def restore_selected(self):
items = [item for item in self.tree.selectedItems()]
model_dict = self.session.filereader_manager.filereader_dict
models = list(model_dict.keys())
for item in items:
parent = item.parent()
mdl = models[self.tree.indexOfTopLevelItem(parent)]
if parent is None:
fr = model_dict[mdl][-1]
else:
fr = model_dict[mdl][parent.indexOfChild(item)]
fr_rescol = ResidueCollection(fr)
fr_rescol.update_chix(mdl)
if fr.all_geom is not None and len(fr.all_geom) > 1:
coordsets = fr_rescol.all_geom_coordsets(fr)
mdl.remove_coordsets()
mdl.add_coordsets(coordsets)
for i, coordset in enumerate(coordsets):
mdl.active_coordset_id = i + 1
for atom, coord in zip(mdl.atoms, coordset):
atom.coord = coord
mdl.active_coordset_id = 1
def fuseRing(session,
selection=None,
rings=None,
newName=None,
modify=True,
minimize=False,
available=False):
if available:
fuseRing_list(session)
return
if not selection:
selection = selected_atoms(session)
if not rings:
session.logger.error("missing required \"rings\" argument")
return
if newName is None:
pass
elif any(len(name.strip()) > 4 for name in newName):
raise RuntimeError("residue names must be 4 characters or less")
elif not all(name.isalnum() for name in newName):
raise RuntimeError("invalid residue name: %s" % newName)
elif len(rings) != len(newName):
raise RuntimeError(
"number of substituents is not the same as the number of new names"
)
if len(selection) < 2:
raise RuntimeWarning("two atoms must be selected per molecule")
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
if len(models[atom.structure]) > 2:
raise RuntimeError("only two atoms can be selected on any model")
first_pass = True
new_structures = []
for i, ringname in enumerate(rings):
ringname = ringname.strip()
for model in models:
atom1 = models[model][0]
atom2 = models[model][1]
if modify and first_pass:
convert = minimal_ring_convert(model, *models[model])
if newName is not None:
for res in convert:
res.name = newName[i]
rescol = ResidueCollection(model, convert_residues=convert)
target = rescol.find(
[AtomSpec(atom1.atomspec),
AtomSpec(atom2.atomspec)])
elif modify and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
a1 = model_copy.atoms[model.atoms.index(models[model][0])]
a2 = model_copy.atoms[model.atoms.index(models[model][1])]
convert = minimal_ring_convert(model_copy, a1, a2)
if newName is not None:
for res in convert:
res.name = newName[i]
rescol = ResidueCollection(model_copy,
convert_residues=convert)
target = rescol.find(
[AtomSpec(a1.atomspec),
AtomSpec(a2.atomspec)])
rescol.ring_substitute(target, ringname, minimize=minimize)
if modify:
rescol.update_chix(model)
else:
rescol.update_chix(model_copy)
new_structures.append(model_copy)
first_pass = False
if not modify:
session.models.add(new_structures)
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 job_finished(self, trigger_name, job):
"""when a job is finished, open or update the structure as requested"""
if self.session.seqcrow_settings.settings.JOB_FINISHED_NOTIFICATION == \
'log and popup notifications' and self.session.ui.is_gui:
#it's just an error message for now
#TODO: make my own logger
self.session.logger.error("%s: %s" % (trigger_name, job))
else:
job.session.logger.info("%s: %s" % (trigger_name, job))
if isinstance(job, LocalJob):
self._thread = None
if not hasattr(job, "output_name") or \
not os.path.exists(job.output_name):
job.error = True
else:
fr = FileReader(job.output_name, just_geom=False)
#XXX: finished is not added to the FileReader for ORCA and Psi4 when finished = False
if 'finished' not in fr.other or not fr.other['finished']:
job.error = True
if job.auto_update and (
job.theory.geometry.chix_atomicstructure is not None
and not job.theory.geometry.chix_atomicstructure.deleted):
if os.path.exists(job.output_name):
finfo = job.output_name
try:
finfo = (job.output_name, job.format_name, None)
fr = FileReader(finfo, get_all=True, just_geom=False)
if len(fr.atoms) > 0:
job.session.filereader_manager.triggers.activate_trigger(
ADD_FILEREADER,
([job.theory.geometry.chix_atomicstructure], [fr]))
rescol = ResidueCollection(fr)
rescol.update_chix(
job.theory.geometry.chix_atomicstructure)
except:
job.update_structure()
if fr.all_geom is not None and len(fr.all_geom) > 1:
coordsets = rescol.all_geom_coordsets(fr)
job.theory.geometry.chix_atomicstructure.remove_coordsets()
job.theory.geometry.chix_atomicstructure.add_coordsets(
coordsets)
for i, coordset in enumerate(coordsets):
job.theory.geometry.chix_atomicstructure.active_coordset_id = i + 1
for atom, coord in zip(
job.theory.geometry.chix_atomicstructure.atoms,
coordset):
atom.coord = coord
job.theory.geometry.chix_atomicstructure.active_coordset_id = job.theory.geometry.chix_atomicstructure.num_coordsets
elif job.auto_open or job.auto_update:
if hasattr(job, "output_name") and os.path.exists(job.output_name):
if job.format_name:
run(
job.session, "open \"%s\" coordsets true format %s" %
(job.output_name, job.format_name))
else:
run(job.session,
"open \"%s\" coordsets true" % job.output_name)
else:
self.session.logger.error("could not open output of %s" %
repr(job))
self.triggers.activate_trigger(JOB_QUEUED, trigger_name)
pass
def substitute(
session,
selection=None,
substituents=None,
