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_edges(session):
from chimerax.atomic import selected_bonds
bonds = selected_bonds(session)
from numpy import array, bool
cbonds = bonds.filter(array([hasattr(b, 'polygon') for b in bonds], bool))
return cbonds
def run_script(session):
from chimerax.atomic import selected_bonds
sel_bonds = selected_bonds(session)
if len(sel_bonds) != 1:
from chimerax.core.errors import UserError
raise UserError('Select exactly one bond first!')
sel_bonds.delete()
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 run_script(session):
from chimerax.atomic import selected_residues, selected_bonds, Residues
sel = selected_residues(session)
if len(sel) != 2 or not all(sel.names=='CYS'):
b = selected_bonds(session)
if len(b) == 1:
b = b[0]
sel = Residues([a.residue for a in b.atoms])
if len(sel) != 2 or not all(sel.names=='CYS'):
from chimerax.core.errors import UserError
raise UserError('Please select exactly two cysteine residues!')
from chimerax.isolde.atomic.building.build_utils import break_disulfide
break_disulfide(*sel)
session.logger.info('Broke disulphide bond between {}.'.format(
' and '.join(['{}{}{}'.format(c.chain_id, c.number, c.insertion_code) for c in sel])
))
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 set_bonds(self, *args):
bonds = selected_bonds(self.session)
if len(bonds) == 0:
self.session.logger.error("no bonds selected")
return
models = [bond.structure for bond in bonds]
if any(models.count(m) > 1 for m in models):
self.session.logger.error(
"multiple bonds selected on the same structure")
return
self.bonds = {
model: (bond.atoms[0].coord - bond.atoms[1].coord)
for model, bond in zip(models, bonds)
}
self.bond_centers = {
model: bond.atoms[1].coord
for model, bond in zip(models, bonds)
}
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
def selected_links(session):
from chimerax import atomic
bonds = atomic.selected_bonds(session)
mask = [isinstance(b.structure, MarkerSet) for b in bonds]
return bonds.filter(mask)
def _ms_del_cb(self, *args):
from chimerax.atomic import selected_atoms, selected_bonds
if not selected_atoms(self.session) and not selected_bonds(self.session):
raise UserError("No atoms or bonds selected")
run(self.session, "del atoms sel; del bonds sel")
