()
contactData = rio.RioData()
c.parseNcontLog(contactData, logfile=logfile, clean_up=False)
sequence = c.helixFromContacts(contactData.contacts, dssplog)
self.assertEqual("NARLKQEIAALEYEIAAL", sequence)
def test_parse8(self):
logfile = os.path.join(self.testfiles_dir, "ncont8.log")
c = rio.Rio()
contactData = rio.RioData()
c.parseNcontLog(contactData, logfile=logfile, clean_up=False)
c.analyseRio(contactData)
self.assertEqual(contactData.numContacts, 9)
self.assertEqual(contactData.rioInRegister, 0)
self.assertEqual(contactData.rioOoRegister, 0)
self.assertEqual(contactData.rioBackwards, 0)
def analyseSolution(amoptd, d, mrinfo):
logger.info("Benchmark: analysing result: {0}".format(d['ensemble_name']))
mrPdb = None
if d['MR_program'] == "PHASER":
mrPdb = d['PHASER_pdbout']
mrMTZ = d['PHASER_mtzout']
elif d['MR_program'] == "MOLREP":
mrPdb = d['MOLREP_pdbout']
elif d['MR_program'] == "unknown":
return
if mrPdb is None or not os.path.isfile(mrPdb):
#logger.critical("Cannot find mrPdb {0} for solution {1}".format(mrPdb,d))
return
# debug - copy into work directory as reforigin struggles with long pathnames
shutil.copy(
mrPdb,
os.path.join(fixpath(amoptd['benchmark_dir']),
os.path.basename(mrPdb)))
mrPdbInfo = pdb_edit.get_info(mrPdb)
d['num_placed_chains'] = mrPdbInfo.numChains()
d['num_placed_atoms'] = mrPdbInfo.numAtoms()
d['num_placed_CA'] = mrPdbInfo.numCalpha()
if amoptd['native_pdb']:
if not d['SHELXE_os']:
logger.critical(
"mrPdb {0} has no SHELXE_os origin shift. Calculating...".
format(mrPdb))
mrinfo.analyse(mrPdb)
mrOrigin = mrinfo.originShift
d['SHELXE_MPE'] = mrinfo.MPE
d['SHELXE_wMPE'] = mrinfo.wMPE
else:
mrOrigin = [c * -1 for c in d['SHELXE_os']]
# Move pdb onto new origin
originPdb = ample_util.filename_append(mrPdb,
astr='offset',
directory=fixpath(
amoptd['benchmark_dir']))
#print(mrPdb, originPdb, mrOrigin)
pdb_edit.translate(mrPdb, originPdb, mrOrigin)
# offset.pdb is the mrModel shifted onto the new origin use csymmatch to wrap onto native
csymmatch.Csymmatch().wrapModelToNative(
originPdb,
amoptd['native_pdb'],
csymmatchPdb=os.path.join(
fixpath(amoptd['benchmark_dir']),
"phaser_{0}_csymmatch.pdb".format(d['ensemble_name'])))
# can now delete origin pdb
os.unlink(originPdb)
# Calculate phase error for the MR PDB
try:
mrinfo.analyse(mrPdb)
d['MR_MPE'] = mrinfo.MPE
d['MR_wMPE'] = mrinfo.wMPE
except Exception as e:
logger.critical("Error analysing mrPdb: {0}\n{1}".format(mrPdb, e))
