break
if clashing:
break
if clashing:
skipped += 1
continue
if args.outfile is None:
s += print_geom.write(outfile=False)
s += "\n"
else:
if os.path.isdir(os.path.expanduser(args.outfile)):
outfile = os.path.join(os.path.expanduser(args.outfile),
"conformer-%i.xyz" % (conf + 1))
else:
outfile = args.outfile.replace("$i", str(conf + 1))
if "$INFILE" in outfile:
outfile = outfile.replace("$INFILE", get_filename(infile))
print_geom.write(outfile=outfile, append="$i" not in args.outfile)
if args.outfile is None or args.list_info:
print(s[:-1])
if skipped > 0:
print("%i conformers skipped because of clashing substituent(s)" % skipped)
geom.change_distance(a1, a2, dist=vals[2], adjust=True)
#print specified bonds
out = ""
for bond in args.measure:
a1 = geom.find(str(bond[0]))[0]
a2 = geom.find(str(bond[1]))[0]
val = a1.dist(a2)
out += "%f\n" % val
out = out.rstrip()
if len(args.set_ang) + len(args.change) > 0:
if args.outfile:
outfile = args.outfile
if "$INFILE" in outfile:
outfile = outfile.replace("$INFILE", get_filename(f))
geom.write(append=True, outfile=outfile)
else:
print(geom.write(outfile=False))
if len(args.measure) > 0:
if not args.outfile:
print(out)
else:
outfile = args.outfile
if "$INFILE" in outfile:
outfile = outfile.replace("$INFILE", get_filename(f))
with open(outfile, "a") as f:
f.write(out)
outfile = outfiles[i].replace("$i", fmt % k)
else:
outfile = outfiles[i]
followed_geom = pathway.geom_func(t)
followed_geom.comment = (
"animating mode %s scaled to displace at most [%s]" % (
repr(mode),
", ".join(
str(pathway.var_func[key](t)) for key in other_vars),
))
if args.outfile:
followed_geom.write(append=False,
outfile=outfile.replace(
"$INFILE",
get_filename(args.input_file)))
else:
print(followed_geom.write(outfile=False))
else:
w = width(len(modes))
fmt = "%0" + "%i" % w + "i"
followed_geom = geom.copy()
followed_geom.update_geometry(geom.coords + dX)
followed_geom.comment = "following mode %s scaled to displace at most %s" % (
repr(mode),
repr(scale[i]),
)
outfile = outfiles[i]
original_ligands = [l for l in ligands]
lig_keys = sum([len(ligand.key_atoms) for ligand in ligands])
while len(key) > lig_keys:
ligands.extend(l.copy() for l in original_ligands)
lig_keys += sum(
[len(ligand.key_atoms) for ligand in original_ligands])
j = 0
while len(key) < sum([len(ligand.key_atoms)
for ligand in ligands]):
if j >= len(cat.components["ligand"]):
raise RuntimeError(
"new ligand appears to have a higher denticity than old ligands combined"
)
key.extend(cat.components["ligand"][j].key_atoms)
j += 1
cat_copy.map_ligand(ligands, key)
if args.outfile:
if "$INFILE" in args.outfile:
outfile = args.outfile.replace("$INFILE",
get_filename(infile))
outfile = outfile.replace("$LIGAND", lig_name)
cat_copy.write(append=False, outfile=outfile)
else:
s = cat_copy.write(outfile=False)
print(s)
def ligandSterimol(session,
selection,
radii="UMN",
showVectors=True,
showRadii=True,
at_L=None,
bisect_L=False,
return_values=False):
models, center, key_atoms = avoidTargets(session.logger, selection)
radii = radii.lower()
targets = []
coord_atoms = []
datas = []
info = "<pre>model\tcoord. atoms\tB1\tB2\tB3\tB4\tB5\tL\n"
# if return_values:
# if len(models.keys()) > 1:
# raise RuntimeError("only one substituent may be selected")
# if any(len(models[key]) > 1 for key in models.keys()):
# raise RuntimeError("only one substituent may be selected")
for model in models:
rescol = ResidueCollection(model)
comp_atoms = [AtomSpec(at.atomspec) for at in models[model]]
key_atomspec = [AtomSpec(at.atomspec) for at in key_atoms[model]]
center_atomspec = [AtomSpec(at.atomspec) for at in center[model]]
if len(center_atomspec) != 1:
session.logger.error(
"ligand sterimol requires one central atom to which " + \
"the ligand is coordinated\n" + \
"%i were found on model %s:\n" % (len(center_atomspec), model.atomspec) + \
"\n".join([at.atomspec for at in center[model]])
)
continue
comp = Component(
rescol.find(comp_atoms),
to_center=rescol.find(center_atomspec),
key_atoms=rescol.find(key_atomspec),
)
data = comp.sterimol(
return_vector=True,
radii=radii,
at_L=at_L,
to_center=rescol.find(center_atomspec),
bisect_L=bisect_L,
)
l = np.linalg.norm(data["L"][1] - data["L"][0])
b1 = np.linalg.norm(data["B1"][1] - data["B1"][0])
b2 = np.linalg.norm(data["B2"][1] - data["B2"][0])
b3 = np.linalg.norm(data["B3"][1] - data["B3"][0])
b4 = np.linalg.norm(data["B4"][1] - data["B4"][0])
b5 = np.linalg.norm(data["B5"][1] - data["B5"][0])
if showVectors:
for key, color in zip(
["B1", "B2", "B3", "B4", "B5", "L"],
["black", "green", "purple", "orange", "red", "blue"]):
start, end = data[key]
s = ".color %s\n" % color
s += ".note Sterimol %s\n" % key
s += ".arrow %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f\n" % (
*start, *end)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(session, stream,
"Sterimol %s" % key)
session.models.add(bild_obj, parent=model)
if showRadii:
s = ".note radii\n"
s += ".transparency 75\n"
color = None
for atom in comp.atoms:
chix_atom = atom.chix_atom
if radii == "umn":
r = VDW_RADII[chix_atom.element.name]
elif radii == "bondi":
r = BONDI_RADII[chix_atom.element.name]
if color is None or chix_atom.color != color:
color = chix_atom.color
rgb = [x / 255. for x in chix_atom.color]
rgb.pop(-1)
s += ".color %f %f %f\n" % tuple(rgb)
s += ".sphere %f %f %f %f\n" % (*chix_atom.coord, r)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(session, stream, "Sterimol radii")
session.models.add(bild_obj, parent=model)
name = get_filename(model.name, include_parent_dir=False)
info += "%-16s\t%-11s\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n" % (
name, ", ".join(at.atomspec
for at in key_atoms[model]), b1, b2, b3, b4, b5, l)
targets.append(name)
coord_atoms.append([at.atomspec for at in key_atoms[model]])
datas.append(data)
info = info.strip()
info += "</pre>"
if not return_values:
session.logger.info(info, is_html=True)
if return_values:
return targets, coord_atoms, datas
def sterimol(
session,
selection,
radii="UMN",
showVectors=True,
showRadii=True,
LCorrection="FORTRAN",
return_values=False
):
models, attached = avoidTargets(session.logger, selection)
radii = radii.lower()
old_L = False
if LCorrection.upper() == "FORTRAN":
old_L = True
model_names = []
targets = []
datas = []
info = "<pre>model\tsubstituent atom\tB1\tB2\tB3\tB4\tB5\tL\n"
# if return_values:
# if len(models.keys()) > 1:
# raise RuntimeError("only one substituent may be selected")
# if any(len(models[key]) > 1 for key in models.keys()):
# raise RuntimeError("only one substituent may be selected")
for model in models:
rescol = ResidueCollection(model, refresh_ranks=False)
for res in models[model]:
for target in models[model][res]:
end_atomspec = AtomSpec(attached[target].atomspec)
start_atomspec = AtomSpec(target.atomspec)
