class BondEditor(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Bond-Editor-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _BondEditorSettings(session, name)
self._build_ui()
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
layout.addWidget(tabs)
ts_bond_tab = QWidget()
ts_options = QFormLayout(ts_bond_tab)
self.tsbond_color = ColorButton(has_alpha_channel=False,
max_size=(16, 16))
self.tsbond_color.set_color(self.settings.tsbond_color)
ts_options.addRow("color:", self.tsbond_color)
self.tsbond_transparency = QSpinBox()
self.tsbond_transparency.setRange(1, 99)
self.tsbond_transparency.setValue(self.settings.tsbond_transparency)
self.tsbond_transparency.setSuffix("%")
ts_options.addRow("transparency:", self.tsbond_transparency)
self.tsbond_radius = QDoubleSpinBox()
self.tsbond_radius.setRange(0.01, 1)
self.tsbond_radius.setDecimals(3)
self.tsbond_radius.setSingleStep(0.005)
self.tsbond_radius.setSuffix(" \u212B")
self.tsbond_radius.setValue(self.settings.tsbond_radius)
ts_options.addRow("radius:", self.tsbond_radius)
draw_tsbonds = QPushButton("draw TS bonds on selected atoms/bonds")
draw_tsbonds.clicked.connect(self.run_tsbond)
ts_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_tsbonds = QPushButton("erase selected TS bonds")
erase_tsbonds.clicked.connect(self.run_erase_tsbond)
ts_options.addRow(erase_tsbonds)
self.erase_tsbonds = erase_tsbonds
bond_tab = QWidget()
bond_options = QFormLayout(bond_tab)
self.bond_halfbond = QCheckBox()
self.bond_halfbond.setChecked(self.settings.bond_halfbond)
self.bond_halfbond.setToolTip(
"each half of the bond will be colored according to the atom's color"
)
bond_options.addRow("half-bond:", self.bond_halfbond)
self.bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.bond_color.set_color(self.settings.bond_color)
self.bond_color.setEnabled(
self.bond_halfbond.checkState() != Qt.Checked)
self.bond_halfbond.stateChanged.connect(
lambda state, widget=self.bond_color: self.bond_color.setEnabled(
state != Qt.Checked))
bond_options.addRow("color:", self.bond_color)
self.bond_radius = QDoubleSpinBox()
self.bond_radius.setRange(0.01, 1)
self.bond_radius.setDecimals(3)
self.bond_radius.setSingleStep(0.005)
self.bond_radius.setSuffix(" \u212B")
self.bond_radius.setValue(self.settings.bond_radius)
bond_options.addRow("radius:", self.bond_radius)
draw_tsbonds = QPushButton("draw bond between selected atoms")
draw_tsbonds.clicked.connect(self.run_bond)
bond_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_bonds = QPushButton("erase selected bonds")
erase_bonds.clicked.connect(
lambda *, ses=self.session: run(ses, "delete bonds sel"))
bond_options.addRow(erase_bonds)
self.erase_bonds = erase_bonds
hbond_tab = QWidget()
hbond_options = QFormLayout(hbond_tab)
self.hbond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.hbond_color.set_color(self.settings.hbond_color)
hbond_options.addRow("color:", self.hbond_color)
self.hbond_radius = QDoubleSpinBox()
self.hbond_radius.setDecimals(3)
self.hbond_radius.setSuffix(" \u212B")
self.hbond_radius.setValue(self.settings.hbond_radius)
hbond_options.addRow("radius:", self.hbond_radius)
self.hbond_dashes = QSpinBox()
self.hbond_dashes.setRange(0, 28)
self.hbond_dashes.setSingleStep(2)
self.hbond_radius.setSingleStep(0.005)
self.hbond_dashes.setValue(self.settings.hbond_dashes)
hbond_options.addRow("dashes:", self.hbond_dashes)
draw_hbonds = QPushButton("draw H-bonds")
draw_hbonds.clicked.connect(self.run_hbond)
hbond_options.addRow(draw_hbonds)
self.draw_hbonds = draw_hbonds
erase_hbonds = QPushButton("erase all H-bonds")
erase_hbonds.clicked.connect(
lambda *, ses=self.session: run(ses, "~hbonds"))
hbond_options.addRow(erase_hbonds)
self.erase_hbonds = erase_hbonds
tm_bond_tab = QWidget()
tm_bond_options = QFormLayout(tm_bond_tab)
self.tm_bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.tm_bond_color.set_color(self.settings.tm_bond_color)
tm_bond_options.addRow("color:", self.tm_bond_color)
self.tm_bond_radius = QDoubleSpinBox()
self.tm_bond_radius.setDecimals(3)
self.tm_bond_radius.setSuffix(" \u212B")
self.tm_bond_radius.setValue(self.settings.tm_bond_radius)
