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(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 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.
"""
## 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
## load struct
struct = FileIO.LoadStructure(file = fobj, distance_bonds = True)
console.kvformat("HEADER", struct.header)
console.kvformat("TITLE", struct.title)
console.kvformat("EXPERIMENTAL METHOD", struct.experimental_method)
## 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:
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
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
def refmac_pure_tls_prep(xyzin, tlsin_list, wilson, xyzout, tlsout):
"""Use TLS model (without Uiso) for each atom. Output xyzout with the
B-factors reset to either the Bmean or the Wilson B value.
"""
## load structure
struct = FileIO.LoadStructure(fil=xyzin)
## load and construct TLS groups
tls_group_list = []
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatPureTLSOUT())
tls_file_format = TLS.TLSFileFormatPureTLSOUT()
for tlsin in tlsin_list:
tls_desc_list = tls_file_format.load(open(tlsin, "r"))
for tls_desc in tls_desc_list:
tls_file.tls_desc_list.append(tls_desc)
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group.tls_desc = tls_desc
tls_group_list.append(tls_group)
## set the extra Uiso for each atom
for tls_group in tls_group_list:
Bmean = 0.0
sum_Biso = 0.0
num_atms = 0
for atm, Utls in tls_group.iter_atm_Utls():
num_atms += 1
sum_Biso += atm.temp_factor
## EAM Aug 2011: num_atms goes to zero if there are atom selection problems.
## The output files will contain empty groups, but at least it doesn't crash.
if num_atms > 0:
Bmean = sum_Biso / num_atms
## reset the TLS tensor values in the TLSDesc object so they can be
## saved
tls_group.tls_desc.set_tls_group(tls_group)
## reset atm.temp_factor to the Bmean for this TLS group
for atm, Utls in tls_group.iter_atm_Utls():
atm.temp_factor = Bmean
atm.temp_factor = wilson
## save the new xyzout file with temp_factors reset to "wilson" value
FileIO.SaveStructure(fil=xyzout, struct=struct)
## save the REFMAC-format file, but without T, L, S, and ORIGIN values
tls_file.save(open(tlsout, "w"))
def phenix_prep(xyzin, phenix_tlsin_list, phenix_tlsout):
"""PHENIX input file. Tells 'phenix.refine' what the TLS groups are.
"""
## load structure
struct = FileIO.LoadStructure(fil=xyzin)
## load and construct TLS groups
tls_group_list = []
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatPHENIX())
tls_file_format = TLS.TLSFileFormatPHENIX()
for tlsin in phenix_tlsin_list:
tls_desc_list = tls_file_format.load(open(tlsin, "r"))
for tls_desc in tls_desc_list:
tls_file.tls_desc_list.append(tls_desc)
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group.tls_desc = tls_desc
tls_group_list.append(tls_group)
## now save the PHENIX file in phenix.refine format
tls_file.save(open(phenix_tlsout, "w"))
def main(tlsin, struct_in, struct_out):
struct = FileIO.LoadStructure(file=struct_in)
## make the TLS groups
fil = open(tlsin, "r")
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatTLSOUT())
tls_file.load(fil)
tls_group_list = []
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)
print tls.origin
for tls in tls_group_list:
for atm, Utls in tls.iter_atm_Utls():
atm.U = Utls + (Constants.B2U * atm.temp_factor *
numpy.identity(3, float))
atm.temp_factor = Constants.U2B * (numpy.trace(atm.U) / 3.0)
## save the struct
FileIO.SaveStructure(file=struct_out, 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.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)
def refmac5_prep(xyzin, tlsin_list, xyzout, tlsout):
"""Use TLS model + Uiso for each atom. Output xyzout with the
residual Uiso only.
"""
## load structure
struct = FileIO.LoadStructure(fil = xyzin)
## load and construct TLS groups
tls_group_list = []
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatTLSOUT())
tls_file_format = TLS.TLSFileFormatTLSOUT()
for tlsin in tlsin_list:
tls_desc_list = tls_file_format.load(open(tlsin, "r"))
for tls_desc in tls_desc_list:
tls_file.tls_desc_list.append(tls_desc)
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group.tls_desc = tls_desc
tls_group_list.append(tls_group)
## set the extra Uiso for each atom
for tls_group in tls_group_list:
## minimal/maximal amount of Uiso which has to be added
## to the group's atoms to to make Uiso == Uiso_tls
min_Uiso = 0.0
max_Uiso = 0.0
for atm, Utls in tls_group.iter_atm_Utls():
tls_tf = numpy.trace(Utls) / 3.0
ref_tf = numpy.trace(atm.get_U()) / 3.0
if ref_tf > tls_tf:
max_Uiso = max(ref_tf - tls_tf, max_Uiso)
else:
min_Uiso = max(tls_tf - ref_tf, min_Uiso)
## reduce the TLS group T tensor by min_Uiso so that
## a PDB file can be written out where all atoms
## Uiso == Uiso_tls
## we must rotate the T tensor to its primary axes before
## subtracting min_Uiso magnitude from it
(T_eval, TR) = numpy.linalg.eig(tls_group.T)
T = numpy.dot(TR, numpy.dot(tls_group.T, numpy.transpose(TR)))
assert numpy.allclose(T[0,1], 0.0)
assert numpy.allclose(T[0,2], 0.0)
assert numpy.allclose(T[1,2], 0.0)
T[0,0] = T[0,0] - min_Uiso
T[1,1] = T[1,1] - min_Uiso
T[2,2] = T[2,2] - min_Uiso
## now take some of the smallest principal component of T and
## move it into the individual atomic temperature factors
min_T = min(T[0,0], min(T[1,1], T[2,2]))
sub_T = min_T * 0.50
add_Uiso = min_T - sub_T
T[0,0] = T[0,0] - sub_T
T[1,1] = T[1,1] - sub_T
T[2,2] = T[2,2] - sub_T
## rotate T back to original orientation
tls_group.T = numpy.dot(
numpy.transpose(TR),
numpy.dot(T, TR))
## reset the TLS tensor values in the TLSDesc object so they can be saved
tls_group.tls_desc.set_tls_group(tls_group)
## set atm.temp_factor
for atm, Utls in tls_group.iter_atm_Utls():
tls_tf = numpy.trace(Utls) / 3.0
ref_tf = numpy.trace(atm.get_U()) / 3.0
if ref_tf > tls_tf:
atm.temp_factor = ((add_Uiso) + ref_tf - tls_tf)*Constants.U2B
atm.U = None
else:
atm.temp_factor = (add_Uiso) * Constants.U2B
atm.U = None
FileIO.SaveStructure(fil = xyzout, struct = struct)
tls_file.save(open(tlsout, "w"))
