def save_verify(struct, stats):
"""Save structure in all supported formats, then reload it and
compare structures.
"""
## pdb
print "[temp.pdb]"
FileIO.SaveStructure(fil="temp.pdb", struct=struct, format="PDB")
pdb_struct = FileIO.LoadStructure(fil="temp.pdb", library_bonds=True)
cmp_struct(struct, pdb_struct)
## mmCIF
print "[temp.cif]"
FileIO.SaveStructure(fil="temp.cif", struct=struct, format="CIF")
cif_struct = FileIO.LoadStructure(fil="temp.cif", library_bonds=True)
cmp_struct(struct, cif_struct)
def construct_animation(self, filename):
"""Save the animated structure to the given filename.
"""
##self.phase_assignment()
for phase in (0.5, 1.0, 0.5, 0.0, -0.5, -1.0, -0.5):
self.construct_frame(phase)
FileIO.SaveStructure(struct=self.struct, fil=filename)
def write_tls_pdb_file(self, chain, cpartition):
"""Write out a PDB file with the TLS predicted anisotropic ADPs for
this segmentation.
"""
basename = "%s_CHAIN%s_NTLS%d_UTLS" % (self.struct_id, chain.chain_id,
cpartition.num_tls_segments())
pdb_path = "%s.pdb" % (basename)
## temporarily set the atom temp_factor and U tensor to the Utls value
old_temp_factor = {}
old_U = {}
for tls in cpartition.iter_tls_segments():
for atm, Utls in tls.tls_group.iter_atm_Utls():
old_temp_factor[atm] = atm.temp_factor
old_U[atm] = atm.U
atm.temp_factor = Constants.U2B * (numpy.trace(Utls) / 3.0)
atm.U = Utls
FileIO.SaveStructure(fil=pdb_path, struct=self.struct)
## restore atom temp_factor and U
for atm, temp_factor in old_temp_factor.iteritems():
atm.temp_factor = temp_factor
atm.U = old_U[atm]
def construct_animation(self, filename, raw_r3d_filename):
"""Save the animated structure to the given filename.
"""
##self.phase_assignment()
raw_r3d_file = open(raw_r3d_filename, "w")
for phase in (0.5, 1.0, 0.5, 0.0, -0.5, -1.0, -0.5):
self.construct_frame(phase, raw_r3d_file)
FileIO.SaveStructure(struct = self.struct, fil = filename)
raw_r3d_file.close()
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 write_cwd(self):
"""Write out all the files in the report.
"""
## write a local copy of the Structure
FileIO.SaveStructure(fil=self.struct_path, struct=self.struct)
## generate small .png images so they can be placed in the
## TLS group tables to identify the TLS group tabular data
## with the generated visualization
self.init_colors()
## a report page comparing the tls group segments of all
## chains against each other
self.write_multi_chain_alignment()
## write out all TLSGraph reports
for chain in self.tlsmd_analysis.iter_chains():
self.write_tls_chain_optimization(chain)
self.write_refinement_prep()
## write out index page
self.write_index()
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"))
print "AUTHORS"
print " Jay Painter <*****@*****.**>"
if __name__ == '__main__':
if "-h" in sys.argv or "--help" in sys.argv:
usage()
sys.exit(0)
cif = "-"
pdb = "-"
if len(sys.argv) == 1:
pass
elif len(sys.argv) == 2:
cif = sys.argv[1]
elif len(sys.argv) == 3:
cif = sys.argv[1]
pdb = sys.argv[2]
else:
usage()
sys.exit(1)
if cif == "-":
cif = sys.stdin
if pdb == "-":
pdb = sys.stdout
struct = FileIO.LoadStructure(file=cif, format="CIF")
FileIO.SaveStructure(file=pdb, structure=struct, format="PDB")
print "AUTHORS"
print " Jay Painter <*****@*****.**>"
if __name__ == '__main__':
if "-h" in sys.argv or "--help" in sys.argv:
usage()
sys.exit(0)
infil = "-"
outfil = "-"
if len(sys.argv) == 1:
pass
elif len(sys.argv) == 2:
infil = sys.argv[1]
elif len(sys.argv) == 3:
infil = sys.argv[1]
outfil = sys.argv[2]
else:
usage()
sys.exit(1)
if infil == "-":
infil = sys.stdin
if outfil == "-":
outfil = sys.stdout
struct = FileIO.LoadStructure(file=infil, format="PDB")
FileIO.SaveStructure(file=outfil, structure=struct, format="CIF")