tm_bond_options.addRow("radius:", self.tm_bond_radius)
self.tm_bond_dashes = QSpinBox()
self.tm_bond_dashes.setRange(0, 28)
self.tm_bond_dashes.setSingleStep(2)
self.tm_bond_radius.setSingleStep(0.005)
self.tm_bond_dashes.setValue(self.settings.tm_bond_dashes)
tm_bond_options.addRow("dashes:", self.tm_bond_dashes)
draw_tm_bonds = QPushButton("draw metal coordination bonds")
draw_tm_bonds.clicked.connect(self.run_tm_bond)
tm_bond_options.addRow(draw_tm_bonds)
self.draw_tm_bonds = draw_tm_bonds
erase_tm_bonds = QPushButton("erase all metal coordination bonds")
erase_tm_bonds.clicked.connect(self.del_tm_bond)
tm_bond_options.addRow(erase_tm_bonds)
self.erase_tm_bonds = erase_tm_bonds
bond_length_tab = QWidget()
bond_length_layout = QFormLayout(bond_length_tab)
self.bond_distance = QDoubleSpinBox()
self.bond_distance.setRange(0.5, 10.0)
self.bond_distance.setSingleStep(0.05)
self.bond_distance.setValue(1.51)
self.bond_distance.setSuffix(" \u212B")
bond_length_layout.addRow("bond length:", self.bond_distance)
self.move_fragment = QComboBox()
self.move_fragment.addItems(["both", "smaller", "larger"])
bond_length_layout.addRow("move side:", self.move_fragment)
bond_lookup = QGroupBox("bond length lookup:")
bond_lookup_layout = QGridLayout(bond_lookup)
bond_lookup_layout.addWidget(
QLabel("elements:"),
0,
0,
)
self.ele1 = ElementButton("C", single_state=True)
self.ele1.clicked.connect(
lambda *args, button=self.ele1: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele1, 0, 1,
Qt.AlignRight | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("-"), 0, 2,
Qt.AlignHCenter | Qt.AlignVCenter)
self.ele2 = ElementButton("C", single_state=True)
self.ele2.clicked.connect(
lambda *args, button=self.ele2: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele2, 0, 3,
Qt.AlignLeft | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("bond order:"), 1, 0)
self.bond_order = BondOrderSpinBox()
self.bond_order.setRange(1., 3.)
self.bond_order.setValue(1)
self.bond_order.setSingleStep(0.5)
self.bond_order.setDecimals(1)
self.bond_order.valueChanged.connect(self.check_bond_lengths)
bond_lookup_layout.addWidget(self.bond_order, 1, 1, 1, 3)
bond_lookup_layout.setColumnStretch(0, 0)
bond_lookup_layout.setColumnStretch(1, 0)
bond_lookup_layout.setColumnStretch(2, 0)
bond_lookup_layout.setColumnStretch(3, 1)
bond_length_layout.addRow(bond_lookup)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
bond_lookup_layout.addWidget(self.status, 2, 0, 1, 4)
self.do_bond_change = QPushButton("change selected bond lengths")
self.do_bond_change.clicked.connect(self.change_bond_length)
bond_length_layout.addRow(self.do_bond_change)
tabs.addTab(bond_tab, "covalent bonds")
tabs.addTab(ts_bond_tab, "TS bonds")
tabs.addTab(hbond_tab, "H-bonds")
tabs.addTab(tm_bond_tab, "coordination bonds")
tabs.addTab(bond_length_tab, "bond length")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def run_tsbond(self, *args):
args = ["tsbond", "sel"]
color = self.tsbond_color.get_color()
args.extend(["color", "rgb(%i, %i, %i)" % tuple(color[:-1])])
self.settings.tsbond_color = tuple([c / 255. for c in color])
radius = self.tsbond_radius.value()
args.extend(["radius", "%.3f" % radius])
self.settings.tsbond_radius = radius
transparency = self.tsbond_transparency.value()
args.extend(["transparency", "%i" % transparency])
self.settings.tsbond_transparency = transparency
run(self.session, " ".join(args))
def run_erase_tsbond(self, *args):
run(self.session, "~tsbond sel")
def run_bond(self, *args):
# TODO: switch to `bond sel` in 1.2
sel = selected_atoms(self.session)
halfbond = self.bond_halfbond.checkState() == Qt.Checked
self.settings.bond_halfbond = halfbond
if not halfbond:
color = self.bond_color.get_color()
color = tuple(x / 255. for x in color)
self.settings.bond_color = color
radius = self.bond_radius.value()
self.settings.bond_radius = radius
for b in selected_bonds(self.session):
b.halfbond = halfbond
if not halfbond:
b.color = np.array([int(x * 255) for x in color])
b.radius = radius
for i, a1 in enumerate(sel):
for a2 in sel[:i]:
if a1.structure is a2.structure and a2 not in a1.neighbors:
