def set_perpendicular(self, *args):
atoms = selected_atoms(self.session)
if len(atoms) == 0:
self.session.logger.error("no atoms selected")
return
self.perpendiculars = {}
self.perp_centers = {}
models = set(atom.structure for atom in atoms)
for model in models:
atom_coords = []
for atom in atoms:
if atom.structure is model:
atom_coords.append(atom.coord)
if len(atom_coords) < 3:
self.session.logger.error("fewer than 3 atoms selected on %s" %
model.atomspec)
continue
xyz = np.array(atom_coords)
xyz -= np.mean(atom_coords, axis=0)
R = np.dot(xyz.T, xyz)
u, s, vh = np.linalg.svd(R, compute_uv=True)
vector = u[:, -1]
self.perpendiculars[model] = vector
self.perp_centers[model] = np.mean(atom_coords, axis=0)
def run_script(session):
from chimerax.atomic import selected_atoms
from chimerax.build_structure import modify_atom
from chimerax.build_structure.mod import ParamError
from chimerax.core.errors import UserError
sel = selected_atoms(session)
if len(sel) != 1:
raise UserError('Please select a single atom!')
sel = sel[0]
current_num_bonds = len(sel.neighbors)
current_color = sel.color
try:
modify_atom(sel,
sel.element,
current_num_bonds + 1,
connect_back=False,
res_name=sel.residue.name)
sel.color = current_color
except ParamError as e:
# If modify_atom throws an error at the previous step, it will have deleted
# any attached hydrogens and not put them back. We need to put them back here.
modify_atom(sel,
sel.element,
current_num_bonds,
connect_back=False,
res_name=sel.residue.name)
sel.color = current_color
raise UserError(str(e))
def run_bond(self, *args):
# TODO: switch to `bond sel` in 1.2
sel = selected_atoms(self.session)
halfbond = self.bond_halfbond.checkState() == Qt.Checked
self.settings.bond_halfbond = halfbond
if not halfbond:
color = self.bond_color.get_color()
color = tuple(x / 255. for x in color)
self.settings.bond_color = color
radius = self.bond_radius.value()
self.settings.bond_radius = radius
for b in selected_bonds(self.session):
b.halfbond = halfbond
if not halfbond:
b.color = np.array([int(x * 255) for x in color])
b.radius = radius
for i, a1 in enumerate(sel):
for a2 in sel[:i]:
if a1.structure is a2.structure and a2 not in a1.neighbors:
new_bond = a1.structure.new_bond(a1, a2)
new_bond.halfbond = halfbond
if not halfbond:
new_bond.color = np.array(
[int(x * 255) for x in color])
new_bond.radius = radius
def selected_vertices(session):
from chimerax.atomic import selected_atoms
atoms = selected_atoms(session)
from numpy import array, bool
catoms = atoms.filter(array([hasattr(a, 'polygon') for a in atoms], bool))
return catoms
def callback(self, session):
from chimerax.atomic import selected_atoms
a1, a2 = selected_atoms(session)
command = "dist %s %s" % (a1.string(style="command line"),
a2.string(style="command line"))
from chimerax.core.commands import run
run(session, command)
def set_ligand(self, *args):
self.ligands = {}
for atom in selected_atoms(self.session):
if atom.structure not in self.ligands:
self.ligands[atom.structure] = []
self.ligands[atom.structure].append(atom)
self.session.logger.status("set ligand to current selection")
def link_consecutive(self, event):
s = self.session
from chimerax.atomic import selected_atoms
atoms1 = selected_atoms(s)
a2 = self.picked_marker(event, select=True)
if a2 is None or len(atoms1) != 1:
return False
a1 = atoms1[0]
if a1.structure != a2.structure:
s.logger.status('Cannot connect atoms from different molecules')
return False
if a1 is a2 or a1.connects_to(a2):
return False
ms = _mouse_marker_settings(self.session)
from .markers import create_link
b = create_link(a1,
a2,
radius=ms['link radius'],
rgba=ms['link color'],
log=True)
s.logger.status('Made connection, distance %.3g' % b.length)
return True
def _mouse_place_marker(session,
center,
link_to_selected=False,
select=True,
log=True):
m = _mouse_markerset(session)
ms = _mouse_marker_settings(session)
a = m.create_marker(center, ms['marker color'], ms['marker radius'],
ms['next_marker_num'])
if log:
_log_place_marker(m, center, ms['marker color'], ms['marker radius'])
ms['next_marker_num'] += 1
session.logger.status('Placed marker')
if link_to_selected:
from chimerax.atomic import selected_atoms
atoms = selected_atoms(session)
if len(atoms) == 1:
al = atoms[0]
if a.structure == al.structure and a is not al:
from .markers import create_link
create_link(al,
a,
radius=ms['link radius'],
rgba=ms['link color'],
log=log)
if select:
session.selection.clear()
a.selected = True
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
if self.action(event) == 'rotate':
self._set_z_rotation(event)
if self.move_atoms:
from chimerax.atomic import selected_atoms
self._atoms = selected_atoms(self.session)
self._undo_start()
def _create_distance(self):
from chimerax.atomic import selected_atoms
sel_atoms = selected_atoms(self.session)
if len(sel_atoms) != 2:
from chimerax.core.errors import UserError
raise UserError("Exactly two atoms must be selected!")
