def iter_fragment_range(chain, frag_id1, frag_id2):
for frag in chain.iter_fragments():
if Structure.fragment_id_lt(frag.fragment_id, frag_id1):
continue
if Structure.fragment_id_gt(frag.fragment_id, frag_id2):
break
yield frag
def iter_fragment_range(chain, frag_id1, frag_id2):
for frag in chain.iter_fragments():
if Structure.fragment_id_lt(frag.fragment_id, frag_id1):
continue
if Structure.fragment_id_gt(frag.fragment_id, frag_id2):
break
yield frag
def copy_struct(self, struct, chain):
"""Make a copy of the argument structure to use for generating
the animation. Only copy the chain specified in chain_id.
"""
cp_struct = Structure.Structure(structure_id = struct.structure_id)
chain_id = chain.chain_id
for chain in struct.iter_chains():
## TODO: Move "200" to conf.py, 2009-06-19
if chain.chain_id == chain_id or chain.count_fragments() < 200:
include_chain = True
else:
include_chain = False
for frag in chain.iter_fragments():
## skip all waters
if frag.is_water() == True:
continue
elif frag.is_standard_residue() == True and include_chain:
for atm in iter_filter_atoms(frag.iter_atoms()):
cp_atom = Structure.Atom(
chain_id = atm.chain_id,
fragment_id = atm.fragment_id,
res_name = atm.res_name,
element = atm.element,
name = atm.name,
temp_factor = atm.temp_factor,
occupancy = atm.occupancy,
position = atm.position.copy())
cp_struct.add_atom(cp_atom, True)
elif frag.is_standard_residue() == False:
for atm in frag.iter_atoms():
cp_atom = Structure.Atom(
chain_id = atm.chain_id,
fragment_id = atm.fragment_id,
res_name = atm.res_name,
element = atm.element,
name = atm.name,
temp_factor = atm.temp_factor,
occupancy = atm.occupancy,
position = atm.position.copy())
cp_struct.add_atom(cp_atom, True)
cp_struct.sort()
return cp_struct
def segment_range_cmp(segrange1, segrange2):
"""Compare two fragment ids.
Performs a proper less than comparison of frament_id strings
according to their sequence number, then insertion code.
Split a string fragment_id into a 2-tuple of:
(sequence_num, insertion_code)
"""
return Structure.fragment_id_cmp(segrange1[0], segrange2[0])
def segment_range_cmp(segrange1, segrange2):
"""Compare two fragment ids.
Performs a proper less than comparison of frament_id strings
according to their sequence number, then insertion code.
Split a string fragment_id into a 2-tuple of:
(sequence_num, insertion_code)
"""
return Structure.fragment_id_cmp(segrange1[0], segrange2[0])
def ConstructSegmentForAnalysis(raw_chain):
"""Returns a list of Segment instance from the
Chain instance which is properly modified for use in
the this application.
"""
## Sets that atm.include attribute for each atom in the chains
## being analyzed by tlsmd
for atm in raw_chain.iter_all_atoms():
atm.include = atom_selection.calc_include_atom(atm)
## ok, use the chain but use a segment and cut off
## any leading and trailing non-amino acid residues
## do not include a fragment with no included atoms
naa = raw_chain.count_amino_acids()
nna = raw_chain.count_nucleic_acids()
if naa > nna:
iter_residues = raw_chain.iter_amino_acids()
elif nna > naa:
iter_residues = raw_chain.iter_nucleic_acids()
segment = Structure.Segment(chain_id = raw_chain.chain_id)
for frag in iter_residues:
for atm in frag.iter_all_atoms():
if atm.include:
segment.add_fragment(frag)
break
## apply data smooth if desired
if conf.globalconf.adp_smoothing > 0:
adp_smoothing.IsotropicADPDataSmoother(segment, conf.globalconf.adp_smoothing)
## this is useful: for each fragment in the minimization
## set a attribute for its index position
for i, frag in enumerate(segment.iter_fragments()):
frag.ifrag = i
## create a TLSModelAnalyzer instance for the chain, and
## attach the instance to the chain for use by the rest of the
## program
segment.tls_analyzer = tlsmdmodule.TLSModelAnalyzer()
xlist = atom_selection.chain_to_xmlrpc_list(segment.iter_all_atoms())
segment.tls_analyzer.set_xmlrpc_chain(xlist)
return segment
def calc_inertia_tensor(atom_iter):
"""Calculate moment of inertia tensor at the centroid
of the atoms.