new_bond = a1.structure.new_bond(a1, a2)
new_bond.halfbond = halfbond
if not halfbond:
new_bond.color = np.array(
[int(x * 255) for x in color])
new_bond.radius = radius
def run_hbond(self, *args):
args = ["hbonds", "reveal", "true"]
color = self.hbond_color.get_color()
args.extend(["color", "rgb(%i, %i, %i)" % tuple(color[:-1])])
self.settings.hbond_color = tuple([c / 255. for c in color])
radius = self.hbond_radius.value()
args.extend(["radius", "%.3f" % radius])
self.settings.hbond_radius = radius
dashes = self.hbond_dashes.value()
args.extend(["dashes", "%i" % dashes])
self.settings.hbond_dashes = dashes
run(self.session, " ".join(args))
def run_tm_bond(self, *args):
color = self.tm_bond_color.get_color()
self.settings.tm_bond_color = tuple([c / 255. for c in color])
radius = self.tm_bond_radius.value()
self.settings.tm_bond_radius = radius
dashes = self.tm_bond_dashes.value()
self.settings.tm_bond_dashes = dashes
models = self.session.models.list(type=AtomicStructure)
for model in models:
rescol = ResidueCollection(model, bonds_matter=False)
try:
tm_list = rescol.find([
AnyTransitionMetal(), "Na", "K", "Rb", "Cs", "Fr", "Mg",
"Ca", "Sr", "Ba", "Ra"
])
for tm in tm_list:
for atom in rescol.atoms:
if atom is tm:
continue
if atom.is_connected(tm):
pbg = model.pseudobond_group(
model.PBG_METAL_COORDINATION,
create_type="normal")
pbg.new_pseudobond(tm.chix_atom, atom.chix_atom)
pbg.dashes = dashes
pbg.color = color
pbg.radius = radius
except LookupError:
pass
def del_tm_bond(self, *args):
models = self.session.models.list(type=AtomicStructure)
for model in models:
pbg = model.pseudobond_group(model.PBG_METAL_COORDINATION,
create_type=None)
if pbg is not None:
pbg.delete()
def open_ptable(self, button):
self.tool_window.create_child_window("select element",
window_class=PTable2,
button=button,
callback=self.check_bond_lengths)
def check_bond_lengths(self, *args):
ele1 = self.ele1.text()
ele2 = self.ele2.text()
key = ORDER_BOND_ORDER.key(ele1, ele2)
order = "%.1f" % self.bond_order.value()
if key in ORDER_BOND_ORDER.bonds and order in ORDER_BOND_ORDER.bonds[
key]:
self.bond_distance.setValue(ORDER_BOND_ORDER.bonds[key][order])
self.status.showMessage("")
else:
self.status.showMessage("no bond data for %s-%s %sx bonds" %
(ele1, ele2, order))
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 _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
layout.addWidget(tabs)
ts_bond_tab = QWidget()
ts_options = QFormLayout(ts_bond_tab)
self.tsbond_color = ColorButton(has_alpha_channel=False,
max_size=(16, 16))
self.tsbond_color.set_color(self.settings.tsbond_color)
ts_options.addRow("color:", self.tsbond_color)
self.tsbond_transparency = QSpinBox()
self.tsbond_transparency.setRange(1, 99)
self.tsbond_transparency.setValue(self.settings.tsbond_transparency)
self.tsbond_transparency.setSuffix("%")
ts_options.addRow("transparency:", self.tsbond_transparency)
self.tsbond_radius = QDoubleSpinBox()
self.tsbond_radius.setRange(0.01, 1)
self.tsbond_radius.setDecimals(3)
self.tsbond_radius.setSingleStep(0.005)
self.tsbond_radius.setSuffix(" \u212B")
self.tsbond_radius.setValue(self.settings.tsbond_radius)
ts_options.addRow("radius:", self.tsbond_radius)
draw_tsbonds = QPushButton("draw TS bonds on selected atoms/bonds")
draw_tsbonds.clicked.connect(self.run_tsbond)
ts_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_tsbonds = QPushButton("erase selected TS bonds")
erase_tsbonds.clicked.connect(self.run_erase_tsbond)
ts_options.addRow(erase_tsbonds)
self.erase_tsbonds = erase_tsbonds
bond_tab = QWidget()
bond_options = QFormLayout(bond_tab)
self.bond_halfbond = QCheckBox()
self.bond_halfbond.setChecked(self.settings.bond_halfbond)
self.bond_halfbond.setToolTip(
"each half of the bond will be colored according to the atom's color"
)
bond_options.addRow("half-bond:", self.bond_halfbond)
self.bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.bond_color.set_color(self.settings.bond_color)
self.bond_color.setEnabled(
self.bond_halfbond.checkState() != Qt.Checked)
self.bond_halfbond.stateChanged.connect(
lambda state, widget=self.bond_color: self.bond_color.setEnabled(
