def calc_superposition(self, tls):
plist = []
msd = 0.0
segment = tls.segment
for frag1 in segment.iter_fragments():
try:
frag2 = self.srctgt_equiv[frag1]
except KeyError:
continue
for name in const.SUPER_ATOMS:
atm1 = frag1.get_atom(name)
atm2 = frag2.get_atom(name)
if atm1 == None or atm2 == None:
console.stdoutln("EEK! No Equivalent Atom %s" % (atm1))
continue
plist.append((atm1.position, atm2.align_position))
d = atm1.position - atm2.align_position
msd += numpy.dot(d, d)
rmsd_pre_alignment = math.sqrt(msd / len(plist))
tls.rmsd_pre_alignment = rmsd_pre_alignment
sresult = Superposition.SuperimposePositions(plist)
tls.sresult = sresult
rotation = math.degrees(2.0 * math.acos(sresult.Q[0]))
if rotation > 180.0:
rotation = 360.0 - rotation
fragstr = "%s:%s-%s" % (self.chain.chain_id, tls.frag_id1,
tls.frag_id2)
console.stdoutln(
"TLS Group::%20s Num Atoms::%4d RMSD PRE ALIGN::%6.2f RMSD::%6.2f TRANSORM ROTATION::%6.2f"
%
(fragstr, len(plist), rmsd_pre_alignment, sresult.rmsd, rotation))
## screw displacement vector
vscrew = AtomMath.normalize(
numpy.array([sresult.Q[1], sresult.Q[2], sresult.Q[3]], float))
console.stdoutln("superposition rotation vector: %s" % (vscrew))
tls.superposition_vscrew = vscrew * rotation
## fit the isotropic TLS model to the group
evals, evecs = numpy.linalg.eig(tls.tls_group.itls_L)
for i in (0, 1, 2):
eval = evals[i]
evec = evecs[i]
lname = "L%d_eigen_val" % (i)
if (eval * Constants.RAD2DEG2) < 1.0:
continue
ang = min(calc_angle(evec, vscrew), calc_angle(-evec, vscrew))
console.stdoutln("%s magnitude::%6.2f vector angle::%6.2f" %
(lname, eval * Constants.RAD2DEG2, ang))
def calc_superposition(self, tls):
plist = []
msd = 0.0
segment = tls.segment
for frag1 in segment.iter_fragments():
try:
frag2 = self.srctgt_equiv[frag1]
except KeyError:
continue
for name in SUPER_ATOMS:
atm1 = frag1.get_atom(name)
atm2 = frag2.get_atom(name)
if atm1 == None or atm2 == None:
console.stdoutln("EEK! No Equivalent Atom %s" % (atm1))
continue
plist.append((atm1.position, atm2.align_position))
d = atm1.position - atm2.align_position
msd += numpy.dot(d,d)
rmsd_pre_alignment = math.sqrt(msd / len(plist))
tls.rmsd_pre_alignment = rmsd_pre_alignment
sresult = Superposition.SuperimposePositions(plist)
tls.sresult = sresult
rotation = math.degrees(2.0 * math.acos(sresult.Q[0]))
if rotation > 180.0:
rotation = 360.0 - rotation
fragstr = "%s:%s-%s" % (self.chain.chain_id, tls.frag_id1, tls.frag_id2)
console.stdoutln(
"TLS Group::%20s Num Atoms::%4d RMSD PRE ALIGN::%6.2f RMSD::%6.2f TRANSORM ROTATION::%6.2f" % (
fragstr, len(plist), rmsd_pre_alignment, sresult.rmsd, rotation))
## screw displacement vector
vscrew = AtomMath.normalize(numpy.array([sresult.Q[1],sresult.Q[2],sresult.Q[3]], float))
console.stdoutln("superposition rotation vector: %s" % (vscrew))
tls.superposition_vscrew = vscrew * rotation
## fit the isotropic TLS model to the group
evals, evecs = numpy.linalg.eig(tls.tls_group.itls_L)
for i in (0,1,2):
eval = evals[i]
evec = evecs[i]
lname = "L%d_eigen_val" % (i)
if (eval * Constants.RAD2DEG2) < 1.0:
continue
ang = min(calc_angle(evec, vscrew), calc_angle(-evec, vscrew))
console.stdoutln("%s magnitude::%6.2f vector angle::%6.2f" % (
lname, eval*Constants.RAD2DEG2, ang))
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 displace_model(self, model, tls, phase):
"""Displace the given model by the tls.
"""
tls_info = tls.model_tls_info
cor = tls_info["COR"]
for n, Lx_rmsd, Lx_vec, Lx_rho, Lx_pitch in [
(1, "L1_rmsd", "L1_eigen_vec", "L1_rho", "L1_pitch"),
(2, "L2_rmsd", "L2_eigen_vec", "L2_rho", "L2_pitch"),
(3, "L3_rmsd", "L3_eigen_vec", "L3_rho", "L3_pitch")
]:
Lrmsd = tls_info[Lx_rmsd]
Lvec = tls_info[Lx_vec]
Lrho = tls_info[Lx_rho]
Lpitch = tls_info[Lx_pitch]
## pre-calculations for screw displacement
Lorigin = cor + Lrho
Lrot = Gaussian.GAUSS3C[settings.ADP_PROB] * Lrmsd * phase
D = AtomMath.dmatrixu(Lvec, Lrot)
d_screw = (Lrot * Lpitch) * Lvec
if n == 1:
chain_id = self.L1_chain.chain_id
elif n == 2:
chain_id = self.L2_chain.chain_id
elif n == 3:
chain_id = self.L3_chain.chain_id
chain = model.get_chain(chain_id)
for frag_id1, frag_id2 in tls.iter_segment_ranges():
for frag in Structure.iter_fragments(chain.iter_fragments(),
frag_id1, frag_id2):
for atm in frag.iter_atoms():
d = numpy.dot(D, atm.position - Lorigin) + d_screw
atm.position += d
def displace_model(self, model, tls, phase):
"""Displace the given model by the tls.
