def write_data_file(self):
"""Generate the data file and return the filename.
"""
nrows = len(self.cpartition.chain)
ncols = 1 + 3 * self.cpartition.num_tls_segments()
tbl = table.StringTable(nrows, ncols, "?")
mpred = lambda f: f.fragment_id
frag_id_iter = itertools.imap(mpred, self.cpartition.chain.iter_fragments())
tbl.set_column(0, 0, frag_id_iter)
for itls, tls in enumerate(self.cpartition.iter_tls_segments()):
tls_group = tls.tls_group
tls_info = tls.model_tls_info
O = tls_info["COR"]
for frag in tls.iter_fragments():
## FIXME: This should be able to handle either one
atm = frag.get_atom("CA") ## for amino acids
# atm = frag.get_atom("P") ## for nucleic acids
if atm is None:
continue
# if frag.get_atom("CA") is not None:
# atm = frag.get_atom("CA")
# console.stdoutln("CA_ATOM: %s" % str(atm))
# elif frag.get_atom("P") is not None:
# atm = frag.get_atom("P")
i = frag.ifrag
for n, Lx_val, Lx_vec, Lx_rho, Lx_pitch in [
(0, "L1_eigen_val", "L1_eigen_vec", "L1_rho", "L1_pitch"),
(1, "L2_eigen_val", "L2_eigen_vec", "L2_rho", "L2_pitch"),
(2, "L3_eigen_val", "L3_eigen_vec", "L3_rho", "L3_pitch"),
]:
Lval = tls_info[Lx_val]
Lvec = tls_info[Lx_vec]
Lrho = tls_info[Lx_rho]
Lpitch = tls_info[Lx_pitch]
if numpy.allclose(Lval, 0.0):
continue
dvec = TLS.calc_LS_displacement(O, Lval, Lvec, Lrho, Lpitch, atm.position, conf.ADP_PROB)
tbl[i, 1 + 3 * itls + n] = AtomMath.length(dvec)
flatfile_write(
"LibrationAnalysis: data", "LIAN", "DATA", str(tbl), self.chain.chain_id, self.cpartition.num_tls_segments()
)
open(self.txt_path, "w").write(str(tbl))
def write_data_file(self):
"""Generate the data file and return the filename.
"""
nrows = len(self.cpartition.chain)
ncols = 1 + 3 * self.cpartition.num_tls_segments()
tbl = table.StringTable(nrows, ncols, "?")
mpred = lambda f: f.fragment_id
frag_id_iter = itertools.imap(mpred, self.cpartition.chain.iter_fragments())
tbl.set_column(0, 0, frag_id_iter)
for itls, tls in enumerate(self.cpartition.iter_tls_segments()):
tls_group = tls.tls_group
tls_info = tls.model_tls_info
O = tls_info["COR"]
for frag in tls.iter_fragments():
atm = frag.get_atom("CA")
if atm is None:
continue
i = frag.ifrag
for n, Lx_val, Lx_vec, Lx_rho, Lx_pitch in [
(0, "L1_eigen_val", "L1_eigen_vec", "L1_rho", "L1_pitch"),
(1, "L2_eigen_val", "L2_eigen_vec", "L2_rho", "L2_pitch"),
(2, "L3_eigen_val", "L3_eigen_vec", "L3_rho", "L3_pitch") ]:
Lval = tls_info[Lx_val]
Lvec = tls_info[Lx_vec]
Lrho = tls_info[Lx_rho]
Lpitch = tls_info[Lx_pitch]
if numpy.allclose(Lval, 0.0):
continue
dvec = TLS.calc_LS_displacement(O, Lval, Lvec, Lrho, Lpitch, atm.position, settings.ADP_PROB)
tbl[i, 1 + 3*itls + n] = AtomMath.length(dvec)
open(self.txt_path, "w").write(str(tbl))
def calc_directional_overlap(a, b):
cos_ab = numpy.dot(a, b) / (AtomMath.length(a) * AtomMath.length(b))
if cos_ab < 0.0:
return 0.0
return abs(cos_ab)
def calc_angle(a, b):
cos_ab = numpy.dot(a, b)/ (AtomMath.length(a) * AtomMath.length(b))
return Constants.RAD2DEG * abs(math.acos(cos_ab))