from chimerax.core.commands import run
run(self.session, "distance %s %s" % tuple(a.string(style="command") for a in sel_atoms))
def wheel(self, event):
d = event.wheel_value()
if self.move_atoms:
from chimerax.atomic import selected_atoms
self._atoms = selected_atoms(self.session)
if self.action(event) == 'rotate':
self._rotate((0, 1, 0), 10 * d)
else:
self._translate((0, 0, 100 * d))
def update_key_atoms(self):
selection = selected_atoms(self.session)
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
else:
self.key_atomspec = selection
self.tool_window.status("key atoms set to %s" %
" ".join(atom.atomspec for atom in selection))
def incr_b_factor(session, b_add, atoms=None):
B_MAX = 500
if atoms is None:
from chimerax.atomic import selected_atoms
atoms = selected_atoms(session)
if any(atoms.bfactors + b_add < 0):
raise UserError(
'Applying this command would reduce the B-factor of at least one atom to below zero.'
)
atoms.bfactors += b_add
atoms[atoms.bfactors > B_MAX].bfactors = B_MAX
def _ms_sel_changed(self, *args):
from chimerax.atomic import selected_atoms
sel_atoms = selected_atoms(self.session)
if len(sel_atoms) != 1:
return
a = sel_atoms[0]
self._ms_update_atom_name(a)
from .mod import unknown_res_name
res_name = unknown_res_name(a.residue)
self.ms_mod_edit.setText(res_name)
self.ms_res_new_name.setText(res_name)
def run_script(session):
from chimerax.atomic import selected_atoms
from chimerax.core.errors import UserError
sel = selected_atoms(session)
if len(sel) != 2:
raise UserError('Must have exactly two atoms selected!')
us = sel.unique_structures
if len(us) != 1:
raise UserError('Both atoms must be from the same structure!')
m = us[0]
from chimerax.atomic.struct_edit import add_bond
add_bond(*sel)
def _fit_atoms(self):
m = self._object_menu.value
if m == 'selected atoms':
from chimerax.atomic import selected_atoms
return selected_atoms(self.session)
from chimerax.atomic import Structure
if isinstance(m, Structure):
return m.atoms
return None
def selection_changed(self, *args):
selection = selected_atoms(self.session)
new_atoms = [atom for atom in selection if atom not in self._selection]
if len(new_atoms) > 1:
self._selection = []
else:
for atom in self._selection:
if atom not in selection:
self._selection.remove(atom)
self._selection.extend(new_atoms)
def change_bond_length(self, *args):
dist = self.bond_distance.value()
atom_pairs = []
sel = selected_atoms(self.session)
if len(sel) == 2 and sel[0].structure is sel[1].structure:
atom_pairs.append(sel)
for bond in selected_bonds(self.session):
if not all(atom in sel for atom in bond.atoms):
atom_pairs.append(bond.atoms)
for bond in selected_pseudobonds(self.session):
if not all(atom in sel for atom in bond.atoms):
atom_pairs.append(bond.atoms)
for pair in atom_pairs:
atom1, atom2 = pair
frag1 = get_fragment(atom1,
stop=atom2,
max_len=atom1.structure.num_atoms)
frag2 = get_fragment(atom2,
stop=atom1,
max_len=atom1.structure.num_atoms)
v = atom2.coord - atom1.coord
cur_dist = np.linalg.norm(v)
change = dist - cur_dist
if self.move_fragment.currentText() == "both":
change = 0.5 * change
frag1.coords -= change * v / cur_dist
frag2.coords += change * v / cur_dist
elif self.move_fragment.currentText() == "smaller":
if len(frag1) < len(frag2) or (len(frag1) == len(frag2)
and sum(frag1.elements.masses) <
sum(frag2.elements.masses)):
frag1.coords -= change * v / cur_dist
else:
frag2.coords += change * v / cur_dist
elif self.move_fragment.currentText() == "larger":
if len(frag1) > len(frag2) or (len(frag1) == len(frag2)
and sum(frag1.elements.masses) >
sum(frag2.elements.masses)):
frag1.coords -= change * v / cur_dist
else:
frag2.coords += change * v / cur_dist
def _ms_update_atom_name(self, a=None):
if a is None:
from chimerax.atomic import selected_atoms
sel_atoms = selected_atoms(self.session)
if len(sel_atoms) != 1:
return
a = sel_atoms[0]
new_element = self.ms_elements_button.text()
from .mod import default_changed_name
new_name = default_changed_name(a, new_element)
self.ms_atom_name.setText(new_name)
if new_name == a.name:
self.ms_retain_atom_name.setChecked(True)
else:
self.ms_change_atom_name.setChecked(True)
def manual_cor(self, *args):
selection = selected_atoms(self.session)
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
self.manual_center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
self.manual_center[model] = np.mean(coords, axis=0)
def set_group(self, *args):
atoms = selected_atoms(self.session)
if len(atoms) == 0:
self.session.logger.error("no atoms selected")
return
self.groups = {}
models = set(atom.structure for atom in atoms)
for model in models:
atom_coords = []
for atom in atoms:
if atom.structure is model:
atom_coords.append(atom.coord)
self.groups[model] = np.mean(atom_coords, axis=0)
def all_connected_selector(session, models, results):
"""select all atoms connected to the current selection"""
# TODO: right mouse mode for this
cur_sel = selected_atoms(session)
bond_sel = selected_bonds(session)
for bond in bond_sel:
cur_sel = cur_sel.merge(Atoms(bond.atoms))
atoms = Atoms()
for atom in cur_sel:
if atom in atoms:
continue
elif atom.structure not in models:
continue
connected_atoms = get_fragment(atom, max_len=len(atom.structure.atoms))
atoms = atoms.merge(connected_atoms)
results.add_atoms(atoms)
def _ms_apply_cb(self):
from chimerax.atomic import selected_atoms
sel_atoms = selected_atoms(self.session)
num_selected = len(sel_atoms)
if num_selected != 1:
raise UserError("You must select exactly one atom to modify.")
