def main():
if len(sys.argv) < 2:
print "Usage: ./bulge_to_fork_graph.py bulge.graph"
bg = BulgeGraph(sys.argv[1])
bg.collapse()
bg.dump()
def main():
if len(sys.argv) < 2:
print >> sys.stderr, "Usage: ./long_range_distances.py temp.comp"
sys.exit(1)
bg = BulgeGraph(sys.argv[1])
output_all_distances(bg)
def main():
parser = OptionParser()
(options, args) = parser.parse_args()
if len(args) < 2:
print >> sys.stderr, "Usage: ./add_sequence.py struct.graph seq_file"
sys.exit(1)
bg = BulgeGraph(args[0])
f = open(args[1])
lines = f.readlines()
bg.seq = lines[0].strip()
f.close()
bg.dump()
def main():
parser = OptionParser()
(options, args) = parser.parse_args()
if len(args) < 2:
print >> sys.stderr, "Usage: ./add_sequence.py struct.graph seq_file"
sys.exit(1)
bg = BulgeGraph(args[0])
f = open(args[1])
lines = f.readlines()
bg.seq = lines[0].strip()
f.close()
bg.dump()
def main():
if len(sys.argv) < 2:
print >> sys.stderr, "Usage: ./bobbins_energy.py temp.comp"
sys.exit(1)
bg = BulgeGraph(sys.argv[1])
lrde = LongRangeDistanceEnergy()
print lrde.naive_energy(bg), lrde.eval_energy(bg)
def main():
if len(sys.argv) < 2:
print "Usage: ./graph_to_distances.py temp.comp"
print
print "Traverse the bulge graph and print statistics on the distances between atoms"
sys.exit(1)
bg = BulgeGraph(sys.argv[1])
print_bulge_distances(bg)
def main():
if len(sys.argv) < 2:
print "Usage: ./graph_to_angles.py struct.graph"
print
print "Traverse a structure and output the stems that are connected by a bulge"
sys.exit(1)
bg = BulgeGraph(sys.argv[1])
print_neato(bg)
def main():
if len(sys.argv) < 2:
print >> sys.stderr, "Usage: ./long_range_interaction_count.py temp.comp"
sys.exit(1)
bg = BulgeGraph(sys.argv[1])
lric_bounded = LongRangeInteractionCount()
lric_naive = LongRangeInteractionCount(DistanceIterator())
print lric_bounded.count_interactions(bg), lric_naive.count_interactions(
bg)
def main():
if len(sys.argv) < 2:
print "Usage: ./check_bulge_integrity.py struct.graph"
print
print "Make sure the bulge graph satisfies the following constraints:"
print "ds[0] < ds[1]"
print "ds[2] < ds[3]"
sys.exit(1)
bg = BulgeGraph(sys.argv[1])
check_define_integrity(bg)
check_connection_integrity(bg)
def main():
if len(sys.argv) < 2:
print "Usage: ./bulge_to_fork_graph.py bulge.graph"
bg = BulgeGraph(sys.argv[1])
bg.collapse()
bg.dump()
def main():
if len(sys.argv) < 3:
print "Usage: ./get-long-range-interactions.py file.graph file.mcannotate"
print
print "Print which graph elements interact with which others"
exit
bg = BulgeGraph(sys.argv[1])
mcannotate_file = open(sys.argv[2], 'r')
for line in iterate_over_interactions(mcannotate_file.readlines()):
(from_chain, from_base, to_chain, to_base) = get_interacting_base_pairs(line)
node1 = bg.get_node_from_residue_num(from_base)
node2 = bg.get_node_from_residue_num(to_base)
if abs(from_base - to_base) > 1 and node1 != node2 and not bg.has_connection(node1, node2): # and not (node1[0] == 's' or node2[0] == 's'):
bg.longrange[node1].add(node2)
bg.longrange[node2].add(node1)
bg.dump()
def main():
if len(sys.argv) < 2:
print "Usage: ./coordinates_to_pymol temp.coordinates"
sys.exit(1)
parser = OptionParser()
parser.add_option('-c', '--centers', dest='centers', default=0, help='Display the centers of each segment.', type='int')
parser.add_option('', '--no-loops', dest='no_loops', default=False, action='store_true', help="Don't display loop region.")
