def main(parser):
args = parser.parse_args()
with fuc.hide_traceback():
cg1, cg2 = fuc.cgs_from_args(args,
nargs=2,
rna_type="3d",
enable_logging=True)
dir1 = np.array(args.directions[0].split(","), dtype=float)
dir2 = np.array(args.directions[1].split(","), dtype=float)
proj1 = ftmp.Projection2D(cg1, dir1)
proj2 = ftmp.Projection2D(cg2, dir2)
vrs1 = np.array(
[x for p in sorted(proj1._coords.keys()) for x in proj1._coords[p]])
vrs2 = np.array(
[x for p in sorted(proj2._coords.keys()) for x in proj2._coords[p]])
print(ftms.rmsd(vrs1, vrs2))
if args.plot:
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
proj1.plot(ax, line2dproperties={"color": "green"})
proj2.plot(ax, line2dproperties={"color": "red"})
plt.show()
def main(args):
with fuc.hide_traceback():
bg, = fuc.cgs_from_args(args, "any", enable_logging=True)
multiloops, _ = bg.find_multiloop_loops()
for multi in multiloops:
shortened = set()
for m in multi:
if m[0] != 'm':
continue
connected_stems = list(bg.edges[m])
for to_shorten in connected_stems:
if to_shorten in shortened:
continue
shortened.add(to_shorten)
# find the stems which are connected to this multiloop
# and pick a random one
db = list(bg.to_dotbracket_string())
# get the side of the stem which is connected to the
# multiloop
(s1b, s1e) = bg.get_sides(to_shorten, m)
# print to_shorten, s1b, "(", bg.defines[to_shorten], ")"
# the nucleotides that need to be changed
to_change = bg.get_side_nucleotides(to_shorten, s1b)
# print bg.defines[to_shorten], to_change
db[to_change[0] - 1] = '.'
db[to_change[1] - 1] = '.'
print("".join(db))
def main(parser):
args = parser.parse_args()
with fuc.hide_traceback():
cg1, cg2 = fuc.cgs_from_args(
args, rna_type="3d", enable_logging=True)
dir1 = np.array(args.directions[0].split(","), dtype=float)
dir2 = np.array(args.directions[1].split(","), dtype=float)
proj1 = ftmp.Projection2D(cg1, dir1)
proj2 = ftmp.Projection2D(cg2, dir2)
vrs1 = np.array([x for p in sorted(proj1._coords.keys())
for x in proj1._coords[p]])
vrs2 = np.array([x for p in sorted(proj2._coords.keys())
for x in proj2._coords[p]])
print(ftms.rmsd(vrs1, vrs2))
if args.plot:
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
proj1.plot(ax, line2dproperties={"color": "green"})
proj2.plot(ax, line2dproperties={"color": "red"})
plt.show()
def main(args):
with fuc.hide_traceback():
cg1, cg2 = fuc.cgs_from_args(args, rna_type="3d", enable_logging=True)
if not (args.acc or args.rmsd or args.pdb_rmsd):
showall = True
else:
showall = False
if showall or args.acc:
if cg1.defines != cg2.defines:
if args.acc:
print(
"Cannot compare two 3d structures that do not correspond to the same RNA."
)
sys.exit(1)
else:
adj = ftms.AdjacencyCorrelation(cg1)
print("ACC:\t{:.3f}".format(ftms.mcc(adj.evaluate(cg2))))
if showall or args.rmsd:
print("RMSD:\t{:.3f}".format(ftms.cg_rmsd(cg1, cg2)))
if showall or args.pdb_rmsd:
if not pdb_rmsd(cg1, cg2):
# If --pdb-rmsd was not given, just don't print it.
# If it was given, we exit with non-zero exit status.
if args.pdb_rmsd:
print(
"Cannot calculate PDB-RMSD: The two files do not contain the same chains."