# We cannot calculate the Reforigin RMSDs or RIO scores for runs where we don't have a full initial model
# to compare to the native to allow us to determine which parts of the ensemble correspond to which parts of
# the native structure.
if not (amoptd['homologs'] or \
amoptd['ideal_helices'] or \
amoptd['import_ensembles'] or \
amoptd['single_model_mode']):
# Get reforigin info
rmsder = reforigin.ReforiginRmsd()
try:
rmsder.getRmsd(nativePdbInfo=amoptd['native_pdb_info'],
placedPdbInfo=mrPdbInfo,
refModelPdbInfo=amoptd['ref_model_pdb_info'],
cAlphaOnly=True,
workdir=fixpath(amoptd['benchmark_dir']))
d['reforigin_RMSD'] = rmsder.rmsd
except Exception as e:
logger.critical("Error calculating RMSD: {0}".format(e))
d['reforigin_RMSD'] = 999
# Score the origin with all-atom and rio
rioData = rio.Rio().scoreOrigin(
mrOrigin,
mrPdbInfo=mrPdbInfo,
nativePdbInfo=amoptd['native_pdb_info'],
resSeqMap=amoptd['res_seq_map'],
workdir=fixpath(amoptd['benchmark_dir']))
# Set attributes
d['AA_num_contacts'] = rioData.aaNumContacts
d['RIO_num_contacts'] = rioData.rioNumContacts
d['RIO_in_register'] = rioData.rioInRegister
d['RIO_oo_register'] = rioData.rioOoRegister
d['RIO_backwards'] = rioData.rioBackwards
d['RIO'] = rioData.rioInRegister + rioData.rioOoRegister
d['RIO_no_cat'] = rioData.rioNumContacts - (rioData.rioInRegister +
rioData.rioOoRegister)
d['RIO_norm'] = float(d['RIO']) / float(
d['native_pdb_num_residues'])
else:
d['AA_num_contacts'] = None
d['RIO_num_contacts'] = None
d['RIO_in_register'] = None
d['RIO_oo_register'] = None
d['RIO_backwards'] = None
d['RIO'] = None
d['RIO_no_cat'] = None
d['RIO_norm'] = None
# # Now get the helix
# helixSequence = contacts.Rio().helixFromContacts( contacts=rioData.contacts,
# dsspLog=dsspLog )
# if helixSequence is not None:
# ampleResult.rioHelixSequence = helixSequence
# ampleResult.rioLenHelix = len( helixSequence )
# hfile = os.path.join( workdir, "{0}.helix".format( ampleResult.ensembleName ) )
# with open( hfile, 'w' ) as f:
# f.write( helixSequence+"\n" )
#
# This purely for checking and so we have pdbs to view
#
# Wrap shelxe trace onto native using Csymmatch
if not d['SHELXE_pdbout'] is None and os.path.isfile(
fixpath(d['SHELXE_pdbout'])):
csymmatch.Csymmatch().wrapModelToNative(
fixpath(d['SHELXE_pdbout']),
amoptd['native_pdb'],
origin=mrOrigin,
workdir=fixpath(amoptd['benchmark_dir']))
if not ('SHELXE_wMPE' in d and d['SHELXE_wMPE']):
try:
mrinfo.analyse(d['SHELXE_pdbout'])
d['SHELXE_MPE'] = mrinfo.MPE
d['SHELXE_wMPE'] = mrinfo.wMPE
except Exception as e:
logger.critical(
"Error analysing SHELXE_pdbout: {0}\n{1}".format(
d['SHELXE_pdbout'], e))
# Wrap parse_buccaneer model onto native
if d['SXRBUCC_pdbout'] and os.path.isfile(fixpath(
d['SXRBUCC_pdbout'])):
# Need to rename Pdb as is just called buccSX_output.pdb
csymmatchPdb = os.path.join(
fixpath(amoptd['benchmark_dir']),
"buccaneer_{0}_csymmatch.pdb".format(d['ensemble_name']))
csymmatch.Csymmatch().wrapModelToNative(
fixpath(d['SXRBUCC_pdbout']),
amoptd['native_pdb'],
origin=mrOrigin,
csymmatchPdb=csymmatchPdb,
workdir=fixpath(amoptd['benchmark_dir']))
# Calculate phase error
try:
mrinfo.analyse(d['SXRBUCC_pdbout'])
d['SXRBUCC_MPE'] = mrinfo.MPE
d['SXRBUCC_wMPE'] = mrinfo.wMPE
except Exception as e:
logger.critical(
"Error analysing SXRBUCC_pdbout: {0}\n{1}".format(
d['SXRBUCC_pdbout'], e))
# Wrap parse_buccaneer model onto native
if d['SXRARP_pdbout'] and os.path.isfile(fixpath(d['SXRARP_pdbout'])):
# Need to rename Pdb as is just called buccSX_output.pdb
csymmatchPdb = os.path.join(
fixpath(amoptd['benchmark_dir']),
"arpwarp_{0}_csymmatch.pdb".format(d['ensemble_name']))
csymmatch.Csymmatch().wrapModelToNative(
fixpath(d['SXRARP_pdbout']),
amoptd['native_pdb'],
origin=mrOrigin,
csymmatchPdb=csymmatchPdb,
workdir=fixpath(amoptd['benchmark_dir']))
# Calculate phase error
try:
mrinfo.analyse(d['SXRARP_pdbout'])
d['SXRARP_MPE'] = mrinfo.MPE
d['SXRARP_wMPE'] = mrinfo.wMPE
except Exception as e:
logger.critical(
"Error analysing SXRARP_pdbout: {0}\n{1}".format(
d['SXRARP_pdbout'], e))
return