sub_atoms = rescol.get_fragment(start_atomspec, end_atomspec)
sub = Substituent(
sub_atoms,
end=rescol.find_exact(end_atomspec)[0],
detect=False,
)
data = sub.sterimol(
return_vector=True,
radii=radii,
old_L=old_L,
)
l = np.linalg.norm(data["L"][1] - data["L"][0])
b1 = np.linalg.norm(data["B1"][1] - data["B1"][0])
b2 = np.linalg.norm(data["B2"][1] - data["B2"][0])
b3 = np.linalg.norm(data["B3"][1] - data["B3"][0])
b4 = np.linalg.norm(data["B4"][1] - data["B4"][0])
b5 = np.linalg.norm(data["B5"][1] - data["B5"][0])
if showVectors:
for key, color in zip(
["B1", "B2", "B3", "B4", "B5", "L"],
["black", "green", "purple", "orange", "red", "blue"]
):
start, end = data[key]
s = ".color %s\n" % color
s += ".note Sterimol %s\n" % key
s += ".arrow %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f\n" % (*start, *end)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(session, stream, "Sterimol %s" % key)
session.models.add(bild_obj, parent=model)
if showRadii:
s = ".note radii\n"
s += ".transparency 75\n"
color = None
for atom in sub.atoms:
chix_atom = atom.chix_atom
if radii == "umn":
r = VDW_RADII[chix_atom.element.name]
elif radii == "bondi":
r = BONDI_RADII[chix_atom.element.name]
if color is None or chix_atom.color != color:
color = chix_atom.color
rgb = [x/255. for x in chix_atom.color]
rgb.pop(-1)
s += ".color %f %f %f\n" % tuple(rgb)
s += ".sphere %f %f %f %f\n" % (*chix_atom.coord, r)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(session, stream, "Sterimol radii")
session.models.add(bild_obj, parent=model)
model_name = get_filename(model.name, include_parent_dir=False)
info += "%-16s\t%-11s\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n" % (
model_name,
target.atomspec,
b1, b2, b3, b4, b5, l
)
model_names.append(model_name)
targets.append(target.atomspec)
datas.append(data)
info = info.strip()
info += "</pre>"
if not return_values:
session.logger.info(info, is_html=True)
if return_values:
return model_names, targets, datas
fig = plt.gcf()
fig.clear()
freq.plot_ir(
fig,
centers=args.centers,
widths=args.widths,
plot_type=args.plot_type,
peak_type=args.peak_type,
reverse_x=args.reverse_x,
fwhm=args.fwhm,
point_spacing=args.point_spacing,
voigt_mixing=args.voigt_mixing,
linear_scale=args.linear_scale,
quadratic_scale=args.quadratic_scale,
exp_data=exp_data,
anharmonic=freq.anharm_data and args.anharmonic,
)
if args.fig_width:
fig.set_figwidth(args.fig_width)
if args.fig_height:
fig.set_figheight(args.fig_height)
if args.outfile:
outfile_name = args.outfile.replace("$INFILE", get_filename(f))
plt.savefig(outfile_name, dpi=300)
else:
plt.show()
s = ""
unique = 0
total = 0
for n_atoms in structures:
for formula in structures[n_atoms]:
formula_unique = len(structures[n_atoms][formula])
unique += formula_unique
s += "%s\n" % formula
for group in structures[n_atoms][formula]:
total += len(group)
if args.directory:
dir_name = os.path.join(
args.directory,
formula,
get_filename(group[0][0].name, include_parent_dir=False),
)
if not os.path.exists(dir_name):
os.makedirs(dir_name)
for geom, rmsd, _ in group:
geom.comment = "RMSD from %s = %.4f" % (
get_filename(group[0][0].name,
include_parent_dir=False),
rmsd,
)
if args.energy_filter and all(
"energy" in g.other for g in [geom, group[0][0]]):
d_nrg = UNIT.HART_TO_KCAL * (
geom.other["energy"] - group[0][0].other["energy"])
geom.comment += " energy from %s = %.1f kcal/mol" % (
get_filename(group[0][0].name,