"""
tls_info = tls.model_tls_info
cor = tls_info["COR"]
for n, Lx_rmsd, Lx_vec, Lx_rho, Lx_pitch in [
(1, "L1_rmsd", "L1_eigen_vec", "L1_rho", "L1_pitch"),
(2, "L2_rmsd", "L2_eigen_vec", "L2_rho", "L2_pitch"),
(3, "L3_rmsd", "L3_eigen_vec", "L3_rho", "L3_pitch") ]:
Lrmsd = tls_info[Lx_rmsd]
Lvec = tls_info[Lx_vec]
Lrho = tls_info[Lx_rho]
Lpitch = tls_info[Lx_pitch]
## pre-calculations for screw displacement
Lorigin = cor + Lrho
Lrot = Gaussian.GAUSS3C[settings.ADP_PROB] * Lrmsd * phase
D = AtomMath.dmatrixu(Lvec, Lrot)
d_screw = (Lrot * Lpitch) * Lvec
if n==1:
chain_id = self.L1_chain.chain_id
elif n==2:
chain_id = self.L2_chain.chain_id
elif n==3:
chain_id = self.L3_chain.chain_id
chain = model.get_chain(chain_id)
for frag_id1, frag_id2 in tls.iter_segment_ranges():
for frag in Structure.iter_fragments(chain.iter_fragments(), frag_id1, frag_id2):
for atm in frag.iter_atoms():
d = numpy.dot(D, atm.position - Lorigin) + d_screw
atm.position += d
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))
def rt_random2(T1, T2):
theta = (random.random() - 0.5) * math.pi
R = AtomMath.rmatrixu(random_vec(), theta)
T1R = numpy.dot(numpy.dot(R, T1), numpy.transpose(R))
T2R = numpy.dot(numpy.dot(R, T2), numpy.transpose(R))
return T1, T2
def rt_random(T):
theta = (random.random() - 0.5) * math.pi
R = AtomMath.rmatrixu(random_vec(), theta)
return numpy.dot(numpy.dot(R, T), numpy.transpose(R))
def random_vec():
rcoord = lambda: random.random() - 0.5
return AtomMath.normalize(numpy.array([rcoord(), rcoord(), rcoord()], float))
def displace_model(self, model, tls, phase, which_ntls, raw_r3d_file):
"""Displace the given model by the tls.
"""
tls_info = tls.model_tls_info
cor = tls_info["COR"]
## figure out which libration eigenvalue is the largest and
## use that value in the animation. Christoph Champ, 2008-08-15
L1_val = float(tls_info["L1_eigen_val"]) * Constants.RAD2DEG2
L2_val = float(tls_info["L2_eigen_val"]) * Constants.RAD2DEG2
L3_val = float(tls_info["L3_eigen_val"]) * Constants.RAD2DEG2
max_libration = 0.00
for val in L1_val, L2_val, L3_val:
if val >= max_libration:
max_libration = val
for n, Lx_rmsd, Lx_val, Lx_vec, Lx_rho, Lx_pitch in [
(1, "L1_rmsd", "L1_eigen_val", "L1_eigen_vec", "L1_rho", "L1_pitch"),
(2, "L2_rmsd", "L2_eigen_val", "L2_eigen_vec", "L2_rho", "L2_pitch"),
(3, "L3_rmsd", "L3_eigen_val", "L3_eigen_vec", "L3_rho", "L3_pitch") ]:
Lrmsd = tls_info[Lx_rmsd]
Lvec = tls_info[Lx_vec]
Lrho = tls_info[Lx_rho]
Lpitch = tls_info[Lx_pitch]
Lval = tls_info[Lx_val] * Constants.RAD2DEG2
## pre-calculations for screw displacement
Lorigin = cor + Lrho
Lrot = Gaussian.GAUSS3C[conf.ADP_PROB] * Lrmsd * phase
D = AtomMath.dmatrixu(Lvec, Lrot)
d_screw = (Lrot * Lpitch) * Lvec
## TODO: Add max(L) chain_id to ANIMATE.txt, 2009-08-06
if n == 1:
chain_id = self.L1_chain.chain_id
elif n == 2:
chain_id = self.L2_chain.chain_id
elif n == 3:
chain_id = self.L3_chain.chain_id
chain = model.get_chain(chain_id)
for frag_id1, frag_id2 in tls.iter_segment_ranges():
for frag in Structure.iter_fragments(chain.iter_fragments(), frag_id1, frag_id2):
for atm in frag.iter_atoms():
d = numpy.dot(D, atm.position - Lorigin) + d_screw
atm.position += d
atm.temp_factor = float(which_ntls)
atm.element = str(model.model_id)
## raw input file for tlsanim2r3d->Raster3D
## E.g., "1 0 A 0 0 7.069 -24.991 -2.991"
if Lval == max_libration:
raw_r3d_file.write("1 ")
else:
raw_r3d_file.write("0 ")
raw_r3d_file.write("%s %s %s %s %.3f %.3f %.3f\n" % (
model.model_id, self.L1_chain.chain_id,
which_ntls, n,
atm.position[0], atm.position[1], atm.position[2]))