a = sel_atoms[0]
element_name = self.ms_elements_button.text()
num_bonds = self.ms_bonds_button.text()
cmd = "build modify %s %s %s" % (a.atomspec, element_name, num_bonds)
geometry = self.ms_geom_button.text()
if geometry != "N/A":
cmd += " geometry " + geometry
if not self.ms_retain_atom_name.isChecked():
new_name = self.ms_atom_name.text().strip()
if not new_name:
raise UserError("Must provide a name for the modified atom")
if new_name != a.name:
cmd += " name " + new_name
if not self.ms_connect_back.isChecked():
cmd += " connectBack false"
if not self.ms_element_color.isChecked():
cmd += " colorByElement false"
if self.ms_res_mod.isChecked():
res_name = self.ms_mod_edit.text().strip()
if not res_name:
raise UserError("Must provided modified residue name")
if res_name != a.residue.name:
cmd += " resName " + res_name
elif self.ms_res_new.isChecked():
res_name = self.ms_res_new_name.text().strip()
if not res_name:
raise UserError("Must provided new residue name")
cmd += " resNewOnly true resName " + res_name
run(self.session, cmd)
if self.ms_focus.isChecked():
run(self.session, "view " + a.residue.atomspec)
def copy_atom_style_from(session, atoms, ref_residue):
from chimerax.atomic import selected_atoms, Atom
from chimerax.core.commands import run
r = ref_residue
atoms.draw_modes = r.atoms[0].draw_mode
residues = atoms.unique_residues
residues.ribbon_displays = r.ribbon_display
residues.ribbon_hide_backbones = r.ribbon_hide_backbone
current_sel = selected_atoms(session)
session.selection.clear()
atoms.selected = True
ref_c = r.atoms[r.atoms.element_names == 'C']
if len(ref_c):
atoms[atoms.element_names == 'C'].colors = ref_c[0].color
else:
run(session, "color sel bychain", log=False)
run(session, "color sel byhetero", log=False)
session.selection.clear()
current_sel.selected = True
def intersect_selection(objects, session, undo_state, full_residues = False):
atoms, bonds, pbonds, models = _atoms_bonds_models(objects, full_residues = full_residues)
from chimerax import atomic
selatoms = atomic.selected_atoms(session)
subatoms = selatoms - atoms
selbonds = atomic.selected_bonds(session)
subbonds = selbonds - bonds
selpbonds = atomic.selected_pseudobonds(session)
subpbonds = selpbonds - pbonds
from chimerax.atomic import Structure, PseudobondGroup
selmodels = set(m for m in session.selection.models()
if not isinstance(m, (Structure, PseudobondGroup)))
submodels = selmodels.difference(models)
undo_state.add(subatoms, "selected", subatoms.selected, False)
undo_state.add(subbonds, "selected", subbonds.selected, False)
undo_state.add(subpbonds, "selected", subpbonds.selected, False)
subatoms.selected = False
subbonds.selected = False
subpbonds.selected = False
for m in submodels:
undo_state.add(m, "selected", m.selected, False)
m.selected = False
from chimerax.core.commands import run
run(session, "open 3fx2 ; sel ligand & aromatic")
from chimerax.atomic import selected_atoms
num_selected = len(selected_atoms(session))
if num_selected != 10:
raise SystemExit("Selecting 3fx2 :FMN aromatic rings selected %d atoms instead of 10!" % num_selected)
run(session, "sel phosphate")
num_selected = len(selected_atoms(session))
if num_selected != 5:
raise SystemExit("Selecting 3fx2 phoshates selected %d atoms instead of 5!" % num_selected)
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 _sel_residues(session, models, results):
from chimerax.atomic import selected_atoms
results.add_atoms(selected_atoms(session).residues.unique().atoms)
def selected_markers(session):
from chimerax import atomic
atoms = atomic.selected_atoms(session)
mask = [isinstance(a.structure, MarkerSet) for a in atoms]
return atoms.filter(mask)
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)