def run(args):
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
for comp_id in args:
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=comp_id)
motif = comp_comp_id.as_geometry_restraints_motif()
motif.show()
def main():
list_cif = mon_lib_list_cif()
geostd_list_cif_obj = geostd_list_cif()
list_cif = merge_and_overwrite_cifs(geostd_list_cif_obj,
list_cif,
)
print(dir(list_cif))
print(dir(list_cif.cif))
cif = list_cif.cif
print(list(cif.blocks.keys()))
j=0
tmp = []
for i, block in enumerate(cif.blocks):
if block in ['link_list']: continue
if block.startswith('link_'):
j+=1
tmp.append([])
tmp[-1].append(block)
tmp[-1].append('Taken from Monomer Library or GeoStd')
#tmp[-1].append('')
#tmp[-1].append([block]*6)
#tmp[-1].append([0,1,2,3,4,5])
print(i, j, block)
outl = 'standard_cif_links = [\n'
for block in sorted(tmp):
outl += ' %s,\n' % block
outl += ']\n'
print(outl)
def exercise():
verbose = "--verbose" in sys.argv[1:]
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
open("tmp.cif", "w").write(tmp_cif)
srv.process_cif(file_name="tmp.cif")
comp_comp_id = srv.get_comp_comp_id_direct(comp_id="tst")
motif = comp_comp_id.as_geometry_restraints_motif()
out = StringIO()
motif.show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), expected_out_tst_comp)
for link_link_id in srv.link_link_id_list:
out = StringIO()
link_link_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (link_link_id.chem_link.id == "tst_lnk"):
assert not show_diff(out.getvalue(), expected_out_tst_lnk)
for mod_mod_id in srv.mod_mod_id_list:
out = StringIO()
mod_mod_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (mod_mod_id.chem_mod.id == "tst_mod"):
assert not show_diff(out.getvalue(), expected_out_tst_mod)
print "OK"
def run(args):
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
for comp_id in args:
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=comp_id)
motif = comp_comp_id.as_geometry_restraints_motif()
motif.show()
def exercise():
verbose = "--verbose" in sys.argv[1:]
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
open("tmp.cif", "w").write(tmp_cif)
srv.process_cif(file_name="tmp.cif")
comp_comp_id = srv.get_comp_comp_id_direct(comp_id="tst")
motif = comp_comp_id.as_geometry_restraints_motif()
out = StringIO()
motif.show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), expected_out_tst_comp)
for link_link_id in srv.link_link_id_list:
out = StringIO()
link_link_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (link_link_id.chem_link.id == "tst_lnk"):
assert not show_diff(out.getvalue(), expected_out_tst_lnk)
for mod_mod_id in srv.mod_mod_id_list:
out = StringIO()
mod_mod_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (mod_mod_id.chem_mod.id == "tst_mod"):
assert not show_diff(out.getvalue(), expected_out_tst_mod)
print "OK"
def exercise():
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
print("srv.root_path:", srv.root_path)
table_of_contents = []
n_get_comp_comp_id_successes = 0
unknown_type_energy_counts = dict_with_default_0()
missing_angle_definitions_counts = dict_with_default_0()
missing_bond_values_counts = dict_with_default_0()
missing_angle_values_counts = dict_with_default_0()
for first_char in string.lowercase + string.digits:
sub_dir = os.path.join(srv.root_path, first_char)
if (not os.path.isdir(sub_dir)): continue
for node in os.listdir(sub_dir):
if (not node.lower().endswith(".cif")): continue
comp_id = node[:-4]
if (comp_id.endswith("_EL")): continue
if (comp_id in ["CON_CON", "PRN_PRN"]):
comp_id = comp_id[:3]
if (comp_id.upper() != comp_id):
print("Mixed case:", os.path.join(first_char, node))
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=comp_id)
if (comp_comp_id is None):
print("Error instantiating comp_comp_id %s (%s)" %
(comp_id, os.path.join(sub_dir, node)))