state != Qt.Checked))
bond_options.addRow("color:", self.bond_color)
self.bond_radius = QDoubleSpinBox()
self.bond_radius.setRange(0.01, 1)
self.bond_radius.setDecimals(3)
self.bond_radius.setSingleStep(0.005)
self.bond_radius.setSuffix(" \u212B")
self.bond_radius.setValue(self.settings.bond_radius)
bond_options.addRow("radius:", self.bond_radius)
draw_tsbonds = QPushButton("draw bond between selected atoms")
draw_tsbonds.clicked.connect(self.run_bond)
bond_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_bonds = QPushButton("erase selected bonds")
erase_bonds.clicked.connect(
lambda *, ses=self.session: run(ses, "delete bonds sel"))
bond_options.addRow(erase_bonds)
self.erase_bonds = erase_bonds
hbond_tab = QWidget()
hbond_options = QFormLayout(hbond_tab)
self.hbond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.hbond_color.set_color(self.settings.hbond_color)
hbond_options.addRow("color:", self.hbond_color)
self.hbond_radius = QDoubleSpinBox()
self.hbond_radius.setDecimals(3)
self.hbond_radius.setSuffix(" \u212B")
self.hbond_radius.setValue(self.settings.hbond_radius)
hbond_options.addRow("radius:", self.hbond_radius)
self.hbond_dashes = QSpinBox()
self.hbond_dashes.setRange(0, 28)
self.hbond_dashes.setSingleStep(2)
self.hbond_radius.setSingleStep(0.005)
self.hbond_dashes.setValue(self.settings.hbond_dashes)
hbond_options.addRow("dashes:", self.hbond_dashes)
draw_hbonds = QPushButton("draw H-bonds")
draw_hbonds.clicked.connect(self.run_hbond)
hbond_options.addRow(draw_hbonds)
self.draw_hbonds = draw_hbonds
erase_hbonds = QPushButton("erase all H-bonds")
erase_hbonds.clicked.connect(
lambda *, ses=self.session: run(ses, "~hbonds"))
hbond_options.addRow(erase_hbonds)
self.erase_hbonds = erase_hbonds
tm_bond_tab = QWidget()
tm_bond_options = QFormLayout(tm_bond_tab)
self.tm_bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.tm_bond_color.set_color(self.settings.tm_bond_color)
tm_bond_options.addRow("color:", self.tm_bond_color)
self.tm_bond_radius = QDoubleSpinBox()
self.tm_bond_radius.setDecimals(3)
self.tm_bond_radius.setSuffix(" \u212B")
self.tm_bond_radius.setValue(self.settings.tm_bond_radius)
tm_bond_options.addRow("radius:", self.tm_bond_radius)
self.tm_bond_dashes = QSpinBox()
self.tm_bond_dashes.setRange(0, 28)
self.tm_bond_dashes.setSingleStep(2)
self.tm_bond_radius.setSingleStep(0.005)
self.tm_bond_dashes.setValue(self.settings.tm_bond_dashes)
tm_bond_options.addRow("dashes:", self.tm_bond_dashes)
draw_tm_bonds = QPushButton("draw metal coordination bonds")
draw_tm_bonds.clicked.connect(self.run_tm_bond)
tm_bond_options.addRow(draw_tm_bonds)
self.draw_tm_bonds = draw_tm_bonds
erase_tm_bonds = QPushButton("erase all metal coordination bonds")
erase_tm_bonds.clicked.connect(self.del_tm_bond)
tm_bond_options.addRow(erase_tm_bonds)
self.erase_tm_bonds = erase_tm_bonds
bond_length_tab = QWidget()
bond_length_layout = QFormLayout(bond_length_tab)
self.bond_distance = QDoubleSpinBox()
self.bond_distance.setRange(0.5, 10.0)
self.bond_distance.setSingleStep(0.05)
self.bond_distance.setValue(1.51)
self.bond_distance.setSuffix(" \u212B")
bond_length_layout.addRow("bond length:", self.bond_distance)
self.move_fragment = QComboBox()
self.move_fragment.addItems(["both", "smaller", "larger"])
bond_length_layout.addRow("move side:", self.move_fragment)
bond_lookup = QGroupBox("bond length lookup:")
bond_lookup_layout = QGridLayout(bond_lookup)
bond_lookup_layout.addWidget(
QLabel("elements:"),
0,
0,
)
self.ele1 = ElementButton("C", single_state=True)
self.ele1.clicked.connect(
lambda *args, button=self.ele1: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele1, 0, 1,
Qt.AlignRight | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("-"), 0, 2,
Qt.AlignHCenter | Qt.AlignVCenter)
self.ele2 = ElementButton("C", single_state=True)
self.ele2.clicked.connect(
lambda *args, button=self.ele2: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele2, 0, 3,
Qt.AlignLeft | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("bond order:"), 1, 0)
self.bond_order = BondOrderSpinBox()
self.bond_order.setRange(1., 3.)
