def test_ring(self):
try:
import rdkit
ring = Ring.from_string(
"benzene", end_length=1, end_atom="C", form="iupac"
)
ref = self.benzene
self.assertTrue(validate(ring, ref, thresh="loose"))
except ImportError:
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
ring = Ring.from_string(
"benzene", end_length=1, end_atom="C", form="iupac"
)
print(ring.comment)
ref = self.benzene
self.assertTrue(
validate(ring, ref, thresh="loose", debug=True)
)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
def ring_substitute(self, target, ring, *args, **kwargs):
"""put a ring on the given targets"""
if not isinstance(ring, Ring):
ring = Ring(ring)
residue = self.find_residue(target[0])[0]
super().ring_substitute(target, ring, *args, **kwargs)
new_atoms = [
atom for atom in self.atoms if not hasattr(atom, "chix_atom")
]
residue.atoms.extend(new_atoms)
for res in self.residues:
deleted_atoms = []
for atom in res.atoms:
if not hasattr(atom, "chix_atom"):
continue
if atom.chix_atom.residue is not res.chix_residue and atom in self.atoms:
deleted_atoms.append(atom)
elif atom not in self.atoms:
deleted_atoms.append(atom)
for atom in deleted_atoms:
res.atoms.remove(atom)
def test_close_ring(self):
mol = Geometry(TestGeometry.benzene)
ref1 = Geometry(TestGeometry.naphthalene)
mol1 = mol.copy()
mol1.ring_substitute(["7", "8"], Ring("benzene"))
self.assertTrue(validate(mol1, ref1, thresh="loose"))
ref2 = Geometry(TestGeometry.tetrahydronaphthalene)
mol2 = mol.copy()
mol2.ring_substitute(["7", "8"], Ring("cyclohexane"))
rmsd = mol2.RMSD(ref2, align=True, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref2, superLoose=True))
mol3 = Geometry(TestGeometry.naphthalene)
ref3 = Geometry(TestGeometry.pyrene)
targets1 = mol3.find(["9", "15"])
targets2 = mol3.find(["10", "16"])
mol3.ring_substitute(targets1, Ring("benzene"))
mol3.ring_substitute(targets2, Ring("benzene"))
rmsd = mol3.RMSD(ref3, align=True, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref3, superLoose=True))
def libadd_ring(self):
"""add ring to library or open it in a new model"""
selection = self.session.seqcrow_ordered_selection_manager.selection
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
rescol = ResidueCollection(selection[0].structure)
walk_atoms = rescol.find(
[AtomSpec(atom.atomspec) for atom in selection])
if len(walk_atoms) < 1:
raise RuntimeError("no walk direction could be determined")
ring_name = self.ring_name.text()
ring = Ring(rescol, name=ring_name, end=walk_atoms)
ring.comment = "E:%s" % ",".join(
[str(rescol.atoms.index(atom) + 1) for atom in walk_atoms])
if len(ring_name) == 0:
chimerax_ring = ResidueCollection(ring).get_chimera(self.session)
chimerax_ring.name = "ring preview"
self.session.models.add([chimerax_ring])
bild_obj = show_walk_highlight(ring, chimerax_ring,
[0.9, 0.4, 0.3, 0.9], self.session)
self.session.models.add(bild_obj, parent=chimerax_ring)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Rings", ring_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" %
ring_name)
else:
self.tool_window.status(
"%s has not been added to ring library" % ring_name)
else:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" % ring_name)
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 do_new_ring(self):
rings = self.ringname.text()
for ring in rings.split(","):
ring = ring.strip()
