def pymol_printer_from_args(args):
pp = ftvp.PymolPrinter()
if args.thin_cylinders:
pp.cylinder_width = 0.5
pp.show_twists = False
pp.display_virtual_residues = args.virtual_residues
pp.virtual_atoms = args.virtual_atoms
if args.only_elements is not None:
pp.only_elements = args.only_elements.split(',')
pp.add_loops = not args.no_loops
pp.add_longrange = args.longrange
pp.stem_color = args.stem_color
pp.multiloop_color = args.multiloop_color
pp.print_text = args.text
pp.encompassing_stems = args.encompassing_stems
pp.sidechain_atoms = args.sidechain_atoms
pp.basis = args.basis
pp.rainbow = args.rainbow
if args.element_colors:
directives = args.element_colors.split(",")
elem_colors = {}
for directive in directives:
elem, _, color = directive.partition(":")
log.debug("Element %s: %s", elem, color)
if not color:
color = "purple"
if color not in ftvp.NAMED_COLORS: # A hex value
try:
color = tuple(
int(color[i:i + 2], 16) / 255 for i in (0, 2, 4))
except:
raise ValueError("Color value '{}' not understood. "
"Either provide a HEX value or "
"one of {}".format(
color,
",".join(ftvp.NAMED_COLORS.keys())))
if elem.lower() == "default":
default_color = color # Color is changed later
elem_colors = defaultdict(lambda: default_color, elem_colors)
else:
elem_colors[elem] = color
log.debug("Element %s", elem_colors)
pp.element_specific_colors = elem_colors
return pp
def main():
usage = """
./visualize_pdb.py pdb_file
Display a pdb file along with its coarse grain representation in pymol.
"""
num_args = 0
parser = OptionParser(usage=usage)
parser.add_option('-s',
'--secondary-structure',
dest='secondary_structure',
default='',
help="Enter a dot-bracket string for the \
secondary structure of this model",
type=str)
parser.add_option('-x',
'--text',
dest='text',
default=False,
action='store_true',
help="Add labels to the figure.")
parser.add_option('-r',
'--longrange',
dest='longrange',
default=False,
action='store_true',
help="Display long-range interactions")
parser.add_option('-p',
'--pseudoknots',
dest='pseudoknots',
default=False,
action='store_true',
help='Allow pseudoknots in the CG structure')
#parser.add_option('', '--batch', dest='batch', default=False, action='store_true', help='Start pymol in batch mode') #Crashes currently
parser.add_option('',
'--virtual-residues',
dest='virtual_residues',
default=False,
action='store_true',
help='Display the virtual residues as spheres')
parser.add_option(
'',
'--color-residues',
dest='color_residues',
default=False,
action='store_true',
help="Color the residues according to the element they're in")
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-l',
'--loops',
dest='loops',
default=True,
action='store_false',
help="Don't display the coarse-grain hairpin loops")
parser.add_option('-d',
'--distance',
dest='distance',
default=None,
help="Draw the lines between specified virtual residues")
parser.add_option('-o',
'--output',
dest='output',
default=None,
help="Create a picture of the scene and exit",
type='str')
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('-v',
'--virtual-atoms',
dest='virtual_atoms',
default=False,
action='store_true',
help='Display the virtual atoms')
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
if not op.exists(args[0]):
print >> sys.stderr, "File doesn't exist: %s" % (args[0])
sys.exit(1)
cg = ftmc.from_pdb(args[0],
options.secondary_structure.strip("\"'"),
remove_pseudoknots=not options.pseudoknots)
pp = ftvp.PymolPrinter()
pp.display_virtual_residues = options.virtual_residues
pp.virtual_atoms = options.virtual_atoms
if options.only_elements is not None:
orig_only_elements = options.only_elements.split(',')
only_elements = set(orig_only_elements[::])
for c in orig_only_elements:
for e in cg.edges[c]:
only_elements.add(e)
pp.only_elements = only_elements
pp.add_loops = options.loops
pp.add_longrange = options.longrange
#sys.exit(1)
pp.coordinates_to_pymol(cg)
pp.print_text = options.text
print >> sys.stderr, "virtual_residues:", options.virtual_residues
#pp.print_text = False
#pp.output_pymol_file()
if options.only_elements is not None:
pp.only_elements = options.only_elements.split(',')
with tf.NamedTemporaryFile() as f:
with tf.NamedTemporaryFile(suffix='.pml') as f1:
with tf.NamedTemporaryFile(suffix='.pdb') as f2:
# extract just the biggest chain and renumber it so
# the nucleotides start at 1
chain = ftup.get_biggest_chain(args[0])
#chain = ftup.renumber_chain(chain)
ftup.output_chain(chain, f2.name)
f2.flush()
# display the distances between nucleotides
if options.distance is not None:
for dist_pair in options.distance.split(':'):
