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
def calc_cone(self, *args):
self.settings.cone_option = self.cone_option.currentText()
self.settings.radii = self.radii_option.currentText()
self.settings.display_radii = self.display_radii.checkState(
) == Qt.Checked
self.settings.display_cone = self.display_cone.checkState(
) == Qt.Checked
if self.cone_option.currentText() == "Tolman (Unsymmetrical)":
method = "tolman"
else:
method = self.cone_option.currentText()
radii = self.radii_option.currentText()
return_cones = self.display_cone.checkState() == Qt.Checked
display_radii = self.display_radii.checkState() == Qt.Checked
# self.table.setRowCount(0)
for center_atom in selected_atoms(self.session):
rescol = ResidueCollection(center_atom.structure)
at_center = rescol.find_exact(AtomSpec(center_atom.atomspec))[0]
if center_atom.structure in self.ligands:
comp = Component(
rescol.find([
AtomSpec(atom.atomspec)
for atom in self.ligands[center_atom.structure]
]),
to_center=rescol.find_exact(AtomSpec(
center_atom.atomspec)),
key_atoms=rescol.find(BondedTo(at_center)),
)
else:
comp = Component(
rescol.find(NotAny(at_center)),
to_center=rescol.find_exact(AtomSpec(
center_atom.atomspec)),
key_atoms=rescol.find(BondedTo(at_center)),
)
cone_angle = comp.cone_angle(
center=rescol.find(AtomSpec(center_atom.atomspec)),
method=method,
radii=radii,
return_cones=return_cones,
)
if return_cones:
cone_angle, cones = cone_angle
s = ".transparency 0.5\n"
for cone in cones:
apex, base, radius = cone
s += ".cone %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %.3f open\n" % (
*apex, *base, radius)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(self.session, stream,
"Cone angle %s" % center_atom)
self.session.models.add(bild_obj, parent=center_atom.structure)
if display_radii:
s = ".note radii\n"
s += ".transparency 75\n"
color = None
for atom in comp.atoms:
chix_atom = atom.chix_atom
if radii.lower() == "umn":
r = VDW_RADII[chix_atom.element.name]
elif radii.lower() == "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(self.session, stream,
"Cone angle radii")
self.session.models.add(bild_obj, parent=center_atom.structure)
row = self.table.rowCount()
self.table.insertRow(row)
name = QTableWidgetItem()
name.setData(Qt.DisplayRole, center_atom.structure.name)
self.table.setItem(row, 0, name)
center = QTableWidgetItem()
center.setData(Qt.DisplayRole, center_atom.atomspec)
self.table.setItem(row, 1, center)
ca = QTableWidgetItem()
ca.setData(Qt.DisplayRole, "%.2f" % cone_angle)
self.table.setItem(row, 2, ca)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
def do_change_element(self):
element = self.element.text()
adjust_bonds = self.change_bonds.isChecked()
self.settings.change_bonds = adjust_bonds
vsepr = self.vsepr.currentText()
if vsepr == "do not change":
vsepr = False
elif vsepr == "linear (1 bond)":
vsepr = "linear 1"
goal = 1
elif vsepr == "linear (2 bonds)":
vsepr = "linear 2"
goal = 2
elif vsepr == "trigonal planar (2 bonds)":
vsepr = "bent 2 planar"
goal = 2
elif vsepr == "tetrahedral (2 bonds)":
vsepr = "bent 2 tetrahedral"
goal = 2
elif vsepr == "trigonal planar":
goal = 3
elif vsepr == "tetrahedral (3 bonds)":
vsepr = "bent 3 tetrahedral"
goal = 3
else:
goal = len(Atom.get_shape(vsepr)) - 1
sel = selected_atoms(self.session)
models, _ = guessAttachmentTargets(sel, self.session, allow_adjacent=False)
for model in models:
conv_res = list(models[model].keys())
for res in models[model]:
for target in models[model][res]:
for neighbor in target.neighbors:
if neighbor.residue not in conv_res:
conv_res.append(neighbor.residue)
for pbg in self.session.models.list(type=PseudobondGroup):
for pbond in pbg.pseudobonds:
if target in pbond.atoms and all(atom.structure is model for atom in pbond.atoms):
other_atom = pbond.other_atom(target)
if other_atom.residue not in conv_res:
conv_res.append(other_atom.residue)
rescol = ResidueCollection(model, convert_residues=conv_res)
for res in models[model]:
residue = [resi for resi in rescol.residues if resi.chix_residue is res][0]
for target in models[model][res]:
targ = rescol.find_exact(AtomSpec(target.atomspec))[0]
adjust_hydrogens = vsepr
if vsepr is not False:
cur_bonds = len(targ.connected)
change_Hs = goal - cur_bonds
adjust_hydrogens = (change_Hs, vsepr)
residue.change_element(targ,
element,
adjust_bonds=adjust_bonds,
adjust_hydrogens=adjust_hydrogens,
)
residue.update_chix(res)
