def main():
usage = """
python average_atom_positions.py file1.pdb file2.pdb ...
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-a', '--all', dest='all_entries', default=False, action='store_true', help='Store all positions')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
poss = c.defaultdict(list)
sources = c.defaultdict(list)
for i,arg in enumerate(args):
cg = ftmc.from_pdb(arg)
for d in cg.defines.keys():
origin, basis = ftug.element_coord_system(cg, d)
if d[0] == 'i' or d[0] == 'm':
conn = cg.connections(d)
conn_type = cg.connection_type(d, conn)
else:
conn_type = 0
for i, r in it.izip(it.count(),
cg.define_residue_num_iterator(d)):
# add only the base atoms which are relevant to the calculation
# of the chi torsion angle
resname = cg.chain[r].resname.strip()
atoms = ftup.nonsidechain_atoms + ftup.chi_torsion_atoms[resname][-2:]
for aname in atoms:
try:
a = cg.chain[r][aname]
except KeyError as ke:
# missing an atom
continue
# The C1'->B1 and B1->B2 vectors define the plane of the base
# The O4'->C1'->B1->B2 sequence defines the torsion
# angle chi
if aname == ftup.chi_torsion_atoms[resname][-2]:
aname = 'B1'
elif aname == ftup.chi_torsion_atoms[resname][-1]:
aname = 'B2'
avec = a.get_vector().get_array()
atom_pos = ftuv.change_basis(avec - origin, basis, ftuv.standard_basis)
identifier = "%s %s %d %d %s" % (d[0],
" ".join(map(str, cg.get_node_dimensions(d))),
conn_type,
i, aname)
poss[identifier] += [atom_pos]
sources[identifier] += [d]
print "import collections as co"
if options.all_entries:
print "all_atom_poss = dict()"
for key in poss.keys():
print 'all_atom_poss["%s"] = [%s] #%d' % (key,
",".join(["[%s]" % (",".join(map(str, pos))) for pos in poss[key]]), len(poss[key]))
else:
print "avg_atom_poss = dict()"
for key in poss.keys():
pos = np.mean(poss[key], axis=0)
print 'avg_atom_poss["%s"] = [%s] #%d' % (key, ",".join(map(str, pos)), len(poss[key]))
print "sources = dict()"
for key in sources.keys():
print 'sources["%s"] = [%s]' % (key, ",".join(sources[key]))
def main():
usage = """
python average_atom_positions.py file1.pdb file2.pdb ...
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-p', '--pseudoknots', dest='pseudoknots', default=False, action='store_true', help='Allow pseudoknots in the CG structure')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
poss = c.defaultdict(list)
sources = c.defaultdict(list)
for i,arg in enumerate(args):
cg = ftmc.from_pdb(arg, remove_pseudoknots=not options.pseudoknots)
if len(list(cg.stem_iterator())) == 0:
print >>sys.stderr, "skipping {}: no stems".format(arg)
continue
for d in cg.defines.keys():
if np.allclose(cg.coords[d][0], cg.coords[d][1]):
print >>sys.stderr, "File {}: Degenerate coordinates for element: {}".format(i, d)
continue
origin, basis = ftug.element_coord_system(cg, d)
if d[0] == 'i' or d[0] == 'm':
conn = cg.connections(d)
conn_type = cg.connection_type(d, conn)
else:
conn_type = 0
for i, r in it.izip(it.count(),
cg.define_residue_num_iterator(d)):
# add only the base atoms which are relevant to the calculation
# of the chi torsion angle
resname = cg.chain[cg.seq_ids[r-1]].resname.strip()
if resname not in ftup.chi_torsion_atoms.keys():
print >>sys.stderr, "Unknown nucleotide name:", resname
continue
atoms = ftup.nonsidechain_atoms + ftup.chi_torsion_atoms[resname][-2:]
scatoms=ftup.side_chain_atoms[resname]
for aname in atoms+scatoms:
try:
a = cg.chain[cg.seq_ids[r-1]][aname]
except KeyError as ke:
# missing an atom
continue
# The C1'->B1 and B1->B2 vectors define the plane of the base
# The O4'->C1'->B1->B2 sequence defines the torsion
# angle chi
if aname == ftup.chi_torsion_atoms[resname][-2]:
aname = 'B1'
elif aname == ftup.chi_torsion_atoms[resname][-1]:
aname = 'B2'
elif aname in scatoms:
aname=resname+"."+aname
avec = a.get_vector().get_array()
atom_pos = ftuv.change_basis(avec - origin, basis, ftuv.standard_basis)