fr, to = dist_pair.split(',')
fr = int(fr)
to = int(to)
try:
vec1 = chain[fr]["C1*"].get_vector().get_array()
vec2 = chain[to]["C1*"].get_vector().get_array()
except KeyError:
# Rosetta produces atoms with non-standard names
vec1 = chain[fr]["C1*"].get_vector().get_array()
vec2 = chain[to]["C1*"].get_vector().get_array()
pp.add_dashed(vec1, vec2, width=1.2)
f.write(pp.pymol_string())
f.flush()
pymol_cmd = 'hide all\n'
pymol_cmd += 'show cartoon, all\n'
pymol_cmd += 'set cartoon_ring_mode\n'
pymol_cmd += 'set cartoon_tube_radius, .3\n'
if options.only_elements is not None:
pymol_cmd += "hide all\n"
for constraint in only_elements:
color = pp.get_element_color(constraint)
for r in cg.define_residue_num_iterator(constraint,
seq_ids=True):
pymol_cmd += "show sticks, resi %r\n" % (r[1])
pymol_cmd += "color %s, resi %r\n" % (color, r[1])
if options.color_residues:
for d in cg.defines:
color = pp.get_element_color(d)
for r in cg.define_residue_num_iterator(d,
seq_ids=True):
pymol_cmd += "color %s, resi %r\n" % (color, r[1])
pymol_cmd += 'run %s\n' % (f.name)
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' #This would lead to an error message
f1.write(pymol_cmd)
f1.flush()
#if options.batch:
# p = sp.Popen(['pymol', '-cq', f2.name, f1.name], stdout=sp.PIPE, stderr=sp.PIPE)
if True: #else:
p = sp.Popen(['pymol', f2.name, f1.name],
stdout=sp.PIPE,
stderr=sp.PIPE)
out, err = p.communicate()
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 main():
usage = """
python plot_average_atom_positions.py
Currently works for certain multiloops (hardcoded).
"""
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_file',
default=None,
help=
'Use a file containing the positions of each entry for this cg element.',
type='str')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
pp = ftvp.PymolPrinter()
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
cmap = plt.get_cmap('gist_rainbow')
stem_len = 3
for aname in ftup.nonsidechain_atoms:
conn_types = [2]
for i in range(3):
all_coords = []
for conn_type in conn_types:
elem_type = 'm'
dimensions = '3 1000'
identifier = "%s %s %d %d %s" % (elem_type, dimensions,
conn_type, i, aname)
if options.all_entries_file is not None:
import imp
fn = op.expanduser(options.all_entries_file)
#fn1 = op.expanduser(op.splitext(options.all_entries_file)[0])
xftua = imp.load_source('xftua', fn)
coords = xftua.all_atom_poss[identifier]
for c in coords:
pp.add_sphere(c,
width=0.2,
color_rgb=cmap(i / float(stem_len)))
all_coords += coords
avg_coord = np.mean(coords, axis=0)
pp.add_sphere(avg_coord,
width=0.6,
color_rgb=cmap(i / float(stem_len)))
else:
coords = ftua.avg_atom_poss[identifier]
pp.add_sphere(coords,
width=0.2,
color_rgb=cmap(i / float(stem_len)))
avg_coord = np.mean(all_coords, axis=0)
pp.add_sphere(avg_coord,
width=0.9,
color_rgb=cmap(i / float(stem_len)))
# Add an axis
pp.add_segment([0, 0, 0], [5, 0, 0], "purple", 0.5)
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'
f1.write(pymol_cmd)
f1.flush()
p = sp.Popen(['pymol', f1.name])
out, err = p.communicate()
def main():
usage = """
./visualize_cg.py cg_file
Display the coarse-grain representation of a structure in pymol.
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
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('-b', '--basis', dest='basis', default=False, action='store_true', help='Display the coordinate basis of each element')
parser.add_option('', '--stem-atoms', dest='stem_atoms', default=False, action='store_true', help='Display the stem 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')
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
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.basis = options.basis
pp.rainbow = options.rainbow
cgs = []
for a in args:
cgs += [cmg.from_file(a)]
if options.align:
align_cgs(cgs)
for i,cg in enumerate(cgs):
if i > 0:
pp.color_modifier = .3
#pp.override_color = 'middle gray'
pp.coordinates_to_pymol(cg)
for d in cg.defines:
if d[0] == 'i' or d[0] == 's' or d[0] == 'm':
if options.stem_atoms:
side = 0
if d[0] == 'm':
side = cg.get_strand(d)
pp.stem_atoms(cg.coords[d], cg.get_twists(d),
cg.get_node_dimensions(d)[0], side=side)
elif d[0] == 's':
for side in range(2):
pp.stem_atoms(cg.coords[d], cg.get_twists(d),
cg.get_node_dimensions(d)[0], side=side)
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'
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()
p = sp.Popen(['pymol', f1.name])
out, err = p.communicate()
def main():
usage = """
./visualize_pdb.py pdb_file
Display a pdb file along with its coarse grain representation in pymol.
