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
class PrecisionRotate(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Rotate-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _PrecisionRotateSettings(session, name)
self.bonds = {}
self.bond_centers = {}
self.groups = {}
self.perpendiculars = {}
self.perp_centers = {}
self.manual_center = {}
self._build_ui()
self._show_rot_vec = self.session.triggers.add_handler(
SELECTION_CHANGED, self.show_rot_vec)
global_triggers = get_triggers()
self._changes = global_triggers.add_handler("changes done",
self.show_rot_vec)
self.show_rot_vec()
def _build_ui(self):
layout = QGridLayout()
layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.cor_button = QComboBox()
self.cor_button.addItems(
["automatic", "select atoms", "view's center of rotation"])
layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop)
self.set_cor_selection = QPushButton("set selection")
self.cor_button.currentTextChanged.connect(
lambda t, widget=self.set_cor_selection: widget.setEnabled(
t == "select atoms"))
self.set_cor_selection.clicked.connect(self.manual_cor)
layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop)
self.set_cor_selection.setEnabled(False)
layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.vector_option = QComboBox()
self.vector_option.addItems([
"axis", "view axis", "bond", "perpendicular to plane",
"centroid of atoms", "custom"
])
layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter)
vector = QWidget()
vector.setToolTip("vector will be normalized before rotating")
vector_layout = QHBoxLayout(vector)
vector_layout.setContentsMargins(0, 0, 0, 0)
self.vector_x = QDoubleSpinBox()
self.vector_y = QDoubleSpinBox()
self.vector_z = QDoubleSpinBox()
self.vector_z.setValue(1.0)
for c, t in zip([self.vector_x, self.vector_y, self.vector_z],
[" x", " y", " z"]):
c.setSingleStep(0.01)
c.setRange(-100, 100)
# c.setSuffix(t)
c.valueChanged.connect(self.show_rot_vec)
vector_layout.addWidget(c)
layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop)
vector.setVisible(self.vector_option.currentText() == "custom")
self.vector_option.currentTextChanged.connect(
lambda text, widget=vector: widget.setVisible(text == "custom"))
self.view_axis = QComboBox()
self.view_axis.addItems(["z", "y", "x"])
layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop)
self.view_axis.setVisible(
self.vector_option.currentText() == "view axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.view_axis: widget.setVisible(text ==
"view axis"))
self.axis = QComboBox()
self.axis.addItems(["z", "y", "x"])
layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop)
self.axis.setVisible(self.vector_option.currentText() == "axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.axis: widget.setVisible(text == "axis"))
self.bond_button = QPushButton("set selected bond")
self.bond_button.clicked.connect(self.set_bonds)
layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop)
self.bond_button.setVisible(self.vector_option.currentText() == "bond")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.bond_button: widget.setVisible(text ==
"bond"))
self.perp_button = QPushButton("set selected atoms")
self.perp_button.clicked.connect(self.set_perpendicular)
layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop)
self.perp_button.setVisible(
self.vector_option.currentText() == "perpendicular to plane")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.perp_button: widget.setVisible(
text == "perpendicular to plane"))
self.group_button = QPushButton("set selected atoms")
self.group_button.clicked.connect(self.set_group)
layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop)
self.group_button.setVisible(
self.vector_option.currentText() == "centroid of atoms")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.group_button: widget.setVisible(
text == "centroid of atoms"))
layout.addWidget(QLabel("angle:"), 2, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.angle = QDoubleSpinBox()
self.angle.setRange(-360, 360)
self.angle.setSingleStep(5)
self.angle.setSuffix("°")
layout.addWidget(self.angle, 2, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.display_rot_vec = QCheckBox()
self.display_rot_vec.setCheckState(Qt.Checked)
self.display_rot_vec.stateChanged.connect(self.show_rot_vec)
layout.addWidget(self.display_rot_vec, 3, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
rotate_button = QPushButton("rotate selected atoms")
rotate_button.clicked.connect(self.do_rotate)
layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop)
self.rotate_button = rotate_button
self.status_bar = QStatusBar()
self.status_bar.setSizeGripEnabled(False)
layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop)
self.vector_option.currentTextChanged.connect(self.show_auto_status)
self.cor_button.currentIndexChanged.connect(
