def to_pdb(cg):
used_chainids = set(cg.chains.keys())
def get_available_chainid():
for c in string.ascii_uppercase:
if c not in used_chainids:
used_chainids.add(c)
return c
raise ValueError("Too many chains. Cannot convert to old PDB format.")
f = StringIO()
for chain in cg.chains.values():
if len(chain.id) > 1:
chain.id = get_available_chainid()
ftup.output_multiple_chains(cg.chains.values(), f, "pdb")
return f.getvalue()
def _get_fragment(self, stat, sm):
key = stat.pdb_name + "__def_" + "-".join(map(str, stat.define))
new_fragment = False
try:
fragment, _, _ = ftup.get_all_chains(op.join(
self.LIBRARY_DIRECTORY, key[2:4], key + ".cif"),
no_annotation=True)
except Exception:
cg, chains = self._get_source_cg_and_chain(stat, sm)
new_fragment = True
else:
fragment = {c.id: c for c in fragment}
log.debug("Used stored fragment for %s", key)
pdb_basename = stat.pdb_name.split(":")[0]
cg_filename = op.expanduser(
op.join(self.cg_library_path, pdb_basename + ".cg"))
cg = self.get_cg(cg_filename) #The cg with the template
try:
elem = cg.get_node_from_residue_num(stat.define[0])
except Exception:
log.error("stat %s with define %s", stat, stat.define)
raise
if stat.define != cg.defines[elem]:
err = ValueError(
"The CG files where the stats where extracted and "
"the cg file used for reconstruction are not consistent!")
with log_to_exception(log, err):
log.error("%s != %s for element %s (%s)", stat.define,
cg.defines[elem], elem, stat.pdb_name)
raise err
if new_fragment:
fragment = ftup.extract_subchains_from_seq_ids(
chains,
cg.define_residue_num_iterator(elem,
seq_ids=True,
adjacent=(elem[0] != "s")))
if self.LIBRARY_DIRECTORY is not None:
log.debug("Storing newly-created fragment for %s", key)
import distutils.dir_util
distutils.dir_util.mkpath(
op.join(self.LIBRARY_DIRECTORY, key[2:4]))
ftup.output_multiple_chains(
fragment.values(),
op.join(self.LIBRARY_DIRECTORY, key[2:4], key + ".cif"),
"cif")
return cg, elem, fragment
def reconstruct(cg, fn, args, rec):
log.info("Processing %s", fn)
stat_source = fbs.from_args(args, cg)
sm = fbm.SpatialModel(cg)
sm.load_sampled_elems(stat_source)
if args.reassign_broken:
sm.bg.traverse_graph()
for ml in sm.bg.mloop_iterator():
if ml not in sm.bg.mst:
try:
del sm.elem_defs[ml]
except KeyError:
pass
fbm._perml_energy_to_sm(sm, "MAX10000[1FJC1]", stat_source)
for ml in sm.bg.mloop_iterator():
if ml not in sm.bg.mst:
e = sm.junction_constraint_energy[ml].eval_energy(sm.bg)
log.info("Deviation for %s is %s", ml, e)
energies = list(sm.junction_constraint_energy[ml].iterate_energies())
if len(energies)==1:
log.debug("Getting used_stat for single energy %s",energies)
used_stat = energies[0].used_stat
else:
log.debug("Multiple energies. Iterating")
for ef in energies:
if ef.element==ml:
used_stat = ef.used_stat
log.info("Used stat for %s is %s", ml, used_stat)
sm.elem_defs[ml] = used_stat
sm.save_sampled_elems()
log.info("Broken stats reassigned. Storing cg.")
