def setUp(self):
try:
cg, = ftmc.CoarseGrainRNA.from_pdb('test/forgi/threedee/data/1y26.pdb', annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("Requires MC-Annotate")
# cg.defines['s0']==[1,9,63,71]
self.va1 = ftug.virtual_atoms(cg, sidechain=False)
self.va2 = ftug.virtual_atoms(cg, sidechain=True)
def setUp(self):
try:
cg, = ftmc.CoarseGrainRNA.from_pdb(
'test/forgi/threedee/data/1y26.pdb',
annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("Requires MC-Annotate")
# cg.defines['s0']==[1,9,63,71]
self.va1 = ftug.virtual_atoms(cg, sidechain=False)
self.va2 = ftug.virtual_atoms(cg, sidechain=True)
def showvirtualAtoms(filename):
sm=get_sm(filename)
cg=sm.bg
clash_energy=fbe.StemVirtualResClashEnergy()
clash_energy.eval_energy(sm)
forJson={ "virtual_atoms":[]}
virtualAtoms = ftug.virtual_atoms(sm.bg, sidechain=True)
for residuePos in virtualAtoms.keys():
stem=cg.get_node_from_residue_num(residuePos)
if stem[0]!="s": continue #Only virtual res for stems!
residue=virtualAtoms[residuePos]
for aname in residue.keys():
isClashing=False
if stem in clash_energy.bad_bulges:
for clashing in clash_energy.bad_atoms[stem]:
if np.allclose(residue[aname], clashing):
isClashing=True
break;
atomInfo={
"atomname":aname,
"center":residue[aname].tolist(),
"is_clashing":isClashing,
"loop": stem
}
forJson["virtual_atoms"].append(atomInfo)
return jsonify(forJson)
def showvirtualAtoms(filename):
sm = get_sm(filename)
cg = sm.bg
clash_energy = fbe.StemVirtualResClashEnergy()
clash_energy.eval_energy(sm)
forJson = {"virtual_atoms": []}
virtualAtoms = ftug.virtual_atoms(sm.bg, sidechain=True)
for residuePos in virtualAtoms.keys():
stem = cg.get_node_from_residue_num(residuePos)
if stem[0] != "s": continue #Only virtual res for stems!
residue = virtualAtoms[residuePos]
for aname in residue.keys():
isClashing = False
if stem in clash_energy.bad_bulges:
for clashing in clash_energy.bad_atoms[stem]:
if np.allclose(residue[aname], clashing):
isClashing = True
break
atomInfo = {
"atomname": aname,
"center": residue[aname].tolist(),
"is_clashing": isClashing,
"loop": stem
}
forJson["virtual_atoms"].append(atomInfo)
return jsonify(forJson)
def reconstruct_from_average(sm):
'''
Reconstruct a molecule using the average positions of each atom in
the elements comprising this structure.
@param sm: A SpatialModel.
'''
atoms = ftug.virtual_atoms(sm.bg, given_atom_names = None)
c = bpdbc.Chain(' ')
anum = 1
for d in sm.bg.defines:
for rnum in sm.bg.define_residue_num_iterator(d):
rname = " " + sm.bg.seq[rnum-1]
r = bpdbr.Residue((' ', rnum, ' '), rname, ' ')
for aname in atoms[rnum]:
atom = bpdba.Atom(aname, atoms[rnum][aname], 0., 1., ' ', aname, 1)
r.add(atom)
c.add(r)
return c
def setUp(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
# cg.defines['s0']==[1,9,63,71]
self.va1 = ftug.virtual_atoms(cg, sidechain=False)
self.va2 = ftug.virtual_atoms(cg, sidechain=True)
def main():
usage = """
./visualize_cg.py cg_file
Display the coarse-grain representation of a structure in pymol.
"""
num_args = 1
parser = OptionParser(usage=usage)
# parser.add_option('-u', '--useless', dest='uselesss',
# default=False, action='store_true', help='Another useless option')
parser.add_option('-g',
'--highlight',
dest='highlight',
default=None,
help="Highlight some elements",
type='str')
parser.add_option('-o',
'--output',
dest='output',
default=None,
help="Create a picture of the scene and exit",
type='str')
parser.add_option('-r',
'--longrange',
dest='longrange',
default=False,
action='store_true',
help="Display long-range interactions")
parser.add_option('-l',
'--loops',
dest='loops',
default=True,
action='store_false',
help="Don't display the coarse-grain hairpin loops")
parser.add_option('-c',
'--cones',
dest='cones',
default=False,
action='store_true',
help="Display cones that portrude from the stems")
parser.add_option('-x',
'--text',
dest='text',
default=False,
action='store_true',
help="Add labels to the figure.")
parser.add_option('-a',
'--align',
dest='align',
default=False,
action='store_true',
help='Align all of the structures with the first')
parser.add_option(
'-e',
'--encompassing-stems',
dest='encompassing_stems',
default=False,
action='store_true',
help='Show the big stems that encompass the colinear ones.')