identifier = "%s %s %d %d %s" % (d[0],
" ".join(map(str, cg.get_node_dimensions(d))),
conn_type,
i, aname)
poss[identifier] += [atom_pos]
sources[identifier] += [d]
print "{}:{}".format(identifier, ",".join(map(str, atom_pos)))
def main(parser):
args = parser.parse_args()
poss = c.defaultdict(list)
sources = c.defaultdict(list)
cgs = fuc.cgs_from_args(args, rna_type="pdb", enable_logging=True)
for i, cg in enumerate(cgs):
if len(list(cg.stem_iterator())) == 0:
log.warning("Skipping RNA %s (%s): no stems", i, cg.pdb_name)
continue
for d in cg.defines.keys():
if np.allclose(cg.coords[d][0], cg.coords[d][1]):
log.warning(
"Skipping element %s of RNA %s (%s): degenerate coordinates.",
d, i, cg.pdb_name)
continue
origin, basis = ftug.element_coord_system(cg, d)
if d[0] == 'i' or d[0] == 'm':
conn = cg.connections(d)
conn_type = cg.connection_type(d, conn)
else:
conn_type = 0
for i, r in it.izip(it.count(), cg.define_residue_num_iterator(d)):
# add only the base atoms which are relevant to the calculation
# of the chi torsion angle
seq_id = cg.seq_ids[r - 1]
resname = cg.chains[seq_id.chain][seq_id.resid].resname.strip()
if resname not in ftup.chi_torsion_atoms.keys():
print("Unknown nucleotide name:", resname, file=sys.stderr)
continue
atoms = ftup.nonsidechain_atoms + \
ftup.chi_torsion_atoms[resname][-2:]
scatoms = ftup.side_chain_atoms[resname]
for aname in atoms + scatoms:
try:
resid = cg.seq_ids[r - 1]
a = cg.chains[resid.chain][resid.resid][aname]
except KeyError as ke:
# missing an atom
continue
# The C1'->B1 and B1->B2 vectors define the plane of the base
# The O4'->C1'->B1->B2 sequence defines the torsion
# angle chi
if aname == ftup.chi_torsion_atoms[resname][-2]:
aname = 'B1'
elif aname == ftup.chi_torsion_atoms[resname][-1]:
aname = 'B2'
elif aname in scatoms:
aname = resname + "." + aname
avec = a.get_vector().get_array()
atom_pos = ftuv.change_basis(avec - origin, basis,
ftuv.standard_basis)
identifier = "%s %s %d %d %s" % (d[0], " ".join(
map(str,
cg.get_node_dimensions(d))), conn_type, i, aname)
poss[identifier] += [atom_pos]
sources[identifier] += [d]
print("{}:{}".format(identifier,
",".join(map(str, atom_pos))))
def add_cg(self, cg, labels, color_modifier=1.0):
"""
:param labels: A dictionary with element names as keys
and labels as values.
"""
rna_plotter = PyMolRNA(cg.name, color_modifier)
for key in cg.coords.keys():
if self.only_elements is not None:
if key not in self.only_elements:
continue
(p, n) = cg.coords[key]
color = self.get_element_color(key)
if key[0] == 's':
try:
text = labels[key]
except KeyError:
text = key
self.add_stem_like(rna_plotter, cg, text, key, color=color)
if self.show_bounding_boxes:
self.draw_bounding_boxes(rna_plotter, cg, key)
else:
if key[0] == 'h':
if self.add_loops:
try:
text = labels[key]
except KeyError:
text = key + " " + str(cg.get_length(key))
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
elif key[0] == 'm':
twists = cg.get_twists(key)
try:
text = labels[key]
except KeyError:
# check if the multiloop is longer than one. If it's not, then
# it has an empty define and its length will be 0
if len(cg.defines[key]) == 0:
text = key + " 0"
else:
text = key + " " + \
str(cg.defines[key][1] -
cg.defines[key][0] + 1)
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
elif key[0] in 'ft':
try:
text = labels[key]
except KeyError:
text = key + " " + \
str(cg.defines[key][1] - cg.defines[key][0] + 1)
if self.visualize_three_and_five_prime:
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
elif key[0] == "i":
try:
text = labels[key]
except KeyError:
text = key
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
if self.display_virtual_residues:
for i in range(1, cg.seq_length + 1):
pos = cg.get_virtual_residue(i, True)
if cg.get_node_from_residue_num(i)[0] == "s":
c = "cyan"
else:
c = "magenta"
rna_plotter.add_sphere(pos, c, 1.)