sm.bg.to_file(fn+".reassigned.cg")
sm.new_traverse_and_build()
chains = rec.reconstruct(sm)
print("Writing", fn+".reconstr.pdb")
chains = ftup.rename_chains_for_pdb(chains)
ftup.output_multiple_chains(chains.values(), fn+".reconstr.pdb")
def main(args):
rnas = fuc.cgs_from_args(args, '+', '3d')
pp = pymol_printer_from_args(args)
if args.align:
align_rnas(rnas)
if args.labels:
label_list = args.labels.split(",")
labels = {}
for label in label_list:
if not label:
continue
try:
elem, lab = label.split(':')
except ValueError:
raise ValueError(
"Please specify --labels with as list of colon-seperated tuples. Found invalid entry {}.".format(repr(label)))
labels[elem] = lab
if not pp.print_text:
labels = defaultdict(lambda: "", labels)
pp.print_text = True
else:
labels = {}
color_modifier = 1.0
log.info("Visualizing {} rnas".format(len(rnas)))
for rna in rnas:
pp.add_cg(rna, labels, color_modifier)
color_modifier *= 0.7
with make_temp_directory() as tmpdir:
# The file describing the cg-structure as cylinders
if args.pymol_file:
stru_filename = args.pymol_file
else:
stru_filename = os.path.join(tmpdir, "structure")
with open(stru_filename, "w") as f:
f.write(pp.pymol_string())
pdb_fns = []
selections = ""
for i, rna in enumerate(rnas):
if rna.chains:
obj_name = "pdb{}_{}".format(i, rna.name.replace("-", "_"))
fn = os.path.join(tmpdir, obj_name + ".cif")
pdb_fns.append(fn)
ftup.output_multiple_chains(rna.chains.values(), fn, "cif")
for d in rna.defines:
resids = list(
rna.define_residue_num_iterator(d, seq_ids=True))
if resids:
chains = {r.chain for r in resids}
sel = []
for c in chains:
sel.append("( %{} and chain {} and resi {}) ".format(
obj_name, c, "+".join(map(str, (r.resid[1] for r in resids)))))
selections += "select {}, ".format(
d + "_" + obj_name) + " or ".join(sel) + "\n"
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 args.only_elements is not None:
pymol_cmd += "hide all\n"
for constraint in args.only_elements.split(','):
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])
pymol_cmd += 'run %s\n' % (stru_filename)
pymol_cmd += 'bg white\n'
pymol_cmd += 'clip slab, 10000\n'
#pymol_cmd += 'orient\n'
pymol_cmd += selections
if args.output is not None:
pymol_cmd += 'ray\n'
pymol_cmd += 'png %s\n' % (args.output)
#pymol_cmd += 'quit\n'
pml_filename = os.path.join(tmpdir, "command.pml")
with open(pml_filename, "w") as f1:
f1.write(pymol_cmd)
if args.batch:
p = sp.Popen(['pymol', '-cq'] + pdb_fns +
[pml_filename], stdout=sp.PIPE, stderr=sp.PIPE)
else:
p = sp.Popen(['pymol'] + pdb_fns + [pml_filename],
stdout=sp.PIPE, stderr=sp.PIPE)
log.info("Now opening pymol")
out, err = p.communicate()
log.info("Out=\n%s", out)
log.info("Errt=\n%s", err)
def update_statistics(self,
sm,
energy,
member_energies=[],
change="",
clashes=[],
bad_mls=[]):
"""
Add a new structure to the statistics.
:param sm: The spatial model.
:param energy: The energy used for sampling of the structure, or None.
:param member_energies: A list of tuples `(energy_shortname, value)`
"""
self.step += 1
line = ["{:6d}\t{:10.3f}".format(self.step, energy)]
if self.options["constituing_energies"] == "no_clash":
ignore_names = [
fbe.RoughJunctionClosureEnergy().shortname,
fbe.StemVirtualResClashEnergy().shortname
]
else:
ignore_names = []
line.append("( " + " ".join("{} {:10.3f}".format(*x)
for x in member_energies
if x[0] not in ignore_names) + " )")
line.append(self.collector.update(sm, self.step))
line.append(change)
if isinstance(clashes, str):
line.append(clashes)
else:
line.append(",".join(["{}+{}".format(*c) for c in clashes])
or "noclash")
if isinstance(bad_mls, str):
line.append(bad_mls)
else:
line.append(",".join(bad_mls) or "noclash")
self.printline("\t".join(line))
if self.best_cgs.can_insert_right((None, energy)):
self.best_cgs.insert_right((sm.bg.to_cg_string(), energy))
if self.step % 10 == 0:
for i, cg_stri in enumerate(self.best_cgs):
with open(
os.path.join(self.out_dir, 'best{:d}.coord'.format(i)),
'w') as f:
f.write(cg_stri[0])
if self.options["step_save"] > 0 and self.step % self.options[
"step_save"] == 0:
cg_stri = sm.bg.to_cg_string()
with open(
os.path.join(self.out_dir,
'step{:06d}.coord'.format(self.step)),
"w") as f:
# print("Opened file", os.path.join(self.out_dir,
# 'step{:06d}.coord'.format(self.step)))
print(cg_stri, file=f)
if self.reconstructor is not None and self.step % self.options[
"reconstruct_n"] == 0:
try:
chains = self.reconstructor.reconstruct(sm)
ftup.output_multiple_chains(
chains.values(),
os.path.join(self.out_dir,
'step{:06d}.reconstr.pdb'.format(self.step)))
except:
log.exception(
"Could not reconstruct all-atom PDB, because of the following error:"
)
def main(args):
rnas = fuc.cgs_from_args(args, '+', '3d')
pp = pymol_printer_from_args(args)
if args.align:
align_rnas(rnas)
if args.labels:
label_list = args.labels.split(",")
labels = {}
for label in label_list:
if not label:
continue
try:
elem, lab = label.split(':')
except ValueError:
raise ValueError(
"Please specify --labels with as list of colon-seperated tuples. Found invalid entry {}."