else:
n_get_comp_comp_id_successes += 1
table_of_contents.append(" ".join(
[comp_id.upper(),
os.path.join(first_char, node)]))
status = detect_unknown_type_energy(comp_id=comp_id,
comp_comp_id=comp_comp_id)
unknown_type_energy_counts[status] += 1
status = detect_missing_angle_definitions(
comp_id=comp_id, comp_comp_id=comp_comp_id)
missing_angle_definitions_counts[status] += 1
status = detect_missing_bond_values(comp_id=comp_id,
comp_comp_id=comp_comp_id)
missing_bond_values_counts[status] += 1
status = detect_missing_angle_values(comp_id=comp_id,
comp_comp_id=comp_comp_id)
missing_angle_values_counts[status] += 1
if (1 and status != "ok"):
print('svn rm "%s"' % os.path.join(first_char, node))
print("number of cif files read successfully:",
n_get_comp_comp_id_successes)
print("unknown type_energy counts:", unknown_type_energy_counts)
print("missing bond angle definitions counts:", \
missing_angle_definitions_counts)
print("missing bond values counts:", missing_bond_values_counts)
print("missing angle values counts:", missing_angle_values_counts)
print("writing file table_of_contents")
open("table_of_contents", "w").write("\n".join(table_of_contents) + "\n")
def exercise():
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
print "srv.root_path:", srv.root_path
table_of_contents = []
n_get_comp_comp_id_successes = 0
unknown_type_energy_counts = dict_with_default_0()
missing_angle_definitions_counts = dict_with_default_0()
missing_bond_values_counts = dict_with_default_0()
missing_angle_values_counts = dict_with_default_0()
for first_char in string.lowercase+string.digits:
sub_dir = os.path.join(srv.root_path, first_char)
if (not os.path.isdir(sub_dir)): continue
for node in os.listdir(sub_dir):
if (not node.lower().endswith(".cif")): continue
comp_id = node[:-4]
if (comp_id.endswith("_EL")): continue
if (comp_id in ["CON_CON", "PRN_PRN"]):
comp_id = comp_id[:3]
if (comp_id.upper() != comp_id):
print "Mixed case:", os.path.join(first_char, node)
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=comp_id)
if (comp_comp_id is None):
print "Error instantiating comp_comp_id %s (%s)" % (
comp_id, os.path.join(sub_dir, node))
else:
n_get_comp_comp_id_successes += 1
table_of_contents.append(
" ".join([comp_id.upper(), os.path.join(first_char, node)]))
status = detect_unknown_type_energy(
comp_id=comp_id, comp_comp_id=comp_comp_id)
unknown_type_energy_counts[status] += 1
status = detect_missing_angle_definitions(
comp_id=comp_id, comp_comp_id=comp_comp_id)
missing_angle_definitions_counts[status] += 1
status = detect_missing_bond_values(
comp_id=comp_id, comp_comp_id=comp_comp_id)
missing_bond_values_counts[status] += 1
status = detect_missing_angle_values(
comp_id=comp_id, comp_comp_id=comp_comp_id)
missing_angle_values_counts[status] += 1
if (1 and status != "ok"):
print 'svn rm "%s"' % os.path.join(first_char, node)
print "number of cif files read successfully:", n_get_comp_comp_id_successes
print "unknown type_energy counts:", unknown_type_energy_counts
print "missing bond angle definitions counts:", \
missing_angle_definitions_counts
print "missing bond values counts:", missing_bond_values_counts
print "missing angle values counts:", missing_angle_values_counts
print "writing file table_of_contents"
open("table_of_contents", "w").write("\n".join(table_of_contents)+"\n")
def run () :
from mmtbx.monomer_library import server
from libtbx.utils import Sorry
try :
cif1 = server.mon_lib_list_cif()
cif2 = server.geostd_list_cif()
cif3 = server.mon_lib_ener_lib_cif()
assert (not None in [cif1, cif2, cif3])
except server.MonomerLibraryServerError :
raise Sorry("The monomer library installation could not be found. If "+
"you are using a Phenix installer, we recommend downloading the "+
"installer again and reinstalling.")
