def run(nativePdb, nativeMtz=None, nativeMap=None, mrPdbs=None, outDir=None):
logging.info("Using native PDB file: %s", os.path.abspath(nativePdb))
logging.info("Using native MTZ file: %s", os.path.abspath(nativeMtz))
logging.info("Wrapping the following MTZ files to the native: %s",
" ".join(mrPdbs))
phenix = False
if outDir is not None:
if not os.path.isdir(outDir):
msg = "Cannot find output directory: {}".format(outDir)
raise RuntimeError(msg)
outDir = os.path.abspath(outDir)
else:
outDir = os.getcwd()
if phenix:
if nativeMap is None:
nativeMap = generateMap(nativePdb, nativeMtz)
if not os.path.isfile(nativeMap):
msg = "Cannot find nativeMap: {}".format(nativeMap)
raise RuntimeError(msg)
else:
shelxeExe = ample_util.find_exe('shelxe')
removables = []
for mrPdb in mrPdbs:
if phenix:
logging.debug("Searching for origin shift using: %s %s", nativeMap,
mrPdb)
origin = phenixer.ccmtzOrigin(nativeMap, mrPdb)
# offset.pdb is the mrPdb moved onto the new origin
offsetPdb = "offset.pdb"
logging.debug("Found origin: %s\nOffset pdb is: %s", origin,
offsetPdb)
else:
mrinfo = shelxe.MRinfo(shelxeExe, nativePdb, nativeMtz)
mrinfo.analyse(mrPdb)
originShift = mrinfo.originShift
logging.debug("Found origin: {0}".format(originShift))
offsetPdb = ample_util.filename_append(mrPdb,
astr='offset',
directory=os.getcwd())
pdb_edit.translate(mrPdb, offsetPdb, originShift)
csymmPdb = ample_util.filename_append(filename=mrPdb,
astr="csymmatch",
directory=outDir)
logging.debug("Running csymmatch to wrap %s onto native %s", offsetPdb,
nativePdb)
csymmatch.Csymmatch().run(refPdb=nativePdb,
inPdb=offsetPdb,
outPdb=csymmPdb,
originHand=False)
removables += [offsetPdb]
logging.info("Matched PDB is: %s", csymmPdb)
map(os.remove, removables + ["shelxe-input.hkl", "shelxe-input.ent"])
def test_shelxe_1BYZ(self):
shelxe_exe = ample_util.find_exe('shelxe' + ample_util.EXE_EXT)
pdb = os.path.join(self.testfiles_dir, "1BYZ.pdb")
mtz = os.path.join(self.testfiles_dir, "1BYZ-cad.mtz")
mrPdb = os.path.join(
self.testfiles_dir,
"1BYZ_phaser_loc0_ALL_poly_ala_trunc_0.486615_rad_1_UNMOD.1.pdb")
mrinfo = shelxe.MRinfo(shelxe_exe, pdb, mtz)
mrinfo.analyse(mrPdb)
self.assertEqual(mrinfo.originShift, [0.326, 0.19, 0.275])
# Need MRBUMP to be updated
#self.assertEqual(mrinfo.MPE,78.5)
self.assertEqual(mrinfo.wMPE, 74.5)
def test_shelxe_1D7M(self):
shelxe_exe = ample_util.find_exe('shelxe' + ample_util.EXE_EXT)
pdb = os.path.join(self.testfiles_dir, "1D7M.pdb")
mtz = os.path.join(self.testfiles_dir, "1D7M-cad.mtz")
mrPdb = os.path.join(
self.testfiles_dir,
"1D7M_phaser_loc0_ALL_SCWRL_reliable_sidechains_trunc_5.241154_rad_1_UNMOD.1.pdb"
)
mrinfo = shelxe.MRinfo(shelxe_exe, pdb, mtz)
mrinfo.analyse(mrPdb)
self.assertEqual(mrinfo.originShift, [-0.0, -0.0, 0.5])
# Need MRBUMP to be updated
#self.assertEqual(mrinfo.MPE,65.5)
self.assertEqual(mrinfo.wMPE, 57.4)
def analyse(amoptd, newroot=None):
if newroot:
assert os.path.isdir(newroot)
global _oldroot, _newroot
_newroot = newroot
_oldroot = amoptd['work_dir']
if not os.path.isdir(fixpath(amoptd['benchmark_dir'])):
os.mkdir(fixpath(amoptd['benchmark_dir']))
os.chdir(fixpath(amoptd['benchmark_dir']))
# AnalysePdb may have already been called from the main script
if amoptd['native_pdb'] and 'native_pdb_std' not in amoptd:
analysePdb(amoptd)
if amoptd['native_pdb_std']:
# Generate an SHELXE HKL and ENT file so that we can calculate phase errors
mtz_util.to_hkl(amoptd['mtz'],
hkl_file=os.path.join(amoptd['benchmark_dir'],
SHELXE_STEM + ".hkl"))
shutil.copyfile(
amoptd['native_pdb_std'],
os.path.join(amoptd['benchmark_dir'], SHELXE_STEM + ".ent"))
if amoptd['native_pdb'] and \
not (amoptd['homologs'] or amoptd['ideal_helices']
or amoptd['import_ensembles'] or amoptd['single_model_mode']):
analyseModels(amoptd)
# Get the ensembling data
if 'ensembles_data' not in amoptd or not len(amoptd['ensembles_data']):
logger.critical("Benchmark cannot find any ensemble data!")