if self.add_longrange:
for key1 in cg.longrange.keys():
for key2 in cg.longrange[key1]:
if self.only_elements is not None:
if key1 not in self.only_elements or key2 not in self.only_elements:
continue
try:
p = cuv.line_segment_distance(cg.coords[key1][0],
cg.coords[key1][1],
cg.coords[key2][0],
cg.coords[key2][1])
rna_plotter.add_dashed(p[0], p[1])
except:
continue
if self.encompassing_stems:
self.add_encompassing_cylinders(rna_plotter, cg, 7.)
if self.max_stem_distances > 0:
for (s1, s2) in it.permutations(cg.stem_iterator(), r=2):
(i1, i2) = cuv.line_segment_distance(cg.coords[s1][0],
cg.coords[s1][1],
cg.coords[s2][0],
cg.coords[s2][1])
if cuv.magnitude(i2 - i1) < self.max_stem_distances:
#self.add_segment(i1, i2, 'cyan', 0.3, s1 + " " + s2, key=key)
rna_plotter.add_segment(i1, i2, 'cyan', 0.3, key=key)
if self.virtual_atoms or self.sidechain_atoms:
cg.add_all_virtual_residues()
va = ftug.virtual_atoms(cg, sidechain=self.sidechain_atoms)
atom_width = 0.5
for i, r in enumerate(sorted(va.keys())):
for a in va[r].keys():
if self.rainbow:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
cmap = plt.get_cmap('gist_rainbow')
rna_plotter.add_sphere(va[r][a],
color=cmap(
i / float(len(va.keys()))),
width=atom_width)
else:
d = cg.get_node_from_residue_num(r)
if d[0] == 's':
if a in ftup.nonsidechain_atoms:
rna_plotter.add_sphere(va[r][a],
self.stem_color,
width=atom_width)
else:
rna_plotter.add_sphere(va[r][a],
'forest',
width=atom_width)
elif d[0] == 'i':
rna_plotter.add_sphere(va[r][a],
'yellow',
width=atom_width)
elif d[0] == 'm':
rna_plotter.add_sphere(va[r][a],
self.multiloop_color,
width=atom_width)
elif d[0] == 'h':
rna_plotter.add_sphere(va[r][a],
'blue',
width=atom_width)
if self.basis:
for d in cg.defines.keys():
origin, basis = ftug.element_coord_system(cg, d)
rna_plotter.add_segment(origin,
origin + 7. * basis[1],
'purple',
0.5,
key=key)
self.plotters.append(rna_plotter)
def coordinates_to_pymol(self, cg):
loops = list(cg.hloop_iterator())
for key in cg.coords.keys():
if self.constraints is not None:
if key not in self.constraints:
continue
(p, n) = cg.coords[key]
color = self.get_element_color(key)
if key[0] == 's':
self.add_stem_like(cg, key)
self.draw_bounding_boxes(cg, key)
else:
if key[0] == 'h':
if self.add_loops:
if key in loops:
self.add_segment(p, n, color, 1.0,
key + " " + str(cg.get_length(key)))
elif key[0] == 'm':
twists = cg.get_twists(key)
# check if the multiloop is longer than one. If it's not, then
# it has an empty define and we its length will be 1
if len(cg.defines[key]) == 0:
self.add_segment(p, n, color, 1.0,
key + " 1")
else:
self.add_segment(p, n, color, 1.0,
key + " " +
str(cg.defines[key][1] -
cg.defines[key][0] + 1))
self.add_segment(p, p+ 7 * twists[0], 'light gray', 0.3)
self.add_segment(n, n+ 7 * twists[1], 'light gray', 0.3)
x = (p + n) / 2
t = ftuv.normalize((twists[0] + twists[1]) / 2.)
