def ghost_connection_highlight(substituent, color, session):
"""returns a bild object with a cylinder pointing along the
x axis towards the substituent and a sphere at the origin"""
s = ".note connection to molecule\n"
s += ".color %f %f %f\n" % tuple(color[:-1])
s += ".transparency %f\n" % (1. - color[-1])
s += ".sphere 0 0 0 %f\n" % 0.15
s += ".cylinder 0 0 0 %f 0 0 %f open\n" % (
substituent.atoms[0].coords[0], 0.15)
stream = BytesIO(bytes(s, 'utf-8'))
bild_obj, status = read_bild(session, stream, "ghost connection")
return bild_obj
def show_walk_highlight(ring, chimera_ring, color, session):
"""returns a bild sphere on the walk atom if there is only one walk atom
returns a set of bild arrows showing the walk direction if there are multiple walk atoms
will also hide any bonds on chimera_ring that are under/over the arrows"""
s = ".note direction to walk around ring\n"
s += ".color %f %f %f\n" % tuple(color[:-1])
s += ".transparency %f\n" % (1. - color[-1])
if len(ring.end) == 1:
if hasattr(ring.end[0], "_radii"):
r = 0.6 * ring.end[0]._radii
else:
r = 1
info = tuple(ring.end[0].coords) + (r, )
s += ".sphere %f %f %f %f\n" % info
else:
r_bd = 0.16
for atom1, atom2 in zip(ring.end[:-1], ring.end[1:]):
v = atom1.bond(atom2)
if hasattr(atom2, "_radii"):
r_sp = 0.4 * atom2._radii
else:
r_sp = 0.4
info = tuple(atom1.coords) + tuple(atom2.coords - r_sp * v) + (
r_bd,
1.5 * r_bd,
)
s += ".arrow %f %f %f %f %f %f %f %f 0.7\n" % info
for bond in chimera_ring.bonds:
bond_atoms = [
chimera_ring.atoms.index(atom) for atom in bond.atoms
]
if ring.atoms.index(atom1) in bond_atoms and ring.atoms.index(
atom2) in bond_atoms:
bond.display = False
break
stream = BytesIO(bytes(s, 'utf-8'))
bild_obj, status = read_bild(session, stream, "walk direction")
return bild_obj
def key_atom_highlight(ligand, color, session):
"""returns a bild object with spheres on top on ligand's key atoms"""
s = ".note coordinating atoms\n"
s += ".color %f %f %f\n" % tuple(color[:-1])
s += ".transparency %f\n" % (1. - color[-1])
for atom in ligand.key_atoms:
if hasattr(atom, "_radii"):
r = 0.6 * atom._radii
else:
r = 0.5
if atom.element == 'H':
r *= 1.5
s += ".sphere %f %f %f %f\n" % (*atom.coords, r)
stream = BytesIO(bytes(s, 'utf-8'))
bild_obj, status = read_bild(session, stream, "highlighting key atoms")
return bild_obj
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 show_rot_vec(self, *args):
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
if self.display_rot_vec.checkState() == Qt.Unchecked:
return
selection = selected_atoms(self.session)
if len(selection) == 0:
return
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
if len(models.keys()) == 0:
return
if self.vector_option.currentText() == "axis":
if self.axis.currentText() == "z":
vector = np.array([0., 0., 1.])
elif self.axis.currentText() == "y":
vector = np.array([0., 1., 0.])
elif self.axis.currentText() == "x":
vector = np.array([1., 0., 0.])