)
sys.exit(1)
def main(args):
with fuc.hide_traceback():
cg1, cg2 = fuc.cgs_from_args(
args, rna_type="3d", enable_logging=True)
if not (args.acc or args.rmsd or args.pdb_rmsd):
showall = True
else:
showall = False
if showall or args.acc:
if cg1.defines != cg2.defines:
if args.acc:
print(
"Cannot compare two 3d structures that do not correspond to the same RNA.")
sys.exit(1)
else:
adj = ftms.AdjacencyCorrelation(cg1)
print("ACC:\t{:.3f}".format(ftms.mcc(adj.evaluate(cg2))))
if showall or args.rmsd:
print("RMSD:\t{:.3f}".format(ftms.cg_rmsd(cg1, cg2)))
if showall or args.pdb_rmsd:
if not pdb_rmsd(cg1, cg2):
# If --pdb-rmsd was not given, just don't print it.
# If it was given, we exit with non-zero exit status.
if args.pdb_rmsd:
print(
"Cannot calculate PDB-RMSD: The two files do not contain the same chains.")
sys.exit(1)
def main(args):
rec = fbr.Reconstructor(args.source_pdb_dir, args.source_cg_dir, args.server)
with fuc.hide_traceback(): # Applies only to WrongFileFormat
cgs, fns = fuc.cgs_from_args(args, rna_type="only_cg", enable_logging=True, return_filenames=True)
# Preprocessing
most_common_pdbs = collections.Counter()
for cg in cgs:
sm = fbm.SpatialModel(cg)
sm.load_sampled_elems(None)
curr_fns = set()
for stat in sm.elem_defs.values():
stat_name = stat.pdb_name
pdb_basename = stat_name.split(":")[0]
pdb_filename = op.expanduser(op.join(rec.pdb_library_path, "_".join(pdb_basename.split("_")[:-1])+".cif"))
try:
with open(pdb_filename): pass
except IOError:
pdb_filename = pdb_filename.rstrip(".cif")+".pdb"
curr_fns.add(pdb_filename)
for fn in curr_fns:
most_common_pdbs[fn]+=1
for fn, count in most_common_pdbs.most_common(250):
if count==1:
break
print("Preloading {}, used {} times".format(fn, count))
rec.get_pdb(fn, True)
print("Preloading of most common PDBs done")
logging.getLogger("forgi").setLevel(logging.ERROR)
logging_exceptions.config_from_args(args)
for i, cg in enumerate(cgs):
try:
fn = fns[i]
reconstruct(cg, fn, args, rec)
except Exception as e:
logging_exceptions.log_exception(e)
log.exception("During reconstruction of cg %s, an error occurred: %s", fn, e)
i=0
help="If this is present, --to-file will automatically be true."
"A target filename (or path) without extention. "
"If it is a filename, use the given filename instead of the RNA's name. "
"If more than one input-RNA is present, appends automatically a increasing number."
"If it is a directory, create files in this directory.")
parser.add_argument(
"-f",
"--force",
action="store_true",
help=
"Overwrite files, if they already exist. Note: In case of race conditions, "
"files could be overwritten even if this flag is not provided.")
if __name__ == "__main__":
args = parser.parse_args()
with fuc.hide_traceback():
cgs = fuc.cgs_from_args(args,
rna_type=FILETYPES[args.target_type].rna_type)
if args.filename:
args.to_file = True
if os.path.isdir(args.filename):
directory = args.filename
filename = None
args.filename = None
else:
directory, filename = os.path.split(args.filename)
else:
filename = None
directory = ""
for i, cg in enumerate(cgs):
help="Store the converted RNA in files instead of printing them to stdout. "
"The file-name will be the RNA's name (if present), otherwise 'rna001' etc.")
parser.add_argument("--filename", type=str,
help="If this is present, --to-file will automatically be true."
"A target filename (or path) without extention. "
"If it is a filename, use the given filename instead of the RNA's name. "
"If more than one input-RNA is present, appends automatically a increasing number."
"If it is a directory, create files in this directory.")
parser.add_argument("-f", "--force", action="store_true",
help="Overwrite files, if they already exist. Note: In case of race conditions, "
"files could be overwritten even if this flag is not provided.")
if __name__ == "__main__":
args = parser.parse_args()
with fuc.hide_traceback():
cgs = fuc.cgs_from_args(
args, rna_type=FILETYPES[args.target_type].rna_type)
if args.filename:
args.to_file = True
if os.path.isdir(args.filename):
directory = args.filename
filename = None
args.filename = None
else:
directory, filename = os.path.split(args.filename)
else:
filename = None
directory = ""
for i, cg in enumerate(cgs):