self.add_segment(x, x + 7 * t, 'middle gray', 0.3)
elif key[0] == 'f':
if self.visualize_three_and_five_prime:
self.add_segment(p, n, color, 1.0,
key + " " +
str(cg.defines[key][1] -
cg.defines[key][0] + 1) + "")
elif key[0] == 't':
if self.visualize_three_and_five_prime:
self.add_segment(p, n, color, 1.0,
key + " " +
str(cg.defines[key][1] -
cg.defines[key][0]) + "")
else:
#self.add_stem_like(cg, key, "yellow", 1.0)
self.add_segment(p, n, color, 1.0, key)
if self.add_longrange:
for key1 in cg.longrange.keys():
for key2 in cg.longrange[key1]:
try:
p = cuv.line_segment_distance(cg.coords[key1][0],
cg.coords[key1][1],
cg.coords[key2][0],
cg.coords[key2][1])
(point1, point2) = p
#point1 = cg.get_point(key1)
#point2 = cg.get_point(key2)
dash_length = 0.6
gap_length = dash_length * 2
direction = ftuv.normalize(point2 - point1)
num_dashes = ftuv.magnitude(point2 - point1) / (dash_length + gap_length)
fud.pv('num_dashes')
for i in range(int(num_dashes)):
self.add_segment(point1 + i * (dash_length + gap_length) * direction,
point1 + (i * (dash_length + gap_length) + dash_length) * direction, "purple",
0.3, "")
'''
self.add_segment(point1, point2, "purple",
0.3, key1 + " " + key2)
'''
except:
continue
if self.encompassing_stems:
self.add_encompassing_cylinders(cg, 7.)
if self.max_stem_distances > 0:
for (s1, s2) in it.permutations(cg.stem_iterator(), r=2):
(i1, i2) = cuv.line_segment_distance(cg.coords[s1][0],
cg.coords[s1][1],
cg.coords[s2][0],
cg.coords[s2][1])
if cuv.magnitude(i2 - i1) < self.max_stem_distances:
#self.add_segment(i1, i2, 'cyan', 0.3, s1 + " " + s2)
self.add_segment(i1, i2, 'cyan', 0.3)
if self.virtual_atoms:
va = ftug.virtual_atoms(cg, sidechain=False)
atom_width = 0.5
for i,r in enumerate(sorted(va.keys())):
for a in va[r].keys():
if self.rainbow:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
cmap = plt.get_cmap('gist_rainbow')
self.add_sphere(va[r][a],
color_rgb = cmap(i / float(len(va.keys()))),
width=atom_width)
else:
d = cg.get_node_from_residue_num(r)
if d[0] == 's':
self.add_sphere(va[r][a], 'green', width=atom_width)
elif d[0] == 'i':
self.add_sphere(va[r][a], 'yellow', width=atom_width)
elif d[0] == 'm':
self.add_sphere(va[r][a], 'red', width=atom_width)
elif d[0] == 'h':
self.add_sphere(va[r][a], 'blue', width=atom_width)
if self.basis:
for d in cg.defines.keys():
origin, basis = ftug.element_coord_system(cg, d)
self.add_segment(origin, origin + 7. * basis[1], 'purple', 2.)
print >>sys.stderr, "energy_function:", self.energy_function
# print the contributions of the energy function, if one is specified
if self.energy_function is not None:
print >>sys.stderr, "key"
sum_energy = 0.