rescol = ResidueCollection(Ring(ring))
model = self.ring_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.ring_model_selector.setCurrentIndex(self.ring_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]))
"if no name is given, the ring will be printed to STDOUT"
)
libaddring_parser.add_argument(
'-w', '--walk',
type=str,
nargs=1,
required=True,
dest='walk',
help="comma-separated list of atoms to define" +
"the direction the ring is traversed (1-indexed)"
)
args = libaddring_parser.parse_args()
ring = Ring(args.infile)
walk_atoms = args.walk.split(',')
ring.find_end(len(walk_atoms), walk_atoms)
ring.comment = "E:%s" % args.walk
if args.name is None:
print(ring.write(outfile=False))
else:
ring_lib = Ring.AARON_LIBS
ring_file = os.path.join(os.path.dirname(Ring.AARON_LIBS), args.name + '.xyz')
if os.path.exists(ring_file):
overwrite = input(
"%s already exists.\nWould you like to overwrite it? (YES/no)\n" % ring_file
)
class TestFromString(TestWithTimer):
"""
these only get run if RDKit is installed
molecules can be fetched from CATCVS, but there can be
discrepencies that make these tests "fail"
"""
COCH3 = Substituent("COCH3")
NO2 = Substituent("NO2")
benzene = Ring("benzene")
chiral_geom = Geometry(
os.path.join(prefix, "test_files", "chiral_ring.xyz")
)
def is_COCH3(self, sub, thresh=0.03):
ref = TestFromString.COCH3
ref.refresh_connected()
sub.refresh_connected()
ref.refresh_ranks()
ref.refresh_ranks()
ref.atoms = ref.reorder(start=ref.atoms[0])[0]
sub.atoms = sub.reorder(start=sub.atoms[0])[0]
self.assertTrue(
validate(
sub,
ref,
thresh=thresh,
heavy_only=True,
sort=False,
debug=False,
)
)
def is_NO2(self, sub):
ref = TestFromString.NO2
self.assertTrue(validate(sub, ref, thresh=2e-1))
def test_substituent(self):
try:
import rdkit
sub = Substituent.from_string(
"acetyl", form="iupac", strict_use_rdkit=True
)
self.is_COCH3(sub)
with self.assertLogs(Substituent.LOG, level="WARNING"):
sub = Substituent.from_string(
"nitro", form="iupac", strict_use_rdkit=True
)
self.is_NO2(sub)
sub = Substituent.from_string(
"O=[N.]=O", form="smiles", strict_use_rdkit=True
)
self.is_NO2(sub)
sub = Substituent.from_string(
"O=[N]=O", form="smiles", strict_use_rdkit=True
)
self.is_NO2(sub)
except (ImportError, ModuleNotFoundError):
# I still want to test CACTVS things because sometimes they change stuff
# that breaks our stuff
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
sub = Substituent.from_string("acetyl", form="iupac")
print(sub.write(outfile=False))
self.is_COCH3(sub, thresh=0.3)
sub = Substituent.from_string("nitro", form="iupac")
print(sub.write(outfile=False))
self.is_NO2(sub)
sub = Substituent.from_string("O=[N.]=O", form="smiles")
print(sub.write(outfile=False))
self.is_NO2(sub)
sub = Substituent.from_string("O=[N]=O", form="smiles")
print(sub.write(outfile=False))
self.is_NO2(sub)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
def test_geometry(self):
try:
import rdkit
geom = Geometry.from_string(
"(1R,2R)-1-Chloro-2-methylcyclohexane", form="iupac"
)
ref = TestFromString.chiral_geom
# really loose threshhold b/c rdkit can give a boat cyclohexane...
self.assertTrue(validate(geom, ref, thresh=0.35, heavy_only=True))
except (ImportError, ModuleNotFoundError):
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
geom = Geometry.from_string(
"(1R,2R)-1-Chloro-2-methylcyclohexane", form="iupac"
)