self.bond_order.setValue(1)
self.bond_order.setSingleStep(0.5)
self.bond_order.setDecimals(1)
self.bond_order.valueChanged.connect(self.check_bond_lengths)
bond_lookup_layout.addWidget(self.bond_order, 1, 1, 1, 3)
bond_lookup_layout.setColumnStretch(0, 0)
bond_lookup_layout.setColumnStretch(1, 0)
bond_lookup_layout.setColumnStretch(2, 0)
bond_lookup_layout.setColumnStretch(3, 1)
bond_length_layout.addRow(bond_lookup)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
bond_lookup_layout.addWidget(self.status, 2, 0, 1, 4)
self.do_bond_change = QPushButton("change selected bond lengths")
self.do_bond_change.clicked.connect(self.change_bond_length)
bond_length_layout.addRow(self.do_bond_change)
tabs.addTab(bond_tab, "covalent bonds")
tabs.addTab(ts_bond_tab, "TS bonds")
tabs.addTab(hbond_tab, "H-bonds")
tabs.addTab(tm_bond_tab, "coordination bonds")
tabs.addTab(bond_length_tab, "bond length")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
self.library_tabs = QTabWidget()
#add a tab for ligands
self.ligand_tab = QWidget()
self.ligand_layout = QVBoxLayout(self.ligand_tab)
self.lig_table = LigandTable()
self.ligand_layout.addWidget(self.lig_table)
showKeyAtomsCheck = QCheckBox('show key atoms')
showKeyAtomsCheck.setToolTip(
"ligand's coordinating atoms will be highlighted")
showKeyAtomsCheck.toggle()
showKeyAtomsCheck.stateChanged.connect(self.showKeyAtoms)
self.ligand_layout.addWidget(showKeyAtomsCheck)
self.lig_color = ColorButton('key atom color', has_alpha_channel=True)
self.lig_color.setToolTip("highlight color for ligand's key atoms")
self.lig_color.set_color(self.settings.key_atom_color)
self.ligand_layout.addWidget(self.lig_color)
openLigButton = QPushButton("open selected ligands")
openLigButton.setToolTip(
"ligands selected in the table will be loaded into ChimeraX")
openLigButton.clicked.connect(self.open_ligands)
self.ligand_layout.addWidget(openLigButton)
self.openLigButton = openLigButton
#add a tab for substituents
self.substituent_tab = QWidget()
self.substituent_layout = QVBoxLayout(self.substituent_tab)
self.sub_table = SubstituentTable()
self.substituent_layout.addWidget(self.sub_table)
showGhostConnectionCheck = QCheckBox('show ghost connection')
showGhostConnectionCheck.setToolTip(
"ligand's coordinating atoms will be highlighted")
showGhostConnectionCheck.toggle()
showGhostConnectionCheck.stateChanged.connect(self.showGhostConnection)
self.substituent_layout.addWidget(showGhostConnectionCheck)
self.sub_color = ColorButton('ghost connection color',
has_alpha_channel=True)
self.sub_color.setToolTip("color of ghost connection")
self.sub_color.set_color(self.settings.ghost_connection_color)
self.substituent_layout.addWidget(self.sub_color)
openSubButton = QPushButton("open selected substituents")
openSubButton.setToolTip(
"substituents selected in the table will be loaded into ChimeraX")
openSubButton.clicked.connect(self.open_substituents)
self.substituent_layout.addWidget(openSubButton)
self.openSubButton = openSubButton
#add a tab for rings
self.ring_tab = QWidget()
self.ring_layout = QVBoxLayout(self.ring_tab)
self.ring_table = RingTable()
self.ring_layout.addWidget(self.ring_table)
showRingWalkCheck = QCheckBox('show ring walk')
showRingWalkCheck.setToolTip(
"arrows will show the way AaronTools traverses the ring")
showRingWalkCheck.toggle()
showRingWalkCheck.stateChanged.connect(self.showRingWalk)
self.ring_layout.addWidget(showRingWalkCheck)
self.ring_color = ColorButton('walk arrow color',
has_alpha_channel=True)
self.ring_color.setToolTip("color of walk arrows")
self.ring_color.set_color(self.settings.ring_walk_color)
self.ring_layout.addWidget(self.ring_color)
openRingButton = QPushButton("open selected rings")
openRingButton.setToolTip(
"rings selected in the table will be loaded into ChimeraX")
openRingButton.clicked.connect(self.open_rings)
self.ring_layout.addWidget(openRingButton)
self.openRingButton = openRingButton
self.library_tabs.resize(300, 200)
self.library_tabs.addTab(self.ligand_tab, "ligands")
self.library_tabs.addTab(self.substituent_tab, "substituents")
self.library_tabs.addTab(self.ring_tab, "rings")
layout.addWidget(self.library_tabs)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
class AaronTools_Library(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Browse-AaronTools-Libraries-Tool"