return
# Get dict of ensemble name -> ensemble result
ensemble_results = {e['name']: e for e in amoptd['ensembles_data']}
# Get mrbump_results for cluster
if 'mrbump_results' not in amoptd or not len(amoptd['mrbump_results']):
logger.critical("Benchmark cannot find any mrbump results!")
return
data = []
mrinfo = shelxe.MRinfo(amoptd['shelxe_exe'], amoptd['native_pdb_info'].pdb,
amoptd['mtz'])
for result in amoptd['mrbump_results']:
# use mrbump dict as basis for result object
d = copy.copy(result)
# Add in the data from the ensemble
d.update(ensemble_results[d['ensemble_name']])
assert d['ensemble_name'] == d['name'], d
# Hack for old results
if 'truncation_num_residues' in d:
d['num_residues'] = d['truncation_num_residues']
del d['truncation_num_residues']
# Hack for ideal helices where num_residues are missing
if amoptd['ideal_helices'] and ('num_residues' not in d
or d['num_residues'] is None):
d['num_residues'] = int(d['ensemble_name'].lstrip('polyala'))
# Get the ensemble data and add to the MRBUMP data
d['ensemble_percent_model'] = int(
(float(d['num_residues']) / float(amoptd['fasta_length'])) * 100)
if amoptd['native_pdb']:
# Add in stuff we've cleaned from the pdb
native_keys = [
'native_pdb_code', 'native_pdb_title', 'native_pdb_resolution',
'native_pdb_solvent_content', 'native_pdb_space_group',
'native_pdb_num_chains', 'native_pdb_num_atoms',
'native_pdb_num_residues'
]
d.update({key: amoptd[key] for key in native_keys})
# Analyse the solution
analyseSolution(amoptd, d, mrinfo)
data.append(d)
# Put everything in a pandas DataFrame
dframe = pd.DataFrame(data)
# General stuff
dframe['ample_version'] = amoptd['ample_version']
dframe['fasta_length'] = amoptd['fasta_length']
# Analyse subcluster centroid models
if 'subcluster_centroid_model' in dframe.columns and amoptd['native_pdb']:
centroid_index = dframe.index
centroid_models = [
fixpath(f) for f in dframe.subcluster_centroid_model
]
native_pdb_std = fixpath(amoptd['native_pdb_std'])
fasta = fixpath(amoptd['fasta'])
# Calculation of TMscores for subcluster centroid models
if amoptd['have_tmscore']:
tm = tm_util.TMscore(amoptd['tmscore_exe'],
wdir=fixpath(amoptd['benchmark_dir']),
**amoptd)
tm_results = tm.compare_structures(centroid_models,
[native_pdb_std], [fasta])
centroid_tmscores = [r['tmscore'] for r in tm_results]
centroid_rmsds = [r['rmsd'] for r in tm_results]
else:
# Use maxcluster
centroid_tmscores = []
for centroid_model in centroid_models:
n = os.path.splitext(os.path.basename(centroid_model))[0]
cm = None
for pdb in amoptd['models']:
if n.startswith(
os.path.splitext(os.path.basename(pdb))[0]):
cm = pdb
break
if cm:
centroid_tmscores.append(_MAXCLUSTERER.tm(cm))
else:
msg = "Cannot find model for subcluster_centroid_model {0}".format(
dframe[0, 'subcluster_centroid_model'])
raise RuntimeError(msg)
# There is an issue here as this is the RMSD over the TM-aligned residues
# NOT the global RMSD, which it is for the tm_util results
centroid_rmsds = [None for _ in centroid_index]
dframe['subcluster_centroid_model_TM'] = pd.Series(
centroid_tmscores, index=centroid_index)
dframe['subcluster_centroid_model_RMSD'] = pd.Series(
centroid_rmsds, index=centroid_index)
# Save the data
file_name = os.path.join(fixpath(amoptd['benchmark_dir']), 'results.csv')
dframe.to_csv(file_name, columns=_CSV_KEYLIST, index=False, na_rep="N/A")
amoptd['benchmark_results'] = dframe.to_dict('records')
return