ref = TestFromString.chiral_geom
# really loose threshhold b/c rdkit can give a boat cyclohexane...
self.assertTrue(
validate(geom, ref, thresh=0.35, heavy_only=True)
)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
def test_ring(self):
try:
import rdkit
ring = Ring.from_string(
"benzene", end_length=1, end_atom="C", form="iupac"
)
ref = self.benzene
self.assertTrue(validate(ring, ref, thresh="loose"))
except ImportError:
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
ring = Ring.from_string(
"benzene", end_length=1, end_atom="C", form="iupac"
)
print(ring.comment)
ref = self.benzene
self.assertTrue(
validate(ring, ref, thresh="loose", debug=True)
)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
def fuseRing_list(session):
s = ""
for ringname in Ring.list():
s += "%s\n" % ringname
session.logger.info(s.strip())
def _build_ui(self):
layout = QGridLayout()
self.alchemy_tabs = QTabWidget()
#substitute
substitute_tab = QWidget()
substitute_layout = QGridLayout(substitute_tab)
sublabel = QLabel("substituent name:")
substitute_layout.addWidget(sublabel, 0, 0, Qt.AlignVCenter)
self.subname = QLineEdit()
# self.subname.setText("Et")
sub_completer = NameCompleter(Substituent.list(), self.subname)
self.subname.setCompleter(sub_completer)
self.subname.setToolTip("name of substituent in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
substitute_layout.addWidget(self.subname, 0, 1, Qt.AlignVCenter)
open_sub_lib = QPushButton("from library...")
open_sub_lib.clicked.connect(self.open_sub_selector)
substitute_layout.addWidget(open_sub_lib, 0, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_sub = QCheckBox()
self.close_previous_sub.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_sub.setChecked(self.settings.modify)
self.close_previous_sub.stateChanged.connect(self.close_previous_change)
substitute_layout.addWidget(self.close_previous_sub, 1, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("relax substituent:"), 2, 0, 1, 1, Qt.AlignVCenter)
self.minimize = QCheckBox()
self.minimize.setToolTip("spin the added substituents to try to minimize the LJ potential energy")
self.minimize.setChecked(self.settings.minimize)
substitute_layout.addWidget(self.minimize, 2, 1, 1, 1, Qt.AlignTop)
substitute_layout.addWidget(QLabel("guess previous substituent:"), 3, 0, 1, 1, Qt.AlignVCenter)
self.guess_old = QCheckBox()
self.guess_old.setToolTip("checked: leave the longest connected fragment in the residue\nunchecked: previous substituent must be selected")
self.guess_old.setChecked(self.settings.guess)
self.guess_old.stateChanged.connect(lambda state, settings=self.settings: settings.__setattr__("guess", True if state == Qt.Checked else False))
substitute_layout.addWidget(self.guess_old, 3, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("new residue:"), 5, 0, 1, 1, Qt.AlignVCenter)
self.new_residue = QCheckBox()
self.new_residue.setToolTip("put the new substituent in its own residue instead\nof adding it to the residue of the old substituent")
self.new_residue.setChecked(self.settings.new_residue)
self.new_residue.stateChanged.connect(lambda state, settings=self.settings: settings.__setattr__("new_residue", True if state == Qt.Checked else False))
substitute_layout.addWidget(self.new_residue, 5, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("use distance names:"), 4, 0, 1, 1, Qt.AlignVCenter)
self.use_greek = QCheckBox()
self.use_greek.setChecked(self.settings.use_greek)
self.use_greek.setToolTip("indicate distance from point of attachment with atom name")
substitute_layout.addWidget(self.use_greek, 4, 1, 1, 1, Qt.AlignTop)
substitute_layout.addWidget(QLabel("change residue name:"), 6, 0, 1, 1, Qt.AlignVCenter)
self.new_sub_name = QLineEdit()
self.new_sub_name.setToolTip("change name of modified residues")
self.new_sub_name.setPlaceholderText("leave blank to keep current")
substitute_layout.addWidget(self.new_sub_name, 6, 1, 1, 2, Qt.AlignTop)
substitute_button = QPushButton("substitute current selection")
substitute_button.clicked.connect(self.do_substitute)
substitute_layout.addWidget(substitute_button, 7, 0, 1, 3, Qt.AlignTop)
self.substitute_button = substitute_button
substitute_layout.setRowStretch(0, 0)
substitute_layout.setRowStretch(1, 0)
substitute_layout.setRowStretch(2, 0)
substitute_layout.setRowStretch(3, 0)
substitute_layout.setRowStretch(4, 0)
substitute_layout.setRowStretch(5, 0)
substitute_layout.setRowStretch(6, 0)
substitute_layout.setRowStretch(7, 1)
#map ligand
maplig_tab = QWidget()
maplig_layout = QGridLayout(maplig_tab)
liglabel = QLabel("ligand name:")
maplig_layout.addWidget(liglabel, 0, 0, Qt.AlignVCenter)
self.ligname = QLineEdit()
lig_completer = NameCompleter(Component.list(), self.ligname)
self.ligname.setCompleter(lig_completer)
self.ligname.setToolTip("name of ligand in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
maplig_layout.addWidget(self.ligname, 0, 1, Qt.AlignVCenter)
open_lig_lib = QPushButton("from library...")
