def write_tlsout_file(self, chain, cpartition):
"""Writes the TLSOUT file for the segmentation.
"""
basename = "%s_CHAIN%s_NTLS%d" % (self.struct_id, chain.chain_id,
cpartition.num_tls_segments())
tlsout_path = "%s.tlsout" % (basename)
struct_id = self.struct_id
chain_id = chain.chain_id
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatTLSOUT())
for tls in cpartition.iter_tls_segments():
## don't write out bypass edges
if tls.method != "TLS":
continue
tls_desc = TLS.TLSGroupDesc()
tls_file.tls_desc_list.append(tls_desc)
tls_desc.set_tls_group(tls.tls_group)
for frag_id1, frag_id2 in tls.iter_segment_ranges():
tls_desc.add_range(chain_id, frag_id1, chain_id, frag_id2,
"ALL")
tls_file.save(open(tlsout_path, "w"))
return tlsout_path
def main(path, opt_dict):
struct = FileIO.LoadStructure(file=path)
tls_group_list = []
## make the TLS groups
if opt_dict.has_key("-t"):
try:
fil = open(opt_dict["-t"], "r")
except IOError:
print "[ERROR]: TLSIN File not found %s" % (opt_dict["-t"])
sys.exit(-1)
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatTLSOUT())
tls_file.load(fil)
for tls_desc in tls_file.tls_desc_list:
tls = tls_desc.construct_tls_group_with_atoms(struct)
tls.tls_desc = tls_desc
tls_group_list.append(tls)
else:
## create one TLS group per chain by default
for chain in struct.iter_chains():
if chain.count_amino_acids() < 10:
continue
try:
chain_id1 = chain.chain_id
frag_id1 = chain[0].fragment_id
frag_id2 = chain[-1].fragment_id
except IndexError:
continue
tls_desc = TLS.TLSGroupDesc()
tls_desc.add_range(chain_id1, frag_id1, chain_id1, frag_id2, "ALL")
tls = tls_desc.construct_tls_group_with_atoms(struct)
tls_group_list.append(tls)
tls.tls_desc = tls_desc
print "Creating TLS Group: %s" % (tls.name)
## fit TLS groups and write output
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatTLSOUT())
## preform a LSQ fit if necessary
for tls in tls_group_list:
print "[TLS GROUP %s]" % (tls.name)
## if the TLS group is null, then perform a LSQ-TLS fit
if tls.is_null():
print "Null Group: Running TLS-LSQ"
if len(tls) < 20:
print "ERROR: Not Enough Atoms in TLS Group."
continue
tls.origin = tls.calc_centroid()
lsq_residual = tls.calc_TLS_least_squares_fit()
tls.shift_COR()
tls.tls_desc.set_tls_group(tls)
tls_file.tls_desc_list.append(tls.tls_desc)
if opt_dict.has_key("-o"):
print "Saving TLSIN: %s" % (opt_dict["-o"])
tls_file.save(open(opt_dict["-o"], "w"))
## write out a PDB file with 0.0 tempature factors for all
## atoms in TLS groups
if opt_dict.has_key("-p"):
for tls in tls_group_list:
for atm, Utls in tls.iter_atm_Utls():
if opt_dict.has_key("-s"):
atm.temp_factor = 0.0
atm.U = None
else:
atm.temp_factor = Constants.U2B * numpy.trace(Utls) / 3.0
atm.U = Utls
## save the struct
print "Saving XYZIN: %s" % (opt_dict["-p"])
FileIO.SaveStructure(file=opt_dict["-p"], struct=struct)
def main(path, opt_dict):
struct = FileIO.LoadStructure(file = path)
tls_group_list = []
## make the TLS groups
if opt_dict.has_key("-t"):
try:
fil = open(opt_dict["-t"], "r")
except IOError:
print "ERROR: TLSIN File not found %s" % (opt_dict["-t"])
sys.exit(-1)
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatTLSOUT())
tls_file.load(fil)
for tls_desc in tls_file.tls_desc_list:
#tls = tls_desc.generate_tls_group(struct) ## old def
tls = tls_desc.construct_tls_group_with_atoms(struct)
tls.tls_desc = tls_desc
tls_group_list.append(tls)
print tls.name
else:
tls_desc = TLS.TLSGroupDesc()
tls_desc.add_range("A", "1", "A", "25", "ALL")
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group_list.append(tls_group)
tls_group.tls_desc = tls_desc
tls_group.origin = tls_group.calc_centroid()
tls_group.T = rt_random(T1)
tls_group.L, tls_group.S = rt_random2(L1, S1)
tls_desc = TLS.TLSGroupDesc()
tls_desc.add_range("A", "26", "A", "35", "ALL")
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group_list.append(tls_group)
tls_group.tls_desc = tls_desc
tls_group.origin = tls_group.calc_centroid()
tls_group.T = rt_random(T2)
tls_group.L, tls_group.S = rt_random2(L2, S1)
tls_desc = TLS.TLSGroupDesc()
tls_desc.add_range("A", "36", "A", "52", "ALL")
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group_list.append(tls_group)
tls_group.tls_desc = tls_desc
tls_group.origin = tls_group.calc_centroid()
tls_group.T = rt_random(T3)
tls_group.L, tls_group.S = rt_random2(L3, S1)
for atm in struct.iter_all_atoms():
atm.U = None
## write out ideal TLS ANISOU records
if opt_dict.has_key("-p"):
for tls_group in tls_group_list:
for atm, Utls in tls_group.iter_atm_Utls():
atm.temp_factor = Constants.U2B * (numpy.trace(Utls) / 3.0)
atm.U = Utls
## save the struct
FileIO.SaveStructure(file = opt_dict["-p"], struct = struct)
