def main(pdb_path, tls_out_path, calc_tls):
struct = FileIO.LoadStructure(file=pdb_path)
## calculate one set of TLS tensors from all the amino acid atoms
if calc_tls == True:
tls = TLS.TLSGroup()
for res in struct.iter_amino_acids():
for atm in res.iter_atoms():
tls.append(atm)
tls.origin = tls.calc_centroid()
tls.calc_tls_tensors()
print_TLSGroup(tls)
else:
tls_file = TLS.TLSFile()
## get TLS groups from REMARK statments in PDB file
if tls_out_path == None:
tls_file.set_file_format(TLS.TLSFileFormatPDB())
try:
tls_file.load(open(pdb_path, "r"), pdb_path)
except IOError, e:
print "[Error] %s: %s" % (str(e), pdb_path)
## or get TLS groups from REFMAC TLSOUT file
else:
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()