SESSION_ENDURING = True
SESSION_SAVE = True
def __init__(self, session, name):
super().__init__(session, name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.settings = _BrowseLibSettings(self.session, name)
self.showLigKeyBool = True
self.showSubGhostBool = True
self.showRingWalkBool = True
self._build_ui()
def _build_ui(self):
layout = QGridLayout()
self.library_tabs = QTabWidget()
#add a tab for ligands
self.ligand_tab = QWidget()
self.ligand_layout = QVBoxLayout(self.ligand_tab)
self.lig_table = LigandTable()
self.ligand_layout.addWidget(self.lig_table)
showKeyAtomsCheck = QCheckBox('show key atoms')
showKeyAtomsCheck.setToolTip(
"ligand's coordinating atoms will be highlighted")
showKeyAtomsCheck.toggle()
showKeyAtomsCheck.stateChanged.connect(self.showKeyAtoms)
self.ligand_layout.addWidget(showKeyAtomsCheck)
self.lig_color = ColorButton('key atom color', has_alpha_channel=True)
self.lig_color.setToolTip("highlight color for ligand's key atoms")
self.lig_color.set_color(self.settings.key_atom_color)
self.ligand_layout.addWidget(self.lig_color)
openLigButton = QPushButton("open selected ligands")
openLigButton.setToolTip(
"ligands selected in the table will be loaded into ChimeraX")
openLigButton.clicked.connect(self.open_ligands)
self.ligand_layout.addWidget(openLigButton)
self.openLigButton = openLigButton
#add a tab for substituents
self.substituent_tab = QWidget()
self.substituent_layout = QVBoxLayout(self.substituent_tab)
self.sub_table = SubstituentTable()
self.substituent_layout.addWidget(self.sub_table)
showGhostConnectionCheck = QCheckBox('show ghost connection')
showGhostConnectionCheck.setToolTip(
"ligand's coordinating atoms will be highlighted")
showGhostConnectionCheck.toggle()
showGhostConnectionCheck.stateChanged.connect(self.showGhostConnection)
self.substituent_layout.addWidget(showGhostConnectionCheck)
self.sub_color = ColorButton('ghost connection color',
has_alpha_channel=True)
self.sub_color.setToolTip("color of ghost connection")
self.sub_color.set_color(self.settings.ghost_connection_color)
self.substituent_layout.addWidget(self.sub_color)
openSubButton = QPushButton("open selected substituents")
openSubButton.setToolTip(
"substituents selected in the table will be loaded into ChimeraX")
openSubButton.clicked.connect(self.open_substituents)
self.substituent_layout.addWidget(openSubButton)
self.openSubButton = openSubButton
#add a tab for rings
self.ring_tab = QWidget()
self.ring_layout = QVBoxLayout(self.ring_tab)
self.ring_table = RingTable()
self.ring_layout.addWidget(self.ring_table)
showRingWalkCheck = QCheckBox('show ring walk')
showRingWalkCheck.setToolTip(
"arrows will show the way AaronTools traverses the ring")
showRingWalkCheck.toggle()
showRingWalkCheck.stateChanged.connect(self.showRingWalk)
self.ring_layout.addWidget(showRingWalkCheck)
self.ring_color = ColorButton('walk arrow color',
has_alpha_channel=True)
self.ring_color.setToolTip("color of walk arrows")
self.ring_color.set_color(self.settings.ring_walk_color)
self.ring_layout.addWidget(self.ring_color)
openRingButton = QPushButton("open selected rings")
openRingButton.setToolTip(
"rings selected in the table will be loaded into ChimeraX")
openRingButton.clicked.connect(self.open_rings)
self.ring_layout.addWidget(openRingButton)
self.openRingButton = openRingButton
self.library_tabs.resize(300, 200)
self.library_tabs.addTab(self.ligand_tab, "ligands")
self.library_tabs.addTab(self.substituent_tab, "substituents")
self.library_tabs.addTab(self.ring_tab, "rings")
layout.addWidget(self.library_tabs)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def showKeyAtoms(self, state):
if state == QtCore.Qt.Checked:
self.showLigKeyBool = True
else:
self.showLigKeyBool = False
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 showGhostConnection(self, state):
if state == QtCore.Qt.Checked:
self.showSubGhostBool = True
else:
self.showSubGhostBool = False
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 showRingWalk(self, state):
if state == QtCore.Qt.Checked:
self.showRingWalkBool = True
else:
self.showRingWalkBool = False
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 display_help(self):
"""Show the help for this tool in the help viewer."""