e_func = self.energy_function
e_func_iter = e_func.interaction_energy_iter(cg, background=False)
int_energies = list(e_func_iter)
max_energy = max(int_energies, key=lambda x: x[1])
print >>sys.stderr, "max_energy:", max_energy
for (interaction, energy) in int_energies:
(p, n) = (cg.get_point(interaction[0]),
cg.get_point(interaction[1]))
scaled_energy = - max_energy[1] + energy
self.add_segment(p, n, 'purple', 3 * np.exp(scaled_energy))
sum_energy += energy
if self.stem_stem_orientations is not None:
for (s1, s2) in it.permutations(cg.stem_iterator(), 2):
'''
if cg.are_adjacent_stems(s1, s2):
continue
'''
if s1 != 's65':
if s2 != 's65':
continue
s1_vec = cg.coords[s1][1] - cg.coords[s1][0]
s2_vec = cg.coords[s2][1] - cg.coords[s2][0]
(i1, i2) = cuv.line_segment_distance(cg.coords[s1][0],
cg.coords[s1][1],
cg.coords[s2][0],
cg.coords[s2][1])
i_vec = i2 - i1
#i_rej will be orthogonal to s1_vec in the direction
#of s2
i_rej = cuv.vector_rejection(i_vec, s1_vec)
#plane_vec will be orthogonal to s1_vec and to the direction
# of s2
plane_vec = np.cross(i_rej, s1_vec)
# s2_proj is in the intersection plane
s2_proj_in = cuv.vector_rejection(s2_vec, plane_vec)
# s2 proj_out is out of the intersection plane
#s2_proj_out = cuv.vector_rejection(s2_vec, i_rej)
start_point = cg.coords[s1][0] + 5 * cg.twists[s1][0]
ortho_offset = cuv.magnitude(i_rej)
dist = cuv.magnitude(i_vec) + 0.0001
lateral_offset = m.sqrt(dist ** 2 - ortho_offset ** 2)
if lateral_offset > 10:
continue
'''
#self.add_segment(start_point,
start_point + 10 * cuv.normalize(s2_vec),
'white', 0.5)
#self.add_segment(start_point,
start_point + 5 * cuv.normalize(plane_vec),
'magenta', 0.5)
#self.add_segment(start_point,
start_point + 5 * cuv.normalize(i_vec),
'cyan', 0.5)
#self.add_segment(i1, i1 + i_rej, 'cyan', 0.5)
'''
self.add_segment(start_point,
start_point + 7 * cuv.normalize(s2_proj_in),
'white', 1.5)
'''
def add_cg(self, cg, labels, color_modifier=1.0):
"""
:param labels: A dictionary with element names as keys
and labels as values.
"""
rna_plotter = PyMolRNA(cg.name, color_modifier)
for key in cg.coords.keys():
if self.only_elements is not None:
if key not in self.only_elements:
continue
(p, n) = cg.coords[key]
color = self.get_element_color(key)
if key[0] == 's':
try:
text = labels[key]
except KeyError:
text = key
self.add_stem_like(rna_plotter, cg, text, key, color=color)
if self.show_bounding_boxes:
self.draw_bounding_boxes(rna_plotter, cg, key)
else:
if key[0] == 'h':
if self.add_loops:
try:
text = labels[key]
except KeyError:
text = key + " " + str(cg.get_length(key))
rna_plotter.add_segment(p, n, color, self.cylinder_width,
text,
key=key)
elif key[0] == 'm':
twists = cg.get_twists(key)
try:
text = labels[key]
except KeyError:
# check if the multiloop is longer than one. If it's not, then
# it has an empty define and its length will be 0
if len(cg.defines[key]) == 0:
text = key + " 0"
else:
text = key + " " + \
str(cg.defines[key][1] -
cg.defines[key][0] + 1)
rna_plotter.add_segment(p, n, color, self.cylinder_width,
text, key=key)
elif key[0] in 'ft':
try:
text = labels[key]
except KeyError:
text = key + " " + \
str(cg.defines[key][1] - cg.defines[key][0] + 1)
if self.visualize_three_and_five_prime:
rna_plotter.add_segment(p, n, color, self.cylinder_width,
text, key=key)
elif key[0] == "i":
try:
text = labels[key]
except KeyError:
text = key
rna_plotter.add_segment(
p, n, color, self.cylinder_width, text, key=key)
if self.display_virtual_residues:
for i in range(1, cg.seq_length + 1):
pos = cg.get_virtual_residue(i, True)
if cg.get_node_from_residue_num(i)[0] == "s":
c = "cyan"
else:
c = "magenta"
rna_plotter.add_sphere(pos, c, 1.)
if self.add_longrange:
for key1 in cg.longrange.keys():
for key2 in cg.longrange[key1]:
if self.only_elements is not None:
if key1 not in self.only_elements or key2 not in self.only_elements:
continue
try:
p = cuv.line_segment_distance(cg.coords[key1][0],
cg.coords[key1][1],
cg.coords[key2][0],
cg.coords[key2][1])
rna_plotter.add_dashed(p[0], p[1])
except:
continue
if self.encompassing_stems:
self.add_encompassing_cylinders(rna_plotter, cg, 7.)