elif self.vector_option.currentText() == "view axis":
if self.view_axis.currentText() == "z":
vector = self.session.view.camera.get_position().axes()[2]
elif self.view_axis.currentText() == "y":
vector = self.session.view.camera.get_position().axes()[1]
elif self.view_axis.currentText() == "x":
vector = self.session.view.camera.get_position().axes()[0]
elif self.vector_option.currentText() == "bond":
vector = self.bonds
elif self.vector_option.currentText() == "perpendicular to plane":
vector = self.perpendiculars
elif self.vector_option.currentText() == "centroid of atoms":
vector = self.groups
elif self.vector_option.currentText() == "custom":
x = self.vector_x.value()
y = self.vector_y.value()
z = self.vector_z.value()
vector = np.array([x, y, z])
angle = np.deg2rad(self.angle.value())
center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
center[model] = np.mean(coords, axis=0)
if self.cor_button.currentText() == "automatic":
if self.vector_option.currentText() == "perpendicular to plane":
center = self.perp_centers
elif self.vector_option.currentText() == "bond":
center = self.bond_centers
elif self.cor_button.currentText() == "select atoms":
center = self.manual_center
else:
center = self.session.main_view.center_of_rotation
for model in models:
if isinstance(vector, dict):
if model not in vector.keys():
continue
else:
v = vector[model]
else:
v = vector
if isinstance(center, dict):
if model not in center.keys():
continue
else:
c = center[model]
else:
c = center
if self.vector_option.currentText(
) == "centroid of atoms" and self.cor_button.currentText(
) != "automatic":
v = v - c
if np.linalg.norm(v) == 0:
continue
residues = []
for atom in models[model]:
if atom.residue not in residues:
residues.append(atom.residue)
v_c = c + v
s = ".color red\n"
s += ".arrow %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f 0.2 0.4 0.7\n" % (
*c, *v_c)
stream = BytesIO(bytes(s, 'utf-8'))
bild_obj, status = read_bild(self.session, stream,
"rotation vector")
self.session.models.add(bild_obj, parent=model)
def pointGroup(
session,
selection,
printElements=False,
displayElements=True,
tolerance=0.1,
axisTolerance=0.5,
maxRotation=6,
):
for model in selection:
rescol = ResidueCollection(model, refresh_ranks=False)
pg = PointGroup(
rescol,
tolerance=tolerance,
rotation_tolerance=np.deg2rad(axisTolerance),
max_rotation=maxRotation,
)
session.logger.info("%s: %s" % (model.name, pg.name))
if printElements:
for ele in sorted(pg.elements, reverse=True):
session.logger.info(repr(ele))
if displayElements:
for ele in sorted(pg.elements, reverse=True):
if isinstance(ele, InversionCenter):
inv = ".note %s\n" % repr(ele)
inv += ".sphere %.5f %.5f %.5f 0.1\n" % tuple(
pg.center)
stream = BytesIO(bytes(inv, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
elif isinstance(ele, ProperRotation):
prots = ".note %s\n" % repr(ele)
prots += ".color red\n"
prots += ".arrow %.5f %.5f %.5f " % tuple(pg.center)
end = pg.center + ele.n * np.sqrt(ele.exp) * ele.axis
prots += "%.5f %.5f %.5f 0.05\n" % tuple(end)
stream = BytesIO(bytes(prots, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
elif isinstance(ele, ImproperRotation):
irots = ".note %s\n" % repr(ele)
irots += ".color blue\n"
irots += ".arrow %.5f %.5f %.5f " % tuple(pg.center)
end = pg.center + np.sqrt(ele.n) * np.sqrt(
ele.exp) * ele.axis
irots += "%.5f %.5f %.5f 0.05\n" % tuple(end)
irots += ".transparency 25\n"
z = ele.axis
x = perp_vector(z)
y = np.cross(x, z)
for angle in np.linspace(0, 2 * np.pi, num=250):
pt2 = ele.n**0.9 * x * np.cos(angle)
pt2 += ele.n**0.9 * y * np.sin(angle)
pt2 += pg.center
if angle > 0:
irots += ".polygon %6.3f %6.3f %6.3f" % tuple(
pt1)
irots += " %6.3f %6.3f %6.3f" % tuple(
pg.center)
irots += " %6.3f %6.3f %6.3f" % tuple(pt2)
irots += "\n"
pt1 = pt2
stream = BytesIO(bytes(irots, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
elif isinstance(ele, MirrorPlane):
mirror = ".note %s\n" % repr(ele)
mirror += ".color purple\n"
mirror += ".transparency 25\n"
z = ele.axis
x = perp_vector(z)
y = np.cross(x, z)
for angle in np.linspace(0, 2 * np.pi, num=250):
pt2 = 5 * x * np.cos(angle)
pt2 += 5 * y * np.sin(angle)
pt2 += pg.center
if angle > 0:
mirror += ".polygon %6.3f %6.3f %6.3f" % tuple(
pt1)
mirror += " %6.3f %6.3f %6.3f" % tuple(
pg.center)
mirror += " %6.3f %6.3f %6.3f" % tuple(pt2)
mirror += "\n"
pt1 = pt2
stream = BytesIO(bytes(mirror, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
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