from chimerax.core.commands import run
run(self.session,
'open %s' % self.help if self.help is not None else "")
def __init__(self, session, tool_name):
self._default_color = (255, 153, 204, 128) # Transparent pink
self._max_slider_value = 1000 # QSlider only handles integer values
self._max_slider_radius = 100.0 # Float maximum radius value, scene units
self._block_text_update = False # Avoid radius slider and text continuous updating each other.
self._block_slider_update = False # Avoid radius slider and text continuous updating each other.
b = session.main_view.drawing_bounds()
vradius = 100 if b is None else b.radius()
self._max_slider_radius = vradius
center = b.center() if b else (0, 0, 0)
self._sphere_model = SphereModel('eraser sphere', session,
self._default_color, center,
0.2 * vradius)
ToolInstance.__init__(self, session, tool_name)
self.display_name = 'Map Eraser'
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
self.tool_window = tw
parent = tw.ui_area
from PyQt5.QtWidgets import QVBoxLayout, QHBoxLayout, QFrame, QCheckBox, QLabel, QPushButton, QLineEdit, QSlider
from PyQt5.QtCore import Qt
layout = QVBoxLayout(parent)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
parent.setLayout(layout)
sf = QFrame(parent)
layout.addWidget(sf)
slayout = QHBoxLayout(sf)
slayout.setContentsMargins(0, 0, 0, 0)
slayout.setSpacing(10)
self._show_eraser = se = QCheckBox('Show map eraser sphere', sf)
se.setCheckState(Qt.Checked)
se.stateChanged.connect(self._show_eraser_cb)
slayout.addWidget(se)
from chimerax.ui.widgets import ColorButton
self._sphere_color = sc = ColorButton(sf,
max_size=(16, 16),
has_alpha_channel=True)
sc.color = self._default_color
sc.color_changed.connect(self._change_color_cb)
slayout.addWidget(sc)
slayout.addStretch(1) # Extra space at end
rf = QFrame(parent)
layout.addWidget(rf)
rlayout = QHBoxLayout(rf)
rlayout.setContentsMargins(0, 0, 0, 0)
rlayout.setSpacing(4)
rl = QLabel('Radius', rf)
rlayout.addWidget(rl)
self._radius_entry = rv = QLineEdit('', rf)
rv.setMaximumWidth(40)
rv.returnPressed.connect(self._radius_changed_cb)
rlayout.addWidget(rv)
self._radius_slider = rs = QSlider(Qt.Horizontal, rf)
smax = self._max_slider_value
rs.setRange(0, smax)
rs.valueChanged.connect(self._radius_slider_moved_cb)
rlayout.addWidget(rs)
rv.setText('%.4g' % self._sphere_model.radius)
self._radius_changed_cb()
ef = QFrame(parent)
layout.addWidget(ef)
elayout = QHBoxLayout(ef)
elayout.setContentsMargins(0, 0, 0, 0)
elayout.setSpacing(30)
eb = QPushButton('Erase inside sphere', ef)
eb.clicked.connect(self._erase_in_sphere)
elayout.addWidget(eb)
eo = QPushButton('Erase outside sphere', ef)
eo.clicked.connect(self._erase_outside_sphere)
elayout.addWidget(eo)
rb = QPushButton('Reduce map bounds', ef)
rb.clicked.connect(self._crop_map)
elayout.addWidget(rb)
elayout.addStretch(1) # Extra space at end
layout.addStretch(1) # Extra space at end
tw.manage(placement="side")
