def main():
usage = """
python get_biggest_rna_chain.py in.pdb out.pdb
Extract the largest RNA chain from the file in.pdb and store it in out.pdb.
"""
num_args = 2
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')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
c = ftup.get_biggest_chain(args[0])
ftup.output_chain(c, args[1])
def main():
usage = """
python get_biggest_rna_chain.py in.pdb out.pdb
Extract the largest RNA chain from the file in.pdb and store it in out.pdb.
"""
num_args= 2
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')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
c = ftup.get_biggest_chain(args[0])
ftup.output_chain(c, args[1])
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 load_cg_from_pdb_in_dir(pdb_filename, output_dir, secondary_structure='',
chain_id=None, remove_pseudoknots=True):
'''
Create the coarse grain model from a pdb file and store all
of the intermediate files in the given directory.
@param pdb_filename: The name of the pdb file to be coarseified
@param output_dir: The name of the output directory
@param secondary_structure: Specify a particular secondary structure
for this coarsification.
@param chain_id: The id of the chain to create the CG model from
'''
#chain = ftup.load_structure(pdb_filename)
if chain_id == None:
chain = ftup.get_biggest_chain(pdb_filename)
else:
chain = ftup.get_particular_chain(pdb_filename, chain_id)
chain = ftup.rename_modified_ress(chain)
chain = ftup.rename_rosetta_atoms(chain)
chain = ftup.remove_hetatm(chain)
# output the biggest RNA chain
pdb_base = op.splitext(op.basename(pdb_filename))[0]
output_dir = op.join(output_dir, pdb_base + "_" + chain.id)
if not op.exists(output_dir):
os.makedirs(output_dir)
with open(op.join(output_dir, 'temp.pdb'), 'w') as f:
ftup.output_chain(chain, f.name)
f.flush()
pdb_base = op.splitext(op.basename(pdb_filename))[0]
pdb_base += "_" + chain.id
cg = CoarseGrainRNA()
cg.name = pdb_base
if len(chain.get_list()) == 0:
return cg
# first we annotate the 3D structure
p = sp.Popen(['MC-Annotate', f.name], stdout=sp.PIPE)
out, err = p.communicate()
with open(op.join(output_dir, 'temp.mcannotate'), 'w') as f3:
f3.write(out)
lines = out.strip().split('\n')
# convert the mcannotate output into bpseq format
try:
(dotplot, residue_map) = ftum.get_dotplot(lines)
except Exception as e:
print >>sys.stderr, e
return cg
# f2 will store the dotbracket notation
with open(op.join(output_dir, 'temp.bpseq'), 'w') as f2:
f2.write(dotplot)
f2.flush()
# remove pseudoknots
'''
p = sp.Popen(['aux/k2n_standalone/knotted2nested.py', '-f', 'bpseq',
'-F', 'vienna', f2.name], stdout = sp.PIPE)
out, err = p.communicate()
'''
if remove_pseudoknots:
out = cak.k2n_main(f2.name, input_format='bpseq',
#output_format = 'vienna',
output_format = 'bpseq',
method = cak.DEFAULT_METHOD,
opt_method = cak.DEFAULT_OPT_METHOD,
verbose = cak.DEFAULT_VERBOSE,
removed= cak.DEFAULT_REMOVED)
out = out.replace(' Nested structure', pdb_base)
else:
out = dotplot
#(out, residue_map) = add_missing_nucleotides(out, residue_map)
'''
if secondary_structure != '':
lines = out.split('\n')
if len(secondary_structure) != len(lines[1].strip()):
print >>sys.stderr, "The provided secondary structure \
does not match the length of the 3D structure"
print >>sys.stderr, "Sequence:", lines[1]
print >>sys.stderr, "ss_struc:", secondary_structure
sys.exit(1)
lines[-1] = secondary_structure
out = "\n".join(lines)
'''
# Add the 3D information about the starts and ends of the stems
# and loops
with warnings.catch_warnings():
warnings.simplefilter("ignore")
s = bpdb.PDBParser().get_structure('temp', f.name)
chains = list(s.get_chains())
if len(chains) < 1:
raise Exception("No chains in the PDB file")
chain = chains[0]
#cg.from_fasta(out, dissolve_length_one_stems=1)
cg.from_bpseq_str(out, dissolve_length_one_stems=False)
cg.name = pdb_base
cg.seqids_from_residue_map(residue_map)
ftug.add_stem_information_from_pdb_chain(cg, chain)
ftug.add_bulge_information_from_pdb_chain(cg, chain)
ftug.add_loop_information_from_pdb_chain(cg, chain)
cg.chain = chain
add_longrange_interactions(cg, lines)
with open(op.join(output_dir, 'temp.cg'), 'w') as f3:
f3.write(cg.to_cg_string())
f3.flush()
return cg
print >>sys.stderr, "Uh oh... couldn't generate the coarse-grain structure."
print >>sys.stderr, "Prepare for an incoming exception."
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 = """
./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_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()