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 random_vec():
rcoord = lambda: random.random() - 0.5
return AtomMath.normalize(numpy.array([rcoord(), rcoord(), rcoord()], float))