newName=None,
guessAttachment=True,
modify=True,
minimize=False,
useRemoteness=False,
available=False,
newResidue=False,
):
if available:
substitute_list(session)
return
if not selection:
selection = selected_atoms(session)
if not substituents:
session.logger.error("missing required \"substituents\" argument")
return
attached = {}
if newName is None:
newName = [None for s in substituents]
elif any(len(name.strip()) > 4 for name in newName):
raise RuntimeError("residue names must be 4 characters or less")
elif not all(name.isalnum() for name in newName):
raise RuntimeError("invalid residue name: %s" % " ".join(newName))
elif len(substituents) != len(newName):
raise RuntimeError(
"number of substituents is not the same as the number of new names"
)
if not guessAttachment:
models, attached = avoidTargets(selection)
else:
models, attached = guessAttachmentTargets(selection, session)
first_pass = True
new_structures = []
for ndx, subname in enumerate(substituents):
subname = subname.strip()
sub = Substituent(subname)
# when minimizing, we only want to deal with residues that are close to the substituent
# determine the size of the new substituent to limit this
if minimize:
size = 5
for atom in sub.atoms:
d = np.linalg.norm(atom.coords)
if d > size:
size = d
for model in models:
if modify and first_pass:
conv_res = []
for res in models[model]:
if res not in conv_res:
conv_res.append(res)
if minimize:
for chix_res in model.residues:
if chix_res in conv_res:
continue
added_res = False
for atom in chix_res.atoms:
for target in models[model][res]:
d = np.linalg.norm(atom.coord -
target.coord)
if d < (size + 3):
conv_res.append(chix_res)
added_res = True
break
if added_res:
break
rescol = ResidueCollection(model, convert_residues=conv_res)
for res in models[model]:
for target in models[model][res]:
if attached is not None:
end = AtomSpec(attached[target].atomspec)
else:
end = None
# call substitute on the ResidueCollection b/c we need to see
# the other residues if minimize=True
rescol.substitute(
sub.copy(),
AtomSpec(target.atomspec),
attached_to=end,
minimize=minimize,
use_greek=useRemoteness,
new_residue=newResidue,
new_name=newName[ndx],
)
rescol.update_chix(model)
elif modify and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
conv_res = [
model_copy.residues[i] for i in
[model.residues.index(res) for res in models[model]]
]
# modifying_residues = [model_copy.residues[i] for i in [model.residues.index(res) for res in models[model]]]
modifying_residues = [r for r in conv_res]
if minimize:
for chix_res in model_copy.residues:
if chix_res in conv_res:
continue
added_res = False
for res in models[model]:
for target in models[model][res]:
for atom in chix_res.atoms:
d = np.linalg.norm(atom.coord -
target.coord)
if d < (size + 3):
conv_res.append(chix_res)
added_res = True
break
if added_res:
break
if added_res:
break
rescol = ResidueCollection(model_copy,
convert_residues=conv_res)
for residue, res in zip(modifying_residues, models[model]):
for target in models[model][res]:
if attached is not None:
end = AtomSpec(model_copy.atoms[model.atoms.index(
attached[target])].atomspec)
else:
end = None
rescol.substitute(
sub.copy(),
AtomSpec(model_copy.atoms[model.atoms.index(
target)].atomspec),
attached_to=end,
minimize=minimize,
use_greek=useRemoteness,
new_residue=newResidue,
new_name=newName[ndx],
)
rescol.update_chix(model_copy)
new_structures.append(model_copy)
first_pass = False
if not modify:
session.models.add(new_structures)
def do_maplig(self):
lignames = self.ligname.text()
selection = selected_atoms(self.session)
if len(selection) < 1:
raise RuntimeWarning("nothing selected")
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [AtomSpec(atom.atomspec)]
else:
models[atom.structure].append(AtomSpec(atom.atomspec))
first_pass = True
new_structures = []
for ligname in lignames.split(','):
ligname = ligname.strip()
lig = Component(ligname)
for model in models:
if self.close_previous_bool and first_pass:
rescol = ResidueCollection(model)
elif self.close_previous_bool and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
rescol = ResidueCollection(model_copy)
for i, atom in enumerate(model.atoms):
rescol.atoms[i].atomspec = atom.atomspec
rescol.atoms[i].add_tag(atom.atomspec)
rescol.atoms[i].chix_atom = atom
target = rescol.find(models[model])
if len(target) % len(lig.key_atoms) == 0:
k = 0
ligands = []
while k != len(target):
res_lig = ResidueCollection(lig.copy(), comment=lig.comment)
res_lig.parse_comment()
res_lig = Component(res_lig, key_atoms = ",".join([str(k + 1) for k in res_lig.other["key_atoms"]]))
ligands.append(res_lig)
k += len(lig.key_atoms)
else:
raise RuntimeError("number of key atoms no not match: %i now, new ligand has %i" % (len(target), len(lig.key_atoms)))
rescol.map_ligand(ligands, target)
for center_atom in rescol.center:
center_atom.connected = set([])
for atom in rescol.atoms:
if atom not in rescol.center:
if center_atom.is_connected(atom):
atom.connected.add(center_atom)
center_atom.connected.add(atom)
if self.close_previous_bool:
rescol.update_chix(model)
else:
struc = rescol.get_chimera(self.session)
new_structures.append(struc)
first_pass = False
if not self.close_previous_bool:
self.session.models.add(new_structures)