else :
print "OK"
def run():
from mmtbx.monomer_library import server
from libtbx.utils import Sorry
try:
cif1 = server.mon_lib_list_cif()
cif2 = server.geostd_list_cif()
cif3 = server.mon_lib_ener_lib_cif()
assert (not None in [cif1, cif2, cif3])
except server.MonomerLibraryServerError:
raise Sorry(
"The monomer library installation could not be found. If " +
"you are using a Phenix installer, we recommend downloading the " +
"installer again and reinstalling.")
else:
print("OK")
def exercise():
verbose = "--verbose" in sys.argv[1:]
quick = "--quick" in sys.argv[1:]
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
print("srv.root_path:", srv.root_path)
default_switch = "--default_off" not in sys.argv[1:]
if (False or default_switch):
monomers_with_commas = {}
atom_id_counts = dicts.with_default_value(0)
for row_id in list_cif.cif["comp_list"]["_chem_comp.id"]:
if (quick and random.random() < 0.95): continue
if (verbose): print("id:", row_id)
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=row_id)
if (comp_comp_id is None):
print("Could not instantiating comp_comp_id(%s)" % row_id)
else:
has_primes = False
has_commas = False
for atom in comp_comp_id.atom_list:
atom_id_counts[atom.atom_id] += 1
if (atom.atom_id.find("'") >= 0):
has_primes = True
if (atom.atom_id.find(",") >= 0):
has_commas = True
if (has_commas):
monomers_with_commas[
comp_comp_id.chem_comp.id] = has_primes
print(monomers_with_commas)
atom_ids = flex.std_string(list(atom_id_counts.keys()))
counts = flex.size_t(list(atom_id_counts.values()))
perm = flex.sort_permutation(data=counts, reverse=True)
atom_ids = atom_ids.select(perm)
counts = counts.select(perm)
for atom_id, count in zip(atom_ids, counts):
print(atom_id, count)
if (False or default_switch):
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
if (quick and random.random() < 0.95): continue
if (verbose): print("id:", row["_chem_comp.id"])
comp_comp_id = srv.get_comp_comp_id_direct(
comp_id=row["_chem_comp.id"])
check_chem_comp(cif_types.chem_comp(**row), comp_comp_id)
if ("--pickle" in sys.argv[1:]):
easy_pickle.dump("mon_lib.pickle", srv)
if (False or default_switch):
comp = srv.get_comp_comp_id_direct("GLY")
comp.show()
mod = srv.mod_mod_id_dict["COO"]
comp.apply_mod(mod).show()
if (False or default_switch):
comp = srv.get_comp_comp_id_direct("LYS")
comp.show()
mod = srv.mod_mod_id_dict["B2C"]
comp.apply_mod(mod).show()
if (False or default_switch):
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
if (quick and random.random() < 0.95): continue
comp_comp_id = srv.get_comp_comp_id_direct(row["_chem_comp.id"])
if (comp_comp_id is not None):
if (comp_comp_id.classification == "peptide"):
print(comp_comp_id.chem_comp.id,
comp_comp_id.chem_comp.name,
end=' ')
print(row["_chem_comp.group"], end=' ')
grp = row["_chem_comp.group"].lower().strip()
if (grp not in ("l-peptide", "d-peptide", "polymer")):
print("LOOK", end=' ')
#if (not os.path.isdir("look")): os.makedirs("look")
#open("look/%s.cif" % row["_chem_comp.id"], "w").write(
#open(comp_comp_id.file_name).read())
print()
elif (row["_chem_comp.group"].lower().find("peptide") >= 0
or comp_comp_id.chem_comp.group.lower().find("peptide")
>= 0):
