def new_atom(self):
element = ChangeElementMouseMode.element
adjust_bonds = True
vsepr = ChangeElementMouseMode.vsepr
if vsepr == "do not change":
vsepr = False
elif vsepr == "linear (1 bond)":
vsepr = "linear 1"
elif vsepr == "linear (2 bonds)":
vsepr = "linear 2"
elif vsepr == "trigonal planar (2 bonds)":
vsepr = "bent 2 planar"
elif vsepr == "tetrahedral (2 bonds)":
vsepr = "bent 2 tetrahedral"
elif vsepr == "tetrahedral (3 bonds)":
vsepr = "bent 3 tetrahedral"
if vsepr:
atoms = Atom.get_shape(vsepr)
atoms[0].element = element
for atom in atoms[1:]:
atom.element = "H"
if adjust_bonds:
# this works b/c all atoms are 1 angstrom from the center
# just multiply by the distance we want
expected_dist = RADII[element] + RADII["H"]
for atom in atoms[1:]:
atom.coords *= expected_dist
for atom in atoms[1:]:
atoms[0].connected.add(atom)
atom.connected.add(atoms[0])
else:
atoms = [Atom(element=element, coords=np.zeros(3))]
rescol = ResidueCollection(atoms, name="new", refresh_connected=False)
rescol.coord_shift(self._coords)
model = self.model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
else:
res = model.new_residue("new", "a", len(model.residues) + 1)
rescol.residues[0].update_chix(res)
run(
self.session, "select add %s" %
" ".join([atom.atomspec for atom in res.atoms]))
self.delete()
def mouse_up(self, event):
if event.shift_down():
_ElementPicker(self.session, "pick element")
return
if not self.element:
self.session.logger.warning(
"no element selected; shift-click to set element")
self.session.logger.status(
"no element selected; shift-click to set element")
_ElementPicker(self.session, "pick element")
return
x, y = event.position()
pick = self.view.picked_object(x, y)
if not pick:
x1, x2 = self.session.main_view.clip_plane_points(x, y)
coords = (x1 + x2) / 2
new_fragment = _ModelSelector(self.session, "place atom in model",
coords)
if new_fragment.model_selector.count() == 1:
new_fragment.new_atom()
return
# import cProfile
#
# profile = cProfile.Profile()
# profile.enable()
vsepr = self.vsepr
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
elif vsepr == "tetrahedral":
goal = 4
else:
goal = len(Atom.get_shape(vsepr)) - 1
if not isinstance(pick, PickedAtom):
return
atom = pick.atom
# # use built-in ChimeraX command for some of the more common things
# # because it's faster for proteins
# if False:
# run(
# self.session,
# "build modify %s %s %i geometry %s" % (
# atom.atomspec,
# self.element,
# goal,
# vsepr,
# )
# )
#
frags = []
for neighbor in atom.neighbors:
frags.append(
get_fragment(neighbor,
stop=atom,
max_len=atom.structure.num_atoms))
residues = [atom.residue]
hold_steady = None
for i, frag in enumerate(sorted(frags, key=len)):
if i == len(frags) - 1:
hold_steady = AtomSpec(frag[0].atomspec)
residues.append(frag[0].residue)
continue
residues.extend(frag.residues)
rescol = ResidueCollection(atom.structure,
convert_residues=set(residues),
refresh_ranks=False)
res = [
residue for residue in rescol.residues
if residue.chix_residue is atom.residue
][0]
target = res.find_exact(AtomSpec(atom.atomspec))[0]
adjust_hydrogens = vsepr
if vsepr is not False:
cur_bonds = len(target.connected)
change_Hs = goal - cur_bonds
adjust_hydrogens = (change_Hs, vsepr)
rescol.change_element(
target,
self.element,
adjust_bonds=True,
adjust_hydrogens=adjust_hydrogens,
hold_steady=hold_steady,
)
res.update_chix(res.chix_residue,
apply_preset=True,
refresh_connected=True)
rescol.update_chix(atom.structure,
apply_preset=False,
refresh_connected=False)
if isinstance(args.change_hs, int):
adjust_hs = args.change_hs
elif args.change_hs is None:
adjust_hs = True
else:
adjust_hs = 0
new_vsepr = None
if args.geometry:
new_vsepr = args.geometry.replace("_", " ")
if adjust_hs == 0 and new_vsepr is None:
adjust_structure = False
elif adjust_hs == 0 and new_vsepr:
goal = len(Atom.get_shape(new_vsepr)) - 1
def goal_func(atom, goal=goal):
return goal - len(atom.connected)
adjust_structure = (goal_func, new_vsepr)
elif adjust_hs is True:
adjust_structure = True
else:
adjust_structure = (adjust_hs, new_vsepr)
for f in glob_files(args.infile, parser=element_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
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)