"""
al = Structure.AtomList(atom_iter)
centroid = al.calc_centroid()
I = numpy.zeros((3, 3), float)
for atm in al:
x = atm.position - centroid
I[0, 0] += x[1]**2 + x[2]**2
I[1, 1] += x[0]**2 + x[2]**2
I[2, 2] += x[0]**2 + x[1]**2
I[0, 1] += -x[0] * x[1]
I[1, 0] += -x[0] * x[1]
I[0, 2] += -x[0] * x[2]
I[2, 0] += -x[0] * x[2]
I[1, 2] += -x[1] * x[2]
I[2, 1] += -x[1] * x[2]
evals, evecs = numpy.linalg.eig(I)
elist = [(evals[0], evecs[0]), (evals[1], evecs[1]), (evals[2], evecs[2])]
elist.sort()
R = numpy.array((elist[0][1], elist[1][1], elist[2][1]), float)
## make sure the tensor uses a right-handed coordinate system
if numpy.allclose(numpy.linalg.det(R), -1.0):
I = numpy.identity(3, float)
I[0, 0] = -1.0
R = numpy.dot(I, R)
assert numpy.allclose(numpy.linalg.det(R), 1.0)
return centroid, R
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 srlcmp(item1, item2):
return Structure.fragment_id_cmp(item1[0][0], item2[0][0])
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]))
def srlcmp(item1, item2):
return Structure.fragment_id_cmp(item1[0][0], item2[0][0])
def ConstructSegmentForAnalysis(raw_chain):
"""Returns a list of Segment instance from the Chain instance which is
properly modified for use in the this application.
"""
console.debug_stdoutln(">tlsmd_analysis->ConstructSegmentForAnalysis(chain %s)" % (
raw_chain.chain_id))
## NOTE: raw_chain = "Chain(1:A, Res(MET,1,A)...Res(VAL,50,A))"
## Sets that atm.include attribute for each atom in the chains
## being analyzed by tlsmd
for atm in raw_chain.iter_all_atoms():
#atm.include = atom_selection.calc_include_atom(atm)
atm.include = atom_selection.calc_include_atom(atm, reject_messages = True)
## ok, use the chain but use a segment and cut off
## any leading and trailing non-amino acid residues
## do not include a fragment with no included atoms
naa = nna = ota = 0
naa = raw_chain.count_amino_acids()
nna = raw_chain.count_nucleic_acids()
ota = raw_chain.count_fragments()
if naa > nna:
## Probably a protein with (possibly) some nucleic acids.
iter_residues = raw_chain.iter_amino_acids()
elif nna > naa:
## Probably a nucleic acid with (possibly) some amino acids.
iter_residues = raw_chain.iter_nucleic_acids()
if naa == 0 and nna == 0 and ota > 0:
## This chain does not have any amino or nucleic acids, so skip.
return ""
segment = Structure.Segment(chain_id = raw_chain.chain_id)
for frag in iter_residues:
for atm in frag.iter_all_atoms():
if atm.include:
segment.add_fragment(frag)
break
## apply data smooth if desired (default is "0")
if conf.globalconf.adp_smoothing > 0:
adp_smoothing.IsotropicADPDataSmoother(segment,
conf.globalconf.adp_smoothing)
## this is useful: for each fragment in the minimization
## set an attribute for its index position
for i, frag in enumerate(segment.iter_fragments()):
## NOTE (by Christoph):
## Example output:
## 0 : Res(MET,1,A)
## 1 : Res(ILE,2,A)
## ...
frag.ifrag = i
## create a TLSModelAnalyzer instance for the chain, and attach the
## instance to the chain for use by the rest of the program
segment.tls_analyzer = tlsmdmodule.TLSModelAnalyzer()
xlist = atom_selection.chain_to_xmlrpc_list(segment.iter_all_atoms())
segment.tls_analyzer.set_xmlrpc_chain(xlist)
## INPUT : raw_chain = "Chain(1:A, Res(MET,1,A)...Res(VAL,50,A))"
## OUTPUT: segment = "Segment(1:A, Res(MET,1,A)...Res(VAL,50,A))"
return segment
def segment_range_cmp(segrange1, segrange2):
return Structure.fragment_id_cmp(segrange1[0], segrange2[0])