print(comp_comp_id.chem_comp.id,
comp_comp_id.chem_comp.name,
end=' ')
print(row["_chem_comp.group"], "MISMATCH")
if (comp_comp_id.classification in ("RNA", "DNA")):
print(comp_comp_id.chem_comp.id,
comp_comp_id.chem_comp.name,
end=' ')
print(row["_chem_comp.group"], end=' ')
if (comp_comp_id.classification !=
row["_chem_comp.group"].strip()):
print(comp_comp_id.classification, "MISMATCH", end=' ')
print()
elif (row["_chem_comp.group"].lower().find("NA") >= 0
or comp_comp_id.chem_comp.group.lower().find("NA") >= 0):
print(comp_comp_id.chem_comp.id,
comp_comp_id.chem_comp.name,
end=' ')
print(row["_chem_comp.group"], "MISMATCH")
if (False or default_switch):
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
if (quick and random.random() < 0.95): continue
comp_comp_id = srv.get_comp_comp_id_direct(row["_chem_comp.id"])
if (comp_comp_id is not None):
planes = comp_comp_id.get_planes()
for plane in planes:
dist_esd_dict = {}
for plane_atom in plane.plane_atoms:
dist_esd_dict[str(plane_atom.dist_esd)] = 0
# FIXME: might break compat for py2/3 because indexing a values call
if (len(dist_esd_dict) != 1
or list(dist_esd_dict.keys())[0] != "0.02"):
print(comp_comp_id.chem_comp.id,
plane.plane_id,
end=' ')
print(list(dist_esd_dict.keys()))
if (False or default_switch):
standard_amino_acids = [
"GLY", "VAL", "ALA", "LEU", "ILE", "PRO", "MET", "PHE", "TRP",
"SER", "THR", "TYR", "CYS", "ASN", "GLN", "ASP", "GLU", "LYS",
"ARG", "HIS"
]
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
is_standard_aa = row["_chem_comp.id"] in standard_amino_acids
if (1 and not is_standard_aa):
continue
comp_comp_id = srv.get_comp_comp_id_direct(row["_chem_comp.id"])
if (is_standard_aa):
assert comp_comp_id is not None
assert comp_comp_id.chem_comp.group.strip() == "L-peptide"
if (comp_comp_id is not None):
print(comp_comp_id.chem_comp.id.strip(), end=' ')
print(comp_comp_id.chem_comp.name.strip(), end=' ')
print(comp_comp_id.chem_comp.group.strip())
for tor in comp_comp_id.tor_list:
print(" tor:", tor.atom_id_1, tor.atom_id_2, end=' ')
print(tor.atom_id_3,
tor.atom_id_4,
tor.value_angle,
end=' ')
print(tor.value_angle_esd, tor.period)
for chir in comp_comp_id.chir_list:
print(" chir:",
chir.atom_id_centre,
chir.atom_id_1,
end=' ')
print(chir.atom_id_2, chir.atom_id_3, chir.volume_sign)
if (False or default_switch):
elib = server.ener_lib()
if (False or default_switch):
for syn in elib.lib_synonym.items():
print(syn)
if (False or default_switch):
for vdw in elib.lib_vdw:
vdw.show()
print("OK")
def exercise():
verbose = "--verbose" in sys.argv[1:]
quick = "--quick" in sys.argv[1:]
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
print "srv.root_path:", srv.root_path
default_switch = "--default_off" not in sys.argv[1:]
if (False or default_switch):
monomers_with_commas = {}
atom_id_counts = dicts.with_default_value(0)
for row_id in list_cif.cif["comp_list"]["_chem_comp.id"]:
if (quick and random.random() < 0.95): continue
if (verbose): print "id:", row_id
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=row_id)
if (comp_comp_id is None):
print "Error instantiating comp_comp_id(%s)" % row_id
else:
has_primes = False
has_commas = False
for atom in comp_comp_id.atom_list:
atom_id_counts[atom.atom_id] += 1
if (atom.atom_id.find("'") >= 0):
has_primes = True
if (atom.atom_id.find(",") >= 0):
has_commas = True
if (has_commas):
monomers_with_commas[comp_comp_id.chem_comp.id] = has_primes
print monomers_with_commas
atom_ids = flex.std_string(atom_id_counts.keys())
counts = flex.size_t(atom_id_counts.values())
perm = flex.sort_permutation(data=counts, reverse=True)
atom_ids = atom_ids.select(perm)
counts = counts.select(perm)
for atom_id,count in zip(atom_ids, counts):
print atom_id, count
if (False or default_switch):
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
if (quick and random.random() < 0.95): continue
if (verbose): print "id:", row["_chem_comp.id"]
comp_comp_id = srv.get_comp_comp_id_direct(comp_id=row["_chem_comp.id"])
check_chem_comp(cif_types.chem_comp(**row), comp_comp_id)
if ("--pickle" in sys.argv[1:]):
easy_pickle.dump("mon_lib.pickle", srv)
if (False or default_switch):
comp = srv.get_comp_comp_id_direct("GLY")
comp.show()
mod = srv.mod_mod_id_dict["COO"]
comp.apply_mod(mod).show()
if (False or default_switch):
comp = srv.get_comp_comp_id_direct("LYS")
comp.show()
mod = srv.mod_mod_id_dict["B2C"]
comp.apply_mod(mod).show()
if (False or default_switch):
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
if (quick and random.random() < 0.95): continue
comp_comp_id = srv.get_comp_comp_id_direct(row["_chem_comp.id"])
if (comp_comp_id is not None):
if (comp_comp_id.classification == "peptide"):
print comp_comp_id.chem_comp.id, comp_comp_id.chem_comp.name,
print row["_chem_comp.group"],
grp = row["_chem_comp.group"].lower().strip()
if (grp not in ("l-peptide", "d-peptide", "polymer")):
print "LOOK",
#if (not os.path.isdir("look")): os.makedirs("look")
#open("look/%s.cif" % row["_chem_comp.id"], "w").write(
#open(comp_comp_id.file_name).read())
print
elif (row["_chem_comp.group"].lower().find("peptide") >= 0
or comp_comp_id.chem_comp.group.lower().find("peptide") >= 0):
print comp_comp_id.chem_comp.id, comp_comp_id.chem_comp.name,
print row["_chem_comp.group"], "MISMATCH"
if (comp_comp_id.classification in ("RNA", "DNA")):
print comp_comp_id.chem_comp.id, comp_comp_id.chem_comp.name,
print row["_chem_comp.group"],
if (comp_comp_id.classification != row["_chem_comp.group"].strip()):
print comp_comp_id.classification, "MISMATCH",
print
elif (row["_chem_comp.group"].lower().find("NA") >= 0
or comp_comp_id.chem_comp.group.lower().find("NA") >= 0):
print comp_comp_id.chem_comp.id, comp_comp_id.chem_comp.name,
print row["_chem_comp.group"], "MISMATCH"
if (False or default_switch):
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
if (quick and random.random() < 0.95): continue
comp_comp_id = srv.get_comp_comp_id_direct(row["_chem_comp.id"])
if (comp_comp_id is not None):
planes = comp_comp_id.get_planes()
for plane in planes:
dist_esd_dict = {}
for plane_atom in plane.plane_atoms:
dist_esd_dict[str(plane_atom.dist_esd)] = 0
if (len(dist_esd_dict) != 1 or dist_esd_dict.keys()[0] != "0.02"):
print comp_comp_id.chem_comp.id, plane.plane_id,
print dist_esd_dict.keys()
if (False or default_switch):
standard_amino_acids = [
"GLY", "VAL", "ALA", "LEU", "ILE", "PRO", "MET", "PHE", "TRP", "SER",