parser.add_option('-v',
'--virtual-atoms',
dest='virtual_atoms',
default=False,
action='store_true',
help='Display the virtual atoms')
parser.add_option('-d',
'--distance',
dest='distance',
default=None,
help="Draw the lines between specified virtual residues")
parser.add_option('-b',
'--basis',
dest='basis',
default=False,
action='store_true',
help='Display the coordinate basis of each element')
parser.add_option('',
'--batch',
dest='batch',
default=False,
action='store_true',
help='Start pymol in batch mode')
parser.add_option(
'',
'--sidechain-atoms',
dest='sidechain_atoms',
default=False,
action='store_true',
help=
'Include the sidechain atoms. Automatically enables --virtual-atoms')
parser.add_option(
'',
'--rainbow',
dest='rainbow',
default=False,
action='store_true',
help=
'Color each of the nucleotide positions (i.e. average atoms) according to the colors of \
the rainbow and their position')
parser.add_option('',
'--only-elements',
dest='only_elements',
default=None,
help='Display only these elements '
'element names should be '
'separated by commas')
parser.add_option('',
'--color-gradual',
dest='color_gradual',
default=None,
help='Color the specified elements'
'gradually from one to the other, example (i1,i4,m1)',
type='str')
(options, args) = parser.parse_args()
print "hi"
if len(args) < num_args:
parser.print_help()
sys.exit(1)
print "hi1"
pp = cvp.PymolPrinter()
pp.add_loops = options.loops
pp.draw_cones = options.cones
# sys.exit(1)
pp.add_longrange = options.longrange
pp.print_text = options.text
pp.encompassing_stems = options.encompassing_stems
pp.virtual_atoms = options.virtual_atoms
pp.sidechain_atoms = options.sidechain_atoms
pp.basis = options.basis
pp.rainbow = options.rainbow
if options.only_elements is not None:
pp.only_elements = options.only_elements.split(',')
cgs = []
for a in args:
cgs += [cmg.CoarseGrainRNA(a)]
if options.align:
align_cgs(cgs)
if options.color_gradual is not None:
pp.element_specific_colors = dict()
import matplotlib.pyplot as plt
cmap = plt.get_cmap('coolwarm')
for d in cgs[0].defines:
pp.element_specific_colors[d] = 'black'
to_color_nodes = options.color_gradual.split(',')
for i, node in enumerate(to_color_nodes):
print node, cmap(i / float(len(to_color_nodes)))
pp.element_specific_colors[node] = cmap(i /
float(len(to_color_nodes)))
for i, cg in enumerate(cgs):
if i > 0:
pp.color_modifier = .3
#pp.override_color = 'middle gray'
pp.coordinates_to_pymol(cg)
# highlight things in purple
if options.highlight is not None:
for s in options.highlight.split(','):
fud.pv('s')
pp.add_twists = False
pp.add_stem_like(cg, s, color='purple', width=3.)
# display the distances between nucleotides
if options.distance is not None:
virtual_atoms = ftug.virtual_atoms(cg, sidechain=False)
for dist_pair in options.distance.split(':'):
fud.pv('dist_pair')
fr, to = dist_pair.split(',')
fr = int(fr)
to = int(to)
pp.add_dashed(virtual_atoms[fr]["C1'"],
virtual_atoms[to]["C1'"],
width=1.2)
with tf.NamedTemporaryFile() as f:
with tf.NamedTemporaryFile(suffix='.pml') as f1:
f.write(pp.pymol_string())
f.flush()
pymol_cmd = 'hide all\n'
pymol_cmd += 'run %s\n' % (f.name)
pymol_cmd += 'show cartoon, all\n'
pymol_cmd += 'bg white\n'
pymol_cmd += 'clip slab, 10000\n'
pymol_cmd += 'orient\n'
if options.output is not None:
pymol_cmd += 'ray\n'
pymol_cmd += 'png %s\n' % (options.output)
pymol_cmd += 'quit\n'
f1.write(pymol_cmd)
f1.flush()
print "f1.name:", f1.name
if options.batch:
p = sp.Popen(['pymol', '-cq', f1.name],
stdout=sp.PIPE,
stderr=sp.PIPE)
else:
p = sp.Popen(['pymol', f1.name],
stdout=sp.PIPE,
stderr=sp.PIPE)
out, err = p.communicate()
print >> sys.stderr, "err:", err
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 = """
./visualize_cg.py cg_file
Display the coarse-grain representation of a structure in pymol.