.format(repr(label)))
labels[elem] = lab
if not pp.print_text:
labels = defaultdict(lambda: "", labels)
pp.print_text = True
else:
labels = {}
color_modifier = 1.0
log.info("Visualizing {} rnas".format(len(rnas)))
for rna in rnas:
pp.add_cg(rna, labels, color_modifier)
color_modifier *= 0.7
with make_temp_directory() as tmpdir:
# The file describing the cg-structure as cylinders
if args.pymol_file:
stru_filename = args.pymol_file
else:
stru_filename = os.path.join(tmpdir, "structure")
with open(stru_filename, "w") as f:
f.write(pp.pymol_string())
pdb_fns = []
selections = ""
for i, rna in enumerate(rnas):
if rna.chains:
obj_name = "pdb{}_{}".format(i, rna.name.replace("-", "_"))
fn = os.path.join(tmpdir, obj_name + ".cif")
pdb_fns.append(fn)
ftup.output_multiple_chains(rna.chains.values(), fn, "cif")
for d in rna.defines:
resids = list(
rna.define_residue_num_iterator(d, seq_ids=True))
if resids:
chains = {r.chain for r in resids}
sel = []
for c in chains:
sel.append(
"( %{} and chain {} and resi {}) ".format(
obj_name, c, "+".join(
map(str,
(r.resid[1] for r in resids)))))
selections += "select {}, ".format(
d + "_" + obj_name) + " or ".join(sel) + "\n"
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 args.only_elements is not None:
pymol_cmd += "hide all\n"
for constraint in args.only_elements.split(','):
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])
pymol_cmd += 'run %s\n' % (stru_filename)
pymol_cmd += 'bg white\n'
pymol_cmd += 'clip slab, 10000\n'
#pymol_cmd += 'orient\n'
pymol_cmd += selections
if args.output is not None:
pymol_cmd += 'ray\n'
pymol_cmd += 'png %s\n' % (args.output)
#pymol_cmd += 'quit\n'
pml_filename = os.path.join(tmpdir, "command.pml")
with open(pml_filename, "w") as f1:
f1.write(pymol_cmd)
if args.batch:
p = sp.Popen(['pymol', '-cq'] + pdb_fns + [pml_filename],
stdout=sp.PIPE,
stderr=sp.PIPE)
else:
p = sp.Popen(['pymol'] + pdb_fns + [pml_filename],
stdout=sp.PIPE,
stderr=sp.PIPE)
log.info("Now opening pymol")
out, err = p.communicate()
log.info("Out=\n%s", out)
log.info("Errt=\n%s", err)
def to_pdb(cg):
chains = ftup.rename_chains_for_pdb(cg.chains)
f = StringIO()
ftup.output_multiple_chains(chains.values(), f, "pdb")
return f.getvalue()
def to_pdb(cg):
chains = ftup.rename_chains_for_pdb(cg.chains)
f = StringIO()
ftup.output_multiple_chains(chains.values(), f, "pdb")
return f.getvalue()
for elem in cg.defines:
if elem in cg.incomplete_elements:
continue
base_name = "{}:{}_".format(cg.name, elem[0])
idnr = next_id[base_name]
next_id[base_name] += 1
name = base_name + str(idnr)
if args.fragment_dir:
fragment_chains = ftup.extract_subchains_from_seq_ids(
cg.chains,
cg.define_residue_num_iterator(elem,
seq_ids=True,
adjacent=elem[0] != "s"))
try:
ftup.output_multiple_chains(
list(fragment_chains.values()),
op.join(args.fragment_dir, name + ".pdb"))
except AttributeError:
continue
direction = "a"
remark = ""
for resid in cg.define_residue_num_iterator(
elem, seq_ids=True, adjacent=elem[0] != "s"):
if resid in cg.seq._modifications:
remark += "# {}={}".format(fgr.resid_to_str(resid),
cg.seq._modifications[resid])
for stat in cg.get_stats(elem):
stat_name = name + direction
stat.pdb_name = stat_name
print(stat, remark)
direction = "b"