"""
num_args = 0
parser = OptionParser(usage=usage)
parser.add_option('-s',
'--secondary-structure',
dest='secondary_structure',
default='',
help="Enter a dot-bracket string for the \
secondary structure of this model",
type=str)
parser.add_option('-x',
'--text',
dest='text',
default=False,
action='store_true',
help="Add labels to the figure.")
parser.add_option('-r',
'--longrange',
dest='longrange',
default=False,
action='store_true',
help="Display long-range interactions")
parser.add_option('-c',
'--constraints',
dest='constraints',
default=None,
help="Only visualize the elements passed as parameters",
type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-l',
'--loops',
dest='loops',
default=True,
action='store_false',
help="Don't display the coarse-grain hairpin loops")
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
if not op.exists(args[0]):
print >> sys.stderr, "File doesn't exist: %s" % (args[0])
sys.exit(1)
cg = ftmc.from_pdb(args[0], options.secondary_structure.strip("\"'"))
pp = ftvp.PymolPrinter()
if options.constraints is not None:
orig_constraints = options.constraints.split(',')
constraints = set(orig_constraints[::])
for c in orig_constraints:
for e in cg.edges[c]:
constraints.add(e)
pp.constraints = constraints
pp.add_loops = options.loops
pp.add_longrange = options.longrange
#sys.exit(1)
pp.coordinates_to_pymol(cg)
pp.print_text = options.text
#pp.print_text = False
#pp.output_pymol_file()
with tf.NamedTemporaryFile() as f:
with tf.NamedTemporaryFile(suffix='.pml') as f1:
with tf.NamedTemporaryFile(suffix='.pdb') as f2:
# extract just the biggest chain and renumber it so
# the nucleotides start at 1
chain = ftup.get_biggest_chain(args[0])
#chain = ftup.renumber_chain(chain)
ftup.output_chain(chain, f2.name)
f2.flush()
f.write(pp.pymol_string())
f.flush()
pymol_cmd = 'hide all\n'
pymol_cmd += 'show cartoon, all\n'
pymol_cmd += 'set cartoon_ring_mode\n'
pymol_cmd += 'set cartoon_tube_radius, .3\n'
if options.constraints is not None:
pymol_cmd += "hide all\n"
for constraint in constraints:
color = pp.get_element_color(constraint)
for r in cg.define_residue_num_iterator(constraint):
pymol_cmd += "show sticks, resi %r\n" % (r)
pymol_cmd += "color %s, resi %r\n" % (color, r)
pymol_cmd += 'run %s\n' % (f.name)
f1.write(pymol_cmd)
f1.flush()
p = sp.Popen(['pymol', f2.name, f1.name])
out, err = p.communicate()
def main():
usage = './bounding_box_coords.py temp.pdb [temp2.pdb ...]'
usage += "Print out the positions of the atoms in coordinates "
usage += "respective to the virtual residue coordinate system."
parser = OptionParser()
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
parser.add_option('-e',
'--edge',
dest='edge',
default=False,
action='store_true',
help='Include the edge nucleotides in the statistics.')
parser.add_option('-p',
'--pymol',
dest='pymol',
default=False,
action='store_true',
help='Output in pymol cgo format.')
parser.add_option('-a',
'--averages',
dest='averages',
default=False,
action='store_true',
help='Output the average coordinates')
parser.add_option(
'-r',
'--residue',
dest='residue',
default='AUGC',
help="The type of residue to calculate the averages for.",
type='str')
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
all_coords = [co.defaultdict(list), co.defaultdict(list)]
pp = cvp.PymolPrinter()
pp.draw_axes = True
for pdbfile in args:
try:
bg = ttmc.from_pdb(pdbfile)
except Exception as e:
log.exception(e)
continue
chain = bg.chain
for s in bg.stem_iterator():
for i in range(bg.stem_length(s)):
if i == 0 or i == bg.stem_length(s) - 1:
if not options.edge:
continue
(origin, basis,
coords) = cgg.stem_vres_reference_atoms(bg, chain, s, i)
# subtract one because the sequence is 0-based
(p1, p2) = (bg.defines[s][0] + i - 1, bg.defines[s][3] - i - 1)
(r1, r2) = (bg.seq[p1], bg.seq[p2])
all_coords[0][r1].append(coords[0])
all_coords[1][r2].append(coords[1])
'''
if options.pymol:
if not options.averages:
add_pymol_coords(coords)
else:
print_atom_positions(coords)
'''
if options.averages:
if options.pymol:
print_average_atom_positions(all_coords, list(options.residue), pp)
pp.output_pymol_file()
else:
print_average_atom_positions(all_coords, list(options.residue),
None)
else:
for i, c in enumerate(all_coords):
for k in c.keys():
for coords in c[k]:
for atom in coords.keys():
print i, k, atom, " ".join(map(str, coords[atom]))
