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 substitute(self, sub, target, *args, attached_to=None, **kwargs):
if attached_to is None:
from SEQCROW.selectors import get_fragment
frags = []
target = self.find(target)[0]
target_chix = target.chix_atom
for bonded_atom in target_chix.neighbors:
frags.append(get_fragment(bonded_atom, target_chix, 1000))
attached_to = None
longest_frag = None
for test_end, (i, frag1) in zip(target_chix.neighbors,
enumerate(frags)):
cyclic = False
for frag2 in frags[i + 1:]:
if frag1.intersects(frag2):
cyclic = True
break
if cyclic:
continue
if attached_to is None or len(longest_frag) < len(frag1):
longest_frag = frag1
attached_to = test_end
if attached_to is not None:
attached_to = self.find(AtomSpec(attached_to.atomspec))[0]
return super().substitute(sub,
target,
*args,
attached_to=attached_to,
**kwargs)
def seqcrow_s(session, models=None, atoms=None):
"""atoms are represented with sticks
atoms colored by Jmol colors"""
from AaronTools.const import RADII
from chimerax.atomic import AtomicStructure, Atom
from chimerax.atomic.colors import element_color
from SEQCROW.selectors import get_fragment
if models is None or atoms is None:
apply_seqcrow_s_lighting(session)
if models is None:
if atoms is None:
models = session.models.list(type=AtomicStructure)
else:
models = list(set([atom.structure for atom in atoms]))
elif isinstance(models, AtomicStructure):
models = [models]
for m in models:
if atoms is None:
m.ball_scale = 0.625
if atoms is None:
atom_list = m.atoms
else:
atom_list = [atom for atom in atoms if atom.structure is m]
for bond in m.bonds:
if any(a in atom_list for a in bond.atoms):
bond.halfbond = True
bond.radius = 0.25
bond.hide = False
tm_bonds = m.pseudobond_group(m.PBG_METAL_COORDINATION,
create_type=None)
ts_bonds = m.pseudobond_group("TS bonds", create_type=None)
h_bonds = m.pseudobond_group("hydrogen bonds", create_type=None)
for atom in atom_list:
ele = atom.element.name
color = element_color(atom.element.number)
atom.color = color
if not atom.neighbors:
atom.draw_mode = Atom.BALL_STYLE
if ele in RADII:
atom.radius = RADII[ele]
else:
atom.draw_mode = Atom.STICK_STYLE
if atom.element.name == "H":
display = len(atom.neighbors) != 1
if tm_bonds:
if any(atom in bond.atoms
for bond in tm_bonds.pseudobonds):
display = True
if h_bonds:
if any(atom in bond.atoms for bond in h_bonds.pseudobonds):
display = True
if ts_bonds:
if any(atom in bond.atoms
for bond in ts_bonds.pseudobonds):
display = True
if not display:
for bonded_atom in atom.neighbors:
if "C" != bonded_atom.element.name or ((
bonded_atom.element.name == "C" and
(
# show H's on terminal carbons that aren't RCH3's
sum(
len(a.neighbors) == 1
for a in bonded_atom.neighbors
) >= bonded_atom.num_bonds - 1
and not (sum(
int(a.element.name == "H")
for a in bonded_atom.neighbors) == 3
and len(bonded_atom.neighbors) == 4)
# show H's in TS bonds or on atoms that are coordinated to a metal
or
(ts_bonds
and any(bonded_atom in bond.atoms
for bond in ts_bonds.pseudobonds)) or
(tm_bonds
and any(bonded_atom in bond.atoms
for bond in tm_bonds.pseudobonds))))
# show H's that are on chiral carbons
# this is a really lazy check and doesn't get everything
or (sum(
a.element.
name == "H"
for a in
bonded_atom.
neighbors
) == 1 and (len(
set(
sum(
get_fragment(
a,
bonded_atom
).
elements
.masses
)
for a in
bonded_atom
.neighbors
)
) == 4 # or any(a.element.name not in "CH" for a in bonded_atom.neighbors)
)
and
bonded_atom.
num_bonds
== 4)):
display = True
break
# show H's on trigonal carbons adjacent to terminal trigonal carbons
if "C" == bonded_atom.element.name and bonded_atom.num_bonds < 4:
for bonded_atom2 in bonded_atom.neighbors:
if bonded_atom2.element.name == "C" and (sum(
len(a.neighbors) == 1
for a in bonded_atom2.neighbors
) >= bonded_atom2.num_bonds - 1 and not (sum(
int(a.element.name == "H")
for a in bonded_atom2.neighbors
) == 3 and len(bonded_atom2.neighbors) == 4)):
display = True
break
atom.display = display
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)
def select_pick(self, pick, set_sel):
if set_sel:
self.session.selection.clear()
if pick:
atoms = Atoms()
bonds = Bonds()
if not hasattr(pick, "__iter__"):
pick = [pick]
first_selected = None
for p in pick:
if isinstance(p, PickedAtoms):
for atom in p.atoms:
if atom in atoms:
continue
connected_atoms = get_fragment(
atom, max_len=atom.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedAtom):
if p.atom in atoms:
continue
connected_atoms = get_fragment(
p.atom, max_len=p.atom.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedBonds):
for bond in p.bonds:
if bond.atoms[0] in atoms:
continue
connected_atoms = get_fragment(
bond.atoms[0], max_len=bond.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedBond):
if p.bond.atoms[0] in atoms:
continue
connected_atoms = get_fragment(
p.bond.atoms[0], max_len=p.bond.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedResidues):
for res in p.residues:
for atom in res:
if atom in atoms:
continue
connected_atoms = get_fragment(
atom, max_len=res.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedResidue):
for atom in p.residue.atoms:
if atoms in atoms:
continue
connected_atoms = get_fragment(
atom, max_len=p.residue.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
for atom in atoms:
for neighbor, bond in zip(atom.neighbors, atom.bonds):
bonds = bonds.merge(Bonds([bond]))
if first_selected is not None:
atoms.selected = not first_selected
bonds.selected = not first_selected
else:
run(self.session, "select clear")