if self.max_stem_distances > 0:
for (s1, s2) in it.permutations(cg.stem_iterator(), r=2):
(i1, i2) = cuv.line_segment_distance(cg.coords[s1][0],
cg.coords[s1][1],
cg.coords[s2][0],
cg.coords[s2][1])
if cuv.magnitude(i2 - i1) < self.max_stem_distances:
#self.add_segment(i1, i2, 'cyan', 0.3, s1 + " " + s2, key=key)
rna_plotter.add_segment(i1, i2, 'cyan', 0.3, key=key)
if self.virtual_atoms or self.sidechain_atoms:
cg.add_all_virtual_residues()
va = ftug.virtual_atoms(cg, sidechain=self.sidechain_atoms)
atom_width = 0.5
for i, r in enumerate(sorted(va.keys())):
for a in va[r].keys():
if self.rainbow:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
cmap = plt.get_cmap('gist_rainbow')
rna_plotter.add_sphere(va[r][a],
color=cmap(
i / float(len(va.keys()))),
width=atom_width)
else:
d = cg.get_node_from_residue_num(r)
if d[0] == 's':
if a in ftup.nonsidechain_atoms:
rna_plotter.add_sphere(
va[r][a], self.stem_color, width=atom_width)
else:
rna_plotter.add_sphere(
va[r][a], 'forest', width=atom_width)
elif d[0] == 'i':
rna_plotter.add_sphere(
va[r][a], 'yellow', width=atom_width)
elif d[0] == 'm':
rna_plotter.add_sphere(
va[r][a], self.multiloop_color, width=atom_width)
elif d[0] == 'h':
rna_plotter.add_sphere(
va[r][a], 'blue', width=atom_width)
if self.basis:
for d in cg.defines.keys():
origin, basis = ftug.element_coord_system(cg, d)
rna_plotter.add_segment(
origin, origin + 7. * basis[1], 'purple', 0.5, key=key)
self.plotters.append(rna_plotter)
def main():
usage = """
python average_atom_positions.py file1.pdb file2.pdb ...
"""
num_args = 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-p',
'--pseudoknots',
dest='pseudoknots',
default=False,
action='store_true',
help='Allow pseudoknots in the CG structure')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
poss = c.defaultdict(list)
sources = c.defaultdict(list)
for i, arg in enumerate(args):
cg = ftmc.from_pdb(arg, remove_pseudoknots=not options.pseudoknots)
if len(list(cg.stem_iterator())) == 0:
print >> sys.stderr, "skipping {}: no stems".format(arg)
continue
for d in cg.defines.keys():
if np.allclose(cg.coords[d][0], cg.coords[d][1]):
print >> sys.stderr, "File {}: Degenerate coordinates for element: {}".format(
i, d)
continue
origin, basis = ftug.element_coord_system(cg, d)
if d[0] == 'i' or d[0] == 'm':
conn = cg.connections(d)
conn_type = cg.connection_type(d, conn)
else:
conn_type = 0
for i, r in it.izip(it.count(), cg.define_residue_num_iterator(d)):
# add only the base atoms which are relevant to the calculation
# of the chi torsion angle
resname = cg.chain[cg.seq_ids[r - 1]].resname.strip()
if resname not in ftup.chi_torsion_atoms.keys():
print >> sys.stderr, "Unknown nucleotide name:", resname
continue
atoms = ftup.nonsidechain_atoms + ftup.chi_torsion_atoms[
resname][-2:]
scatoms = ftup.side_chain_atoms[resname]
for aname in atoms + scatoms:
try:
a = cg.chain[cg.seq_ids[r - 1]][aname]
except KeyError as ke:
# missing an atom
continue
# The C1'->B1 and B1->B2 vectors define the plane of the base
# The O4'->C1'->B1->B2 sequence defines the torsion
# angle chi
if aname == ftup.chi_torsion_atoms[resname][-2]:
aname = 'B1'
elif aname == ftup.chi_torsion_atoms[resname][-1]:
aname = 'B2'
elif aname in scatoms:
aname = resname + "." + aname
avec = a.get_vector().get_array()
atom_pos = ftuv.change_basis(avec - origin, basis,
ftuv.standard_basis)
identifier = "%s %s %d %d %s" % (d[0], " ".join(
map(str,
cg.get_node_dimensions(d))), conn_type, i, aname)
poss[identifier] += [atom_pos]
sources[identifier] += [d]
print "{}:{}".format(identifier,
",".join(map(str, atom_pos)))