open_lig_lib.clicked.connect(self.open_lig_selector)
maplig_layout.addWidget(open_lig_lib, 0, 2, Qt.AlignTop)
maplig_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_lig = QCheckBox()
self.close_previous_lig.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_lig.setChecked(self.settings.modify)
self.close_previous_lig.stateChanged.connect(self.close_previous_change)
maplig_layout.addWidget(self.close_previous_lig, 1, 1, 1, 2, Qt.AlignTop)
maplig_button = QPushButton("swap ligand with selected coordinating atoms")
maplig_button.clicked.connect(self.do_maplig)
maplig_layout.addWidget(maplig_button, 2, 0, 1, 3, Qt.AlignTop)
self.maplig_button = maplig_button
start_structure_button = QPushButton("place in:")
self.lig_model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_lig)
maplig_layout.addWidget(start_structure_button, 3, 0, 1, 1, Qt.AlignTop)
maplig_layout.addWidget(self.lig_model_selector, 3, 1, 1, 2, Qt.AlignTop)
maplig_layout.setRowStretch(0, 0)
maplig_layout.setRowStretch(1, 0)
maplig_layout.setRowStretch(2, 0)
maplig_layout.setRowStretch(3, 1)
#close ring
closering_tab = QWidget()
closering_layout = QGridLayout(closering_tab)
ringlabel = QLabel("ring name:")
closering_layout.addWidget(ringlabel, 0, 0, Qt.AlignVCenter)
self.ringname = QLineEdit()
ring_completer = NameCompleter(Ring.list(), self.ringname)
self.ringname.setCompleter(ring_completer)
self.ringname.setToolTip("name of ring in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
closering_layout.addWidget(self.ringname, 0, 1, Qt.AlignVCenter)
open_ring_lib = QPushButton("from library...")
open_ring_lib.clicked.connect(self.open_ring_selector)
closering_layout.addWidget(open_ring_lib, 0, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_ring = QCheckBox()
self.close_previous_ring.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_ring.setChecked(self.settings.modify)
self.close_previous_ring.stateChanged.connect(self.close_previous_change)
closering_layout.addWidget(self.close_previous_ring, 1, 1, 1, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("try multiple:"), 2, 0, 1, 1, Qt.AlignVCenter)
self.minimize_ring = QCheckBox()
self.minimize_ring.setToolTip("try to use other versions of this ring in the library to find the one that fits best")
self.minimize_ring.setChecked(self.settings.minimize_ring)
closering_layout.addWidget(self.minimize_ring, 2, 1, 1, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("new residue name:"), 3, 0, 1, 1, Qt.AlignVCenter)
self.new_ring_name = QLineEdit()
self.new_ring_name.setToolTip("change name of modified residues")
self.new_ring_name.setPlaceholderText("leave blank to keep current")
closering_layout.addWidget(self.new_ring_name, 3, 1, 1, 2, Qt.AlignTop)
closering_button = QPushButton("put a ring on current selection")
closering_button.clicked.connect(self.do_fusering)
closering_layout.addWidget(closering_button, 4, 0, 1, 3, Qt.AlignTop)
self.closering_button = closering_button
start_structure_button = QPushButton("place in:")
self.ring_model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_ring)
closering_layout.addWidget(start_structure_button, 5, 0, 1, 1, Qt.AlignTop)
closering_layout.addWidget(self.ring_model_selector, 5, 1, 1, 2, Qt.AlignTop)
closering_layout.setRowStretch(0, 0)
closering_layout.setRowStretch(1, 0)
closering_layout.setRowStretch(2, 0)
closering_layout.setRowStretch(3, 0)
closering_layout.setRowStretch(4, 0)
