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 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]))