"THR", "TYR", "CYS", "ASN", "GLN", "ASP", "GLU", "LYS", "ARG", "HIS"]
for row in list_cif.cif["comp_list"]["_chem_comp"].iterrows():
is_standard_aa = row["_chem_comp.id"] in standard_amino_acids
if (1 and not is_standard_aa):
continue
comp_comp_id = srv.get_comp_comp_id_direct(row["_chem_comp.id"])
if (is_standard_aa):
assert comp_comp_id is not None
assert comp_comp_id.chem_comp.group.strip() == "L-peptide"
if (comp_comp_id is not None):
print comp_comp_id.chem_comp.id.strip(),
print comp_comp_id.chem_comp.name.strip(),
print comp_comp_id.chem_comp.group.strip()
for tor in comp_comp_id.tor_list:
print " tor:", tor.atom_id_1, tor.atom_id_2,
print tor.atom_id_3, tor.atom_id_4, tor.value_angle,
print tor.value_angle_esd, tor.period
for chir in comp_comp_id.chir_list:
print " chir:", chir.atom_id_centre, chir.atom_id_1,
print chir.atom_id_2, chir.atom_id_3, chir.volume_sign
if (False or default_switch):
elib = server.ener_lib()
if (False or default_switch):
for syn in elib.lib_synonym.items():
print syn
if (False or default_switch):
for vdw in elib.lib_vdw:
vdw.show()
print "OK"
def _generate_restraints(self, res_ids):
list = server.mon_lib_list_cif()
self._residues = [ row["_chem_comp.id"] for row in list.cif["comp_list"]["_chem_comp"].iterrows() ]
self._srv = server.server(list_cif=list)
bonds = {}
output = []
for r in res_ids:
if not r in self._residues:
self._generate_ligand_restraints()
break
for r in res_ids:
res = self._srv.get_comp_comp_id_direct(r)
if res is not None:
for b in res.bond_list:
if not (b.atom_id_1.startswith('H') or b.atom_id_2.startswith('H')):
if not b.atom_id_1 in bonds:
bonds[b.atom_id_1] = {}
bonds[b.atom_id_1][b.atom_id_2] = b.value_dist
output.append('DFIX_%s %.3f %s %s' % (r, b.value_dist, b.atom_id_1, b.atom_id_2))
for a in res.angle_list:
if not (a.atom_id_1.startswith('H') or a.atom_id_2.startswith('H') or a.atom_id_3.startswith('H')):
ang = None
dist1 = None
dist2 = None
if a.atom_id_1 in bonds:
if a.atom_id_2 in bonds[a.atom_id_1]:
dist1 = bonds[a.atom_id_1][a.atom_id_2]
if a.atom_id_2 in bonds:
if a.atom_id_1 in bonds[a.atom_id_2]:
dist1 = bonds[a.atom_id_2][a.atom_id_1]
if a.atom_id_2 in bonds:
if a.atom_id_3 in bonds[a.atom_id_2]:
dist2 = bonds[a.atom_id_2][a.atom_id_3]
if a.atom_id_3 in bonds:
if a.atom_id_2 in bonds[a.atom_id_3]:
dist2 = bonds[a.atom_id_3][a.atom_id_2]
if a.value_angle is not None and dist1 is not None and dist2 is not None:
dang = math.sqrt(math.pow(dist1,2)+math.pow(dist2,2)-(2*dist1*dist2*math.cos((math.pi/180)*a.value_angle)))
output.append('DANG_%s %.3f %s %s' % (r, dang, a.atom_id_1, a.atom_id_3))
for p in res.get_planes():
atoms = []
for a in p.plane_atoms:
if not a.atom_id.startswith('H'):
atoms.append(a.atom_id)
if len(atoms) > 2:
output.append('FLAT_' + r + ' ' + ' '.join(atoms))
output.append('CHIV_%s C' % r)
for c in res.chir_list:
output.append('CHIV_%s %.3f %s' % (r, res.get_chir_volume_ideal(c) * (1 if c.volume_sign == 'positiv' else -1), c.atom_id_centre))
for t in res.tor_list:
if t.id.startswith('chi'):
output.append('RTAB_%s %s %s %s %s %s' % (r, t.id.capitalize(), t.atom_id_1, t.atom_id_2, t.atom_id_3, t.atom_id_4))
output.append('\n')
return '\n'.join(output)