lambda *args: self.show_auto_status("select atoms"))
self.cor_button.currentIndexChanged.connect(self.show_rot_vec)
self.set_cor_selection.clicked.connect(self.show_rot_vec)
self.vector_option.currentIndexChanged.connect(self.show_rot_vec)
self.axis.currentIndexChanged.connect(self.show_rot_vec)
self.view_axis.currentIndexChanged.connect(self.show_rot_vec)
self.bond_button.clicked.connect(self.show_rot_vec)
self.perp_button.clicked.connect(self.show_rot_vec)
self.group_button.clicked.connect(self.show_rot_vec)
layout.setRowStretch(0, 0)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 0)
layout.setRowStretch(3, 0)
layout.setRowStretch(4, 0)
layout.setRowStretch(5, 1)
layout.setColumnStretch(0, 0)
layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 1)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def manual_cor(self, *args):
selection = selected_atoms(self.session)
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
self.manual_center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
self.manual_center[model] = np.mean(coords, axis=0)
def show_auto_status(self, text):
if self.cor_button.currentText() == "automatic":
if text == "bond":
self.status_bar.showMessage(
"center set to one of the bonded atoms")
elif text == "perpendicular to plane":
self.status_bar.showMessage("center set to centroid of atoms")
else:
self.status_bar.showMessage(
"center set to centroid of rotating atoms")
elif self.cor_button.currentText() == "select atoms":
self.status_bar.showMessage(
"center set to centroid of specified atoms")
else:
self.status_bar.showMessage(
"center set to view's center of rotation")
def set_bonds(self, *args):
bonds = selected_bonds(self.session)
if len(bonds) == 0:
self.session.logger.error("no bonds selected")
return
models = [bond.structure for bond in bonds]
if any(models.count(m) > 1 for m in models):
self.session.logger.error(
"multiple bonds selected on the same structure")
return
self.bonds = {
model: (bond.atoms[0].coord - bond.atoms[1].coord)
for model, bond in zip(models, bonds)
}
self.bond_centers = {
model: bond.atoms[1].coord
for model, bond in zip(models, bonds)
}
def set_perpendicular(self, *args):
atoms = selected_atoms(self.session)
if len(atoms) == 0:
self.session.logger.error("no atoms selected")
return
self.perpendiculars = {}
self.perp_centers = {}
models = set(atom.structure for atom in atoms)
for model in models:
atom_coords = []
for atom in atoms:
if atom.structure is model:
atom_coords.append(atom.coord)
if len(atom_coords) < 3:
self.session.logger.error("fewer than 3 atoms selected on %s" %
model.atomspec)
continue
xyz = np.array(atom_coords)
xyz -= np.mean(atom_coords, axis=0)
R = np.dot(xyz.T, xyz)
u, s, vh = np.linalg.svd(R, compute_uv=True)
vector = u[:, -1]
self.perpendiculars[model] = vector
self.perp_centers[model] = np.mean(atom_coords, axis=0)
def set_group(self, *args):
atoms = selected_atoms(self.session)
if len(atoms) == 0:
self.session.logger.error("no atoms selected")
return
self.groups = {}
models = set(atom.structure for atom in atoms)
for model in models:
atom_coords = []
for atom in atoms:
if atom.structure is model:
atom_coords.append(atom.coord)
self.groups[model] = np.mean(atom_coords, axis=0)
def do_rotate(self, *args):
selection = selected_atoms(self.session)
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
if len(models.keys()) == 0:
return
if self.vector_option.currentText() == "axis":
if self.axis.currentText() == "z":
vector = np.array([0., 0., 1.])
elif self.axis.currentText() == "y":
vector = np.array([0., 1., 0.])
elif self.axis.currentText() == "x":
vector = np.array([1., 0., 0.])
elif self.vector_option.currentText() == "view axis":
if self.view_axis.currentText() == "z":
vector = self.session.view.camera.get_position().axes()[2]
elif self.view_axis.currentText() == "y":
vector = self.session.view.camera.get_position().axes()[1]
elif self.view_axis.currentText() == "x":
vector = self.session.view.camera.get_position().axes()[0]
elif self.vector_option.currentText() == "bond":
vector = self.bonds
elif self.vector_option.currentText() == "perpendicular to plane":
vector = self.perpendiculars
elif self.vector_option.currentText() == "centroid of atoms":
vector = self.groups
elif self.vector_option.currentText() == "custom":
x = self.vector_x.value()
y = self.vector_y.value()
z = self.vector_z.value()
vector = np.array([x, y, z])
angle = np.deg2rad(self.angle.value())
center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
center[model] = np.mean(coords, axis=0)
if self.cor_button.currentText() == "automatic":
if self.vector_option.currentText() == "perpendicular to plane":
center = self.perp_centers
elif self.vector_option.currentText() == "bond":
center = self.bond_centers
elif self.cor_button.currentText() == "select atoms":
center = self.manual_center
else:
center