def create_complexes(self):
c2_symmetric = []
ligands = []
minimize = self.minimize.checkState() == Qt.Checked
for i in range(0, self.ligand_table.rowCount() - 1):
ligand_name = self.ligand_table.item(i, 0).text()
ligands.append(ligand_name)
checkbox = self.ligand_table.cellWidget(i, 1).layout().itemAt(0).widget()
c2 = checkbox.checkState() == Qt.Checked
c2_symmetric.append(c2)
rescols, formula = ResidueCollection.get_coordination_complexes(
self.element.text(),
ligands,
self.vsepr.currentText(),
c2_symmetric=c2_symmetric,
minimize=minimize,
session=self.session,
)
self.session.logger.info("generic formula is %s" % formula)
models = [rescol.get_chimera(self.session) for rescol in rescols]
self.session.models.add(models)
for model in models:
apply_seqcrow_preset(model, fallback="Ball-Stick-Endcap")
def open_substituents(self):
for row in self.sub_table.table.selectionModel().selectedRows():
if self.sub_table.table.isRowHidden(row.row()):
continue
sub_name = row.data()
substituent = Substituent(sub_name, name=sub_name)
chimera_substituent = ResidueCollection(substituent).get_chimera(
self.session)
self.session.models.add([chimera_substituent])
apply_seqcrow_preset(chimera_substituent,
fallback="Ball-Stick-Endcap")
if self.showSubGhostBool:
color = self.sub_color.get_color()
color = [c / 255. for c in color]
self.settings.ghost_connection_color = tuple(color)
bild_obj = ghost_connection_highlight(substituent, color,
self.session)
self.session.models.add(bild_obj, parent=chimera_substituent)
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 do_new_lig(self):
ligands = self.ligname.text()
for lig in ligands.split(","):
lig = lig.strip()
rescol = ResidueCollection(Component(lig))
model = self.lig_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")
self.lig_model_selector.setCurrentIndex(self.lig_model_selector.count()-1)
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]))
def open_ligands(self):
for row in self.lig_table.table.selectionModel().selectedRows():
if self.lig_table.table.isRowHidden(row.row()):
continue
lig_name = row.data()
ligand = Component(lig_name)
chimera_ligand = ResidueCollection(
ligand, name=lig_name).get_chimera(self.session)
self.session.models.add([chimera_ligand])
apply_seqcrow_preset(chimera_ligand, fallback="Ball-Stick-Endcap")
if self.showLigKeyBool:
color = self.lig_color.get_color()
color = [c / 255. for c in color]
self.settings.key_atom_color = tuple(color)
bild_obj = key_atom_highlight(ligand, color, self.session)
self.session.models.add(bild_obj, parent=chimera_ligand)
def open_rings(self):
for row in self.ring_table.table.selectionModel().selectedRows():
if self.ring_table.table.isRowHidden(row.row()):
continue
ring_name = row.data()
ring = Ring(ring_name, name=ring_name)
chimera_ring = ResidueCollection(ring.copy()).get_chimera(
self.session)
self.session.models.add([chimera_ring])
apply_seqcrow_preset(chimera_ring, fallback="Ball-Stick-Endcap")
if self.showRingWalkBool:
color = self.ring_color.get_color()
color = [c / 255. for c in color]
self.ring_walk_color = tuple(color)
bild_obj = show_walk_highlight(ring, chimera_ring, color,
self.session)
self.session.models.add(bild_obj, parent=chimera_ring)
def handle_scheme(self, url):
query = urllib.parse.parse_qs(url.query())
# tool has URL's to acknowledge how we get the structure
# clicking those opens these links
if "link" in query:
link = query["link"][0]
if link == "AmberTools":
run(self.session,
"open \"https://ambermd.org/AmberTools.php\"")
elif link == "NCI/CADD":
run(self.session, "open \"https://cactus.nci.nih.gov/\"")
return
# this is the 2D mol file that we will convert to a 3D structure
# as some point in the HTML file, spaces are turned into sPaCe so they don't get nuked
molfile = query["molfile"][0].replace("sPaCe",
" ").replace("\\n", "\n")
# copy-paste from AaronTools.from_string
# instead of smiles, we have a file
url = "https://cactus.nci.nih.gov/cgi-bin/translate.tcl?smiles=&format=sdf&astyle=kekule&dim=3D&file=%s" % urllib.parse.quote_plus(
molfile)
s_sd_get = urlopen(url, context=ssl.SSLContext())
msg, status = s_sd_get.msg, s_sd_get.status
if msg != "OK":
self.session.logger.error(
"Issue contacting %s for MOL lookup (status: %s)",
CACTUS_HOST,
status,
)
raise IOError
s_sd_get = s_sd_get.read().decode("utf8")
try:
tmp_url = re.search(
'User-defined exchange format file: <a href="(.*)"',
s_sd_get,
).group(1)
except AttributeError as err:
if re.search("You entered an invalid MOL file", s_sd_get):
self.session.logger.error(
"Invalid format encountered: %s (consult %s for syntax help)",
molfile,
"https://cactus.nci.nih.gov/translate/smiles.html",
)
raise IOError(err)
new_url = "{}{}".format(CACTUS_HOST, tmp_url)
s_sd = (urlopen(new_url,
context=ssl.SSLContext()).read().decode("utf8"))
name = query["name"][0]
fr = FileReader((name, "sd", s_sd))
rescol = ResidueCollection(fr)
# if not optimization was requested, open the new molecule
if query["method"][0] == "no":
struc = rescol.get_chimera(self.session, filereader=fr)
self.session.models.add([struc])
apply_seqcrow_preset(
struc,
fallback="Ball-Stick-Endcap",
)
return
# if optimization was requested, run the SQM job with auto_open=True
theory = Theory(
method=query["method"][0],
charge=fr.other["charge"],
job_type=OptimizationJob(),
)
job = SQMJob(
name,
self.session,
theory,
rescol,
auto_open=True,
)
self.session.logger.info(
"structure will appear when optimization completes")
self.session.logger.status(
"structure will appear when optimization completes")
self.session.seqcrow_job_manager.add_job(job)
def update_chix(self, chix_residue, refresh_connected=True):
"""changes chimerax residue to match self"""
elements = {}
known_atoms = []
new_atoms = []
#print("updating residue", self.name, chix_residue.name)
chix_residue.name = self.name
#print("updating residue:")
#print(self.write(outfile=False))
for atom in self.atoms:
#print(atom, hasattr(atom, "chix_atom"))
if not hasattr(atom, "chix_atom") or \
atom.chix_atom is None or \
atom.chix_atom.deleted or atom.chix_atom not in chix_residue.atoms:
#if not hasattr(atom, "chix_atom"):
# print("no chix atom", atom)
#elif atom.chix_atom is None:
# print("no chix atom yet", atom)
#elif atom.chix_atom.deleted:
# print("chix_atom deleted", atom)
#else:
# print("atoms do not match", atom.chix_atom)
#print("new chix atom for", atom)
if hasattr(atom, "chix_name"):
atom_name = atom.chix_name
# print("atom has chix name:", atom_name)
else:
atom_name = atom.name
# print("atom does not have chix name:", atom_name)
if "." in atom_name or len(atom_name) > 4:
# print("previous atom name was illegal, using", atom.element)
atom_name = atom.element
new_atom = chix_residue.structure.new_atom(
atom_name, atom.element)
new_atom.coord = atom.coords
chix_residue.add_atom(new_atom)
atom.chix_atom = new_atom
known_atoms.append(new_atom)
new_atoms.append(new_atom)
else:
if atom.chix_atom.element.name != atom.element:
atom.chix_atom.element = Element.get_element(atom.element)
new_atoms.append(atom.chix_atom)
atom.chix_atom.coord = atom.coords
known_atoms.append(atom.chix_atom)
for atom in chix_residue.atoms:
if atom not in known_atoms:
#print("deleting %s" % atom.atomspec)
atom.delete()
for atom in new_atoms:
# print("starting name:", atom.name)
if ([a.name for a in known_atoms].count(atom.name) == 1
and atom.name.startswith(atom.element.name)
and atom.name != atom.element.name
and "." not in atom.name):
# print("skipping", atom.name, atom.serial_number, atom.atomspec)
continue
if not atom.name.startswith(atom.element.name):
atom.name = atom.element.name
atom_name = "%s1" % atom.name
k = 1
while k == 1 or any(
[chix_atom.name == atom_name for chix_atom in known_atoms]):
atom_name = "%s%i" % (atom.name, k)
k += 1
if len(atom_name) > 4:
if atom.name == atom.element.name:
# print("breaking:", k, atom.name)
break
atom.name = atom.element.name
k = 1
# print("name:", atom_name)
if len(atom_name) <= 4:
atom.name = atom_name
else:
atom.name = atom.element.name
# print("final name:", atom.name)
if refresh_connected:
self.refresh_chix_connected(chix_residue)
for atom in chix_residue.atoms:
if atom.serial_number == -1:
atom.serial_number = atom.structure.atoms.index(atom) + 1
apply_seqcrow_preset(chix_residue.structure, atoms=new_atoms)
