def fit_to_chain(self, chain):
"""Re-sets all derived information in the TLSSegment.
"""
## cut segment from chain using segment ranges
segments = []
for frag_id1, frag_id2 in self.segment_ranges:
segments.append(chain[frag_id1:frag_id2])
self.segments = segments
## put all atoms in the segment into a new TLSGroup instance
tls_group = TLS.TLSGroup()
for segment in self.segments:
for atm in segment.iter_all_atoms():
if atm.include is True:
tls_group.append(atm)
self.tls_group = tls_group
if len(self.tls_group) != self.num_atoms():
console.stderrln(
"fit_to_chain: EEK! (%s) len(self.tls_group)=%d != self.num_atoms()=%d" % (
self, len(self.tls_group), self.num_atoms()))
raise SystemExit
## fit the TLS group parameters
try:
self.fit_tls_parameters(chain)
except:
print console.formatExceptionInfo()
## helpful additions
tls_info = self.tls_group.calc_tls_info()
itls_info = TLS.calc_itls_center_of_reaction(
self.tls_group.itls_T,
self.tls_group.itls_L,
self.tls_group.itls_S,
self.tls_group.origin)
self.tls_info = tls_info
self.itls_info = itls_info
if conf.globalconf.tls_model in ["ISOT", "NLISOT"]:
self.tls_group.model = "ISOT"
self.model_tls_info = itls_info
elif conf.globalconf.tls_model in ["ANISO", "NLANISO"]:
self.tls_group.model = "ANISO"
self.model_tls_info = tls_info
try:
self.rmsd_b = tls_calcs.calc_rmsd_tls_biso(self.tls_group)
except:
print console.formatExceptionInfo()
def fit_to_chain(self, chain):
"""Re-sets all derived information in the TLSSegment.
"""
## cut segment from chain using segment ranges
segments = []
for frag_id1, frag_id2 in self.segment_ranges:
segments.append(chain[frag_id1:frag_id2])
self.segments = segments
## put all atoms in the segment into a new TLSGroup instance
tls_group = TLS.TLSGroup()
for segment in self.segments:
for atm in segment.iter_all_atoms():
if atm.include is True:
tls_group.append(atm)
self.tls_group = tls_group
if len(self.tls_group) != self.num_atoms():
console.stderrln(
"fit_to_chain: EEK! (%s) len(self.tls_group)=%d != self.num_atoms()=%d"
% (self, len(self.tls_group), self.num_atoms()))
raise SystemExit
## fit the TLS group parameters
try:
self.fit_tls_parameters(chain)
except:
print console.formatExceptionInfo()
## helpful additions
tls_info = self.tls_group.calc_tls_info()
itls_info = TLS.calc_itls_center_of_reaction(self.tls_group.itls_T,
self.tls_group.itls_L,
self.tls_group.itls_S,
self.tls_group.origin)
self.tls_info = tls_info
self.itls_info = itls_info
if conf.globalconf.tls_model in ["ISOT", "NLISOT"]:
self.tls_group.model = "ISOT"
self.model_tls_info = itls_info
elif conf.globalconf.tls_model in ["ANISO", "NLANISO"]:
self.tls_group.model = "ANISO"
self.model_tls_info = tls_info
try:
self.rmsd_b = tls_calcs.calc_rmsd_tls_biso(self.tls_group)
except:
print console.formatExceptionInfo()
def FitConstrainedTLSModel(analysis):
"""Calculates constrained TLS model for visualization.
"""
console.endln()
console.debug_stdoutln(">tlsmd_analysis->FitConstrainedTLSModel()")
console.stdoutln("CALCULATING CONSTRAINED TLS MODEL FOR VISUALIZATION")
## EAM Feb 2008 User job was getting stuck in fit_to_chain()
## Obviously it would be nice to fix the actual error, but at least we would
## like to be able to give it a swift non-fatal kick by sending SIGUSR1
signal.signal(signal.SIGUSR1, SIGUSR1_handler)
## Progress tracking
## - assume this portion of the run occupies 0.1 -> 0.5 of the total time
progress = 0.1
for chain in analysis.iter_chains():
console.stdoutln("CHAIN %s" % (chain.chain_id))
for cpartition in chain.partition_collection.iter_chain_partitions():
## cpartition.chain = "Segment(1:A, Res(MET,1,A)...Res(VAL,50,A))"
console.stdoutln("TLS GROUPS: %d" % (cpartition.num_tls_segments()))
for tls in cpartition.iter_tls_segments():
try:
tls.fit_to_chain(cpartition.chain)
## TODO: Write out data for residual plots.
#gp = gnuplots.LSQR_vs_TLS_Segments_Pre_Plot(cpartition.chain)
#console.stdoutln("FIT_TO_CHAIN_PATH: %s" % analysis.struct2_file_path)
except (RuntimeError, numpy.linalg.linalg.LinAlgError), e:
msg = " Runtime error for [%s]: %s, " % (
tls, e)
msg += "trying to continue..."
console.stdoutln(msg)
print console.formatExceptionInfo()
pass
## Track progress
progress += 0.4/analysis.num_chains()
progress_report = open("progress","w+")
print >> progress_report, progress
## progress_report.write(progress)
progress_report.close()
def LoadStructure(struct_source):
"""Loads Structure, chooses a unique struct_id string.
Also, search the REMARK records for TLS group records. If they
are found, then add the TLS group ADP magnitude to the B facors of
the ATOM records.
"""
console.debug_stdoutln(">tlsmd_analysis->LoadStructure()")
## determine the argument type
if isinstance(struct_source, str):
file_path = struct_source
console.kvformat("LOADING STRUCTURE", file_path)
fobj = open(file_path, "r")
elif hasattr(struct_source, "__iter__") and hasattr(struct_source, "seek"):
console.kvformat("LOADING STRUCTURE", str(struct_source))
fobj = struct_source
else:
raise ValueError
## TODO: Is this the same load struct used during the sanity checks? 2009-05-28
## load struct
struct = FileIO.LoadStructure(file = fobj, distance_bonds = True)
job_dir = str(os.path.dirname(str(struct_source)))
console.kvformat("HEADER", struct.header)
console.kvformat("TITLE", struct.title)
console.kvformat("EXPERIMENTAL METHOD", struct.experimental_method)
console.kvformat("PATH", job_dir)
## set the structure ID
if conf.globalconf.struct_id is not None:
struct_id = conf.globalconf.struct_id
else:
struct_id = struct.structure_id
conf.globalconf.struct_id = struct_id
struct.structure_id = struct_id
console.endln()
## if there are REFMAC5 TLS groups in the REMARK records of
## the PDB file, then add those in
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatPDB())
## return to the beginning of the file and read the REMARK/TLS records
fobj.seek(0)
tls_file.load(fobj)
if len(tls_file.tls_desc_list) > 0:
console.stdoutln("ADDING TLS GROUP Bequiv TO ATOM TEMPERATURE FACTORS")
console.stdoutln(" NUM TLS GROUPS: %d" % (
len(tls_file.tls_desc_list)))
## assume REFMAC5 groups where Utotal = Utls + Biso(temp_factor)
for tls_desc in tls_file.tls_desc_list:
try:
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
except:
print console.formatExceptionInfo()
console.stdoutln(" TLS GROUP: %s" % (tls_group.name))
for atm, Utls in tls_group.iter_atm_Utls():
bresi = atm.temp_factor
atm.temp_factor = bresi + (Constants.U2B * numpy.trace(Utls) / 3.0)
atm.U = (Constants.B2U * bresi * numpy.identity(3, float)) + Utls
console.endln()
return struct