parser.add_option('-f', '--flexibility', dest='flex', default=None, help='Location of the flexibility statistics file.', type='string')
parser.add_option('-x', '--text', dest='print_text', default=False, action='store_true', help='Print the names of the segments in the pymol output')
parser.add_option('-t', '--twists', dest='add_twists', default=True, action='store_false', help='Hide the twist indicators')
parser.add_option('-l', '--longrange', dest='add_longrange', default=False, action='store_true', help='Display the longrange interactions')
parser.add_option('-e', '--energy', dest='energy', default='', help='Location of an energy function to visualize', type='string')
parser.add_option('-i', '--img-energy', dest='img_energy', default=False, action='store_true', help="Visualize the distance energy")
parser.add_option('-s', '--stem-stem-energy', dest='stem_stem_energy', default=False, action='store_true', help="Visualize the distance energy")
parser.add_option('', '--loop-loop-energy', dest='loop_loop_energy', default=False, action='store_true', help='Visualize the loop-loop energy')
parser.add_option('', '--cylinder-intersect-energy', dest='cylinder_intersect_energy', default=False, action='store_true', help="Visualize the distance energy")
parser.add_option('-m', '--max-stem-distances', dest='max_stem_distances', default=0, help='Draw the vectors between the closest points on two different stems', type='float')
parser.add_option('-p', '--pdb', dest='pdb_file', default=None, help='Include a pdb file for drawing bouding boxes.', type='string')
parser.add_option('', '--hide-cg', dest='hide_cg', default=False, action='store_true', help='Hide the coarse grain model.')
parser.add_option('', '--stem-atoms', dest='stem_atoms', default=False, action='store_true', help='Display the approximate locations of the atoms of the nucleotides that are parts of stems.')
parser.add_option('', '--stem-atom-distances', dest='stem_atom_distances', default=False, action='store_true', help='Check the distances between the stem atoms.')
parser.add_option('', '--movie', dest='movie', default=False, action='store_true')
parser.add_option('', '--align-to-longest-stem', dest='align_to_longest_stem', default=False, action='store_true', help='Align all of the models to the longest stem of the first one')
parser.add_option('', '--include-pdb', dest='include_pdb', default=False, action='store_true', help='Include the pdb files in a movie. The pdb files should be named just like the graph files except with a .pdb appended.')
parser.add_option('-a', '--align', dest='align', default=False, action='store_true', help="Align all of the structure so as to minimize the rmsd")
parser.add_option('', '--letters', dest='letters', default=False, action='store_true', help="Print the letters of each base in the approximate positions")
parser.add_option('', '--stem-stem-orientations', dest='stem_stem_orientations', default=False, action='store_true', help="show vectors indicating the stem stem orientations")
parser.add_option('', '--pairwise-distances', dest='pairwise_distances', default=False, action='store_true')
(options, args) = parser.parse_args()
bgs = []
for arg in args:
bgs += [BulgeGraph(arg)]
pymol_printer = PymolPrinter()
pymol_printer.print_text = options.print_text
pymol_printer.add_twists = options.add_twists
pymol_printer.add_longrange = options.add_longrange
pymol_printer.add_letters = options.letters
pymol_printer.add_loops = not options.no_loops
pymol_printer.max_stem_distances = options.max_stem_distances
pymol_printer.movie = options.movie
pymol_printer.stem_stem_orienations = options.stem_stem_orientations
if len(options.energy) > 0:
for bg in bgs:
bg.calc_bp_distances()
pymol_printer.energy_function = pickle.load(open(options.energy, 'r'))
if options.img_energy:
pymol_printer.energy_function = cbe.ImgHelixOrientationEnergy()
if options.loop_loop_energy:
for bg in bgs:
bg.add_all_virtual_residues()
pymol_printer.energy_function = cbe.LoopLoopEnergy()
if options.stem_stem_energy:
for bg in bgs:
bg.add_all_virtual_residues()
pymol_printer.energy_function = cbe.StemStemOrientationEnergy()
if options.cylinder_intersect_energy:
for bg in bgs:
bg.add_all_virtual_residues()
pymol_printer.energy_function = cbe.CylinderIntersectionEnergy()
if options.pdb_file:
pymol_printer.pdb_file = options.pdb_file
if options.hide_cg:
pymol_printer.draw_segments = False
translation_matrix = np.zeros(3)
rotation_matrix = np.identity(3)
for i in range(len(bgs)):
bg = bgs[i]
pymol_printer.reset()
centroid0 = cuv.get_vector_centroid(cgg.bg_virtual_residues(bgs[0]))
centroid1 = cuv.get_vector_centroid(cgg.bg_virtual_residues(bg))
crds0 = cuv.center_on_centroid(cgg.bg_virtual_residues(bgs[0]))
crds1 = cuv.center_on_centroid(cgg.bg_virtual_residues(bg))
if options.align:
rot_mat = cbr.optimal_superposition(crds0, crds1)
for k in bg.coords.keys():
bg.coords[k] = (np.dot(rot_mat, bg.coords[k][0] - centroid1),
np.dot(rot_mat, bg.coords[k][1] - centroid1))
if k[0] == 's':
bg.twists[k] = (np.dot(rot_mat, bg.twists[k][0]),
np.dot(rot_mat, bg.twists[k][1]))
if i > 0:
if options.pairwise_distances:
for d in bg.defines.keys():
pymol_printer.add_segment(bgs[0].get_point(d), bgs[i].get_point(d), 'cyan', 0.5)
if not options.movie:
if len(bgs) > 1 and i == 0:
pymol_printer.override_color = 'green'
elif len(bgs) > 1 and i > 0:
pymol_printer.override_color = 'red'
#pymol_printer.override_color = 'red'
bg = bgs[i]
if options.centers == 1:
pymol_printer.centers_to_pymol(bg)
elif options.flex != None:
pymol_printer.flex_to_pymol(bg, options.flex)
pymol_printer.coordinates_to_pymol(bg)
if options.align_to_longest_stem:
sm = cbm.SpatialModel(bg)
longest_stem = bgs[0].get_longest_stem()
sm.stems[longest_stem] = cbm.StemModel(name=longest_stem)
sm.stems[longest_stem].mids = bg.coords[longest_stem]
sm.stems[longest_stem].twists = bg.twists[longest_stem]
translation_matrix = sm.get_transform(longest_stem)
rotation_matrix = sm.get_rotation(longest_stem)
#cud.pv('translation_matrix')
#cud.pv('rotation_matrix')
pymol_printer.transform_segments(translation_matrix, rotation_matrix)
if options.stem_atoms:
bg.add_all_virtual_residues()
for (s,i) in bg.virtual_residues():
vra = []
vra += [cgg.virtual_residue_atoms(bg, s, i,0)]
vra += [cgg.virtual_residue_atoms(bg, s, i,1)]
#(vpos1, vvec1, vvec1_l, vvec1_r) = cgg.virtual_res_3d_pos(bg, s, i)
(vpos1, vvec1, vvec1_l, vvec1_r) = bg.v3dposs[s][i]
'''
print >> sys.stderr, "************************"
if s == 's1' and i == 1:
print >> sys.stderr, "----------------------"
cud.pv('vpos1')
cud.pv('vvec1_l')
cud.pv('vpos1 + mult * vvec1_l')
'''
for x in range(2):
for a in vra[x].values():
pymol_printer.add_sphere(a, 'purple', 0.3)
if not options.stem_atom_distances:
continue
#cud.pv('(s,i, s2, i2)')
for (s2, i2) in bg.virtual_residues():
vra2 = []
vra2 += [cgg.virtual_residue_atoms(bg, s2, i2,0)]
vra2 += [cgg.virtual_residue_atoms(bg, s2, i2,1)]
#(vpos2, vvec2, vvec2_l, vvec2_r) = cgg.virtual_res_3d_pos(bg, s2, i2)
(vpos2, vvec2, vvec2_l, vvec2_r) = bg.v3dposs[s2][i2]
if s == s2:
continue
#for atoms1 in vra:
#for atoms2 in vra2:
for k in range(2):
atoms1 = vra[k]
for m in range(2):
atoms2 = vra2[m]
for a1 in atoms1.values():
for a2 in atoms2.values():
if cuv.magnitude(a1 - a2) < 2.0:
mult = 8.
cud.pv('(s,i,k,s2,i2,m)')
'''
cud.pv('(k,m)')
cud.pv('vpos1')
cud.pv('vvec1_l')
cud.pv('vpos1 + mult * vvec1_l')
cud.pv('vpos1 + mult * vvec1_r')
cud.pv('vpos2 + mult * vvec2_l')
cud.pv('vpos2 + mult * vvec2_r')
'''
cud.pv('cuv.magnitude((vpos1 + mult * vvec1_l) - (vpos2 + mult * vvec2_l))')
cud.pv('cuv.magnitude((vpos1 + mult * vvec1_l) - (vpos2 + mult * vvec2_r))')
cud.pv('cuv.magnitude((vpos1 + mult * vvec1_r) - (vpos2 + mult * vvec2_l))')
cud.pv('cuv.magnitude((vpos1 + mult * vvec1_r) - (vpos2 + mult * vvec2_r))')
cud.pv('cuv.magnitude(a1 - a2)')
pymol_printer.add_segment(a1, a2, 'yellow', 0.5)
pymol_printer.output_pymol_file()
if options.include_pdb:
print 'cmd.load("%s", "sxs%s", state=%d)' % (args[i] + ".pdb", pymol_printer.prev_obj_name, pymol_printer.state-1)
print 'cmd.color("grey50", "all")'