"""
num_args = 1
parser = OptionParser(usage=usage)
# parser.add_option('-u', '--useless', dest='uselesss',
# default=False, action='store_true', help='Another useless option')
parser.add_option('-g', '--highlight', dest='highlight', default=None, help="Highlight some elements", type='str')
parser.add_option('-o', '--output', dest='output', default=None, help="Create a picture of the scene and exit",
type='str')
parser.add_option('-r', '--longrange', dest='longrange', default=False, action='store_true',
help="Display long-range interactions")
parser.add_option('-l', '--loops', dest='loops', default=True, action='store_false',
help="Don't display the coarse-grain hairpin loops")
parser.add_option('-c', '--cones', dest='cones', default=False, action='store_true',
help="Display cones that portrude from the stems")
parser.add_option('-x', '--text', dest='text', default=False, action='store_true', help="Add labels to the figure.")
parser.add_option('-a', '--align', dest='align', default=False, action='store_true',
help='Align all of the structures with the first')
parser.add_option('-e', '--encompassing-stems', dest='encompassing_stems', default=False, action='store_true',
help='Show the big stems that encompass the colinear ones.')
parser.add_option('-v', '--virtual-atoms', dest='virtual_atoms', default=False, action='store_true',
help='Display the virtual atoms')
parser.add_option('-d', '--distance', dest='distance', default=None,
help="Draw the lines between specified virtual residues")
parser.add_option('-b', '--basis', dest='basis', default=False, action='store_true',
help='Display the coordinate basis of each element')
parser.add_option('', '--batch', dest='batch', default=False, action='store_true', help='Start pymol in batch mode')
parser.add_option('', '--sidechain-atoms', dest='sidechain_atoms', default=False, action='store_true',
help='Include the sidechain atoms. Automatically enables --virtual-atoms')
parser.add_option('', '--rainbow', dest='rainbow', default=False, action='store_true',
help='Color each of the nucleotide positions (i.e. average atoms) according to the colors of \
the rainbow and their position')
parser.add_option('', '--only-elements', dest='only_elements', default=None, help='Display only these elements '
'element names should be '
'separated by commas')
parser.add_option('', '--color-gradual', dest='color_gradual', default=None, help='Color the specified elements'
'gradually from one to the other, example (i1,i4,m1)', type='str')
(options, args) = parser.parse_args()
print "hi"
if len(args) < num_args:
parser.print_help()
sys.exit(1)
print "hi1"
pp = cvp.PymolPrinter()
pp.add_loops = options.loops
pp.draw_cones = options.cones
# sys.exit(1)
pp.add_longrange = options.longrange
pp.print_text = options.text
pp.encompassing_stems = options.encompassing_stems
pp.virtual_atoms = options.virtual_atoms
pp.sidechain_atoms = options.sidechain_atoms
pp.basis = options.basis
pp.rainbow = options.rainbow
if options.only_elements is not None:
pp.only_elements = options.only_elements.split(',')
cgs = []
for a in args:
cgs += [cmg.CoarseGrainRNA(a)]
if options.align:
align_cgs(cgs)
if options.color_gradual is not None:
pp.element_specific_colors = dict()
import matplotlib.pyplot as plt
cmap = plt.get_cmap('coolwarm')
for d in cgs[0].defines:
pp.element_specific_colors[d]= 'black'
to_color_nodes = options.color_gradual.split(',')
for i,node in enumerate(to_color_nodes):
print node, cmap(i / float(len(to_color_nodes)))
pp.element_specific_colors[node] = cmap(i / float(len(to_color_nodes)))
for i, cg in enumerate(cgs):
if i > 0:
pp.color_modifier = .3
#pp.override_color = 'middle gray'
pp.coordinates_to_pymol(cg)
# highlight things in purple
if options.highlight is not None:
for s in options.highlight.split(','):
fud.pv('s')
pp.add_twists = False
pp.add_stem_like(cg, s, color='purple', width=3.)
# display the distances between nucleotides
if options.distance is not None:
virtual_atoms = ftug.virtual_atoms(cg, sidechain=False)
for dist_pair in options.distance.split(':'):
fud.pv('dist_pair')
fr, to = dist_pair.split(',')
fr = int(fr)
to = int(to)
pp.add_dashed(virtual_atoms[fr]["C1'"], virtual_atoms[to]["C1'"], width=1.2)
with tf.NamedTemporaryFile() as f:
with tf.NamedTemporaryFile(suffix='.pml') as f1:
f.write(pp.pymol_string())
f.flush()
pymol_cmd = 'hide all\n'
pymol_cmd += 'run %s\n' % (f.name)
pymol_cmd += 'show cartoon, all\n'
pymol_cmd += 'bg white\n'
pymol_cmd += 'clip slab, 10000\n'
pymol_cmd += 'orient\n'
if options.output is not None:
pymol_cmd += 'ray\n'
pymol_cmd += 'png %s\n' % (options.output)
pymol_cmd += 'quit\n'
f1.write(pymol_cmd)
f1.flush()
print "f1.name:", f1.name
if options.batch:
p = sp.Popen(['pymol', '-cq', f1.name], stdout=sp.PIPE, stderr=sp.PIPE)
else:
p = sp.Popen(['pymol', f1.name], stdout=sp.PIPE, stderr=sp.PIPE)
out, err = p.communicate()
print >>sys.stderr, "err:", err
def setUp(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
# cg.defines['s0']==[1,9,63,71]
self.va1=ftug.virtual_atoms(cg, sidechain=False)
self.va2=ftug.virtual_atoms(cg, sidechain=True)
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)