# When displayed models change update radius slider range.
from chimerax.core.models import MODEL_DISPLAY_CHANGED
h = session.triggers.add_handler(MODEL_DISPLAY_CHANGED,
self._model_display_change)
self._model_display_change_handler = h
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self.display_name = 'Marker Placement'
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self, close_destroys=False)
self.tool_window = tw
parent = tw.ui_area
from PyQt5.QtWidgets import QFrame, QVBoxLayout, QHBoxLayout, QLabel, QPushButton, QLineEdit, QSizePolicy, QCheckBox
playout = QVBoxLayout(parent)
playout.setContentsMargins(0,0,0,0)
playout.setSpacing(0)
parent.setLayout(playout)
f = QFrame(parent)
f.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
playout.addWidget(f)
layout = QVBoxLayout(f)
layout.setContentsMargins(0,0,0,0)
layout.setSpacing(0)
f.setLayout(layout)
# Marker and link color and radius
mf = QFrame(f)
mf.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
layout.addWidget(mf)
mm_layout = QHBoxLayout(mf)
mm_layout.setContentsMargins(0,0,0,0)
mm_layout.setSpacing(5)
mf.setLayout(mm_layout)
ml = QLabel('Marker color', mf)
mm_layout.addWidget(ml)
from chimerax.ui.widgets import ColorButton
self._marker_color = mc = ColorButton(mf, max_size = (16,16))
mc.color_changed.connect(self._marker_color_changed)
mm_layout.addWidget(mc)
rl = QLabel(' radius', mf)
mm_layout.addWidget(rl)
self._marker_radius = mr = QLineEdit('', mf)
mr.setMaximumWidth(40)
mr.returnPressed.connect(self._marker_radius_changed)
mm_layout.addWidget(mr)
mm_layout.addSpacing(20)
ml = QLabel('Link color', mf)
mm_layout.addWidget(ml)
from chimerax.ui.widgets import ColorButton
self._link_color = lc = ColorButton(mf, max_size = (16,16))
lc.color_changed.connect(self._link_color_changed)
mm_layout.addWidget(lc)
rl = QLabel(' radius', mf)
mm_layout.addWidget(rl)
self._link_radius = lr = QLineEdit('', mf)
lr.setMaximumWidth(40)
lr.returnPressed.connect(self._link_radius_changed)
mm_layout.addWidget(lr)
mm_layout.addStretch(1) # Extra space at end
# Link consecutive markers checkbutton
self.link_new_button = lm = QCheckBox('Link new marker to selected marker', f)
lm.stateChanged.connect(self.link_new_cb)
layout.addWidget(lm)
layout.addSpacing(5)
hl = QLabel('Place markers using mouse modes in the Markers toolbar')
layout.addWidget(hl)
self.update_settings()
tw.manage(placement="side")
def __init__(self, session, tool_name):
self._default_color = (0, 0, 204, 255)
self._default_box_color = (0, 255, 0, 255)
ToolInstance.__init__(self, session, tool_name)
self.display_name = 'Measure and Color Blobs'
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
self.tool_window = tw
parent = tw.ui_area
from PyQt5.QtWidgets import QVBoxLayout, QHBoxLayout, QFrame, QCheckBox, QLabel, QPushButton, QSizePolicy
from PyQt5.QtCore import Qt
layout = QVBoxLayout(parent)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
parent.setLayout(layout)
cf = QFrame(parent)
# cf.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
layout.addWidget(cf)
clayout = QHBoxLayout(cf)
clayout.setContentsMargins(0, 0, 0, 0)
clayout.setSpacing(10)
self._color_blob = cb = QCheckBox('Color blob', cf)
cb.setCheckState(Qt.Checked)
clayout.addWidget(cb)
from chimerax.ui.widgets import ColorButton
self._blob_color = cbut = ColorButton(cf, max_size=(16, 16))
cbut.color = self._default_color
clayout.addWidget(cbut)
clayout.addSpacing(10)
self._change_color = cc = QCheckBox('Change color automatically', cf)
cc.setCheckState(Qt.Checked)
clayout.addWidget(cc)
clayout.addStretch(1) # Extra space at end
af = QFrame(parent)
# af.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
layout.addWidget(af)
aflayout = QHBoxLayout(af)
aflayout.setContentsMargins(0, 0, 0, 0)
aflayout.setSpacing(10)
self._show_box = bb = QCheckBox('Show principal axes box', af)
bb.setCheckState(Qt.Checked)
aflayout.addWidget(bb)
self._box_color = bc = ColorButton(af, max_size=(16, 16))
bc.color = self._default_box_color
aflayout.addWidget(bc)
aflayout.addSpacing(10)
eb = QPushButton('Erase boxes', af)
eb.clicked.connect(self._erase_boxes)
aflayout.addWidget(eb)
aflayout.addStretch(1) # Extra space at end
self._message_label = ml = QLabel(parent)
layout.addWidget(ml)
layout.addStretch(1) # Extra space at end
tw.manage(placement="side")