closering_layout.setRowStretch(5, 1)
#change element
changeelement_tab = QWidget()
changeelement_layout = QFormLayout(changeelement_tab)
self.element = ElementButton("C", single_state=True)
self.element.clicked.connect(self.open_ptable)
changeelement_layout.addRow("element:", self.element)
self.vsepr = QComboBox()
self.vsepr.addItems([
"do not change", # 0
"linear (1 bond)", # 1
"linear (2 bonds)", # 2
"trigonal planar (2 bonds)", # 3
"tetrahedral (2 bonds)", # 4
"trigonal planar", # 5
"tetrahedral (3 bonds)", # 6
"T-shaped", # 7
"trigonal pyramidal", # 8
"tetrahedral", # 9
"sawhorse", #10
"seesaw", #11
"square planar", #12
"trigonal bipyramidal", #13
"square pyramidal", #14
"pentagonal", #15
"octahedral", #16
"hexagonal", #17
"trigonal prismatic", #18
"pentagonal pyramidal", #19
"capped octahedral", #20
"capped trigonal prismatic", #21
"heptagonal", #22
"hexagonal pyramidal", #23
"pentagonal bipyramidal", #24
"biaugmented trigonal prismatic", #25
"cubic", #26
"elongated trigonal bipyramidal", #27
"hexagonal bipyramidal", #28
"heptagonal pyramidal", #29
"octagonal", #30
"square antiprismatic", #31
"trigonal dodecahedral", #32
"capped cube", #33
"capped square antiprismatic", #34
"enneagonal", #35
"heptagonal bipyramidal", #36
"hula-hoop", #37
"triangular cupola", #38
"tridiminished icosahedral", #39
"muffin", #40
"octagonal pyramidal", #41
"tricapped trigonal prismatic", #42
])
self.vsepr.setCurrentIndex(9)
self.vsepr.insertSeparator(33)
self.vsepr.insertSeparator(25)
self.vsepr.insertSeparator(20)
self.vsepr.insertSeparator(16)
self.vsepr.insertSeparator(13)
self.vsepr.insertSeparator(8)
self.vsepr.insertSeparator(5)
self.vsepr.insertSeparator(2)
self.vsepr.insertSeparator(1)
self.vsepr.insertSeparator(0)
changeelement_layout.addRow("geometry:", self.vsepr)
self.change_bonds = QCheckBox()
self.change_bonds.setChecked(self.settings.change_bonds)
changeelement_layout.addRow("adjust bond lengths:", self.change_bonds)
change_element_button = QPushButton("change selected elements")
change_element_button.clicked.connect(self.do_change_element)
changeelement_layout.addRow(change_element_button)
self.change_element_button = change_element_button
start_structure_button = QPushButton("place in:")
self.model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_atom)
changeelement_layout.addRow(start_structure_button, self.model_selector)
delete_atoms_button = QPushButton("delete selected atoms")
delete_atoms_button.clicked.connect(self.delete_atoms)
changeelement_layout.addRow(delete_atoms_button)
self.alchemy_tabs.addTab(substitute_tab, "substitute")
self.alchemy_tabs.addTab(maplig_tab, "swap ligand")
self.alchemy_tabs.addTab(closering_tab, "fuse ring")
self.alchemy_tabs.addTab(changeelement_tab, "change element")
layout.addWidget(self.alchemy_tabs)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
help="try to minimize structure difference")
ring_parser.add_argument("-f",
"--flip-rings",
action="store_const",
const=True,
default=False,
required=False,
dest="flip",
help="also try swapping target order when minimizing")
args = ring_parser.parse_args()
if args.list_avail:
s = ""
for i, name in enumerate(sorted(Ring.list())):
s += "%-20s" % name
# if (i + 1) % 3 == 0:
if (i + 1) % 1 == 0:
s += "\n"
print(s.strip())
exit(0)
for infile in glob_files(args.infile, parser=ring_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format, infile))
else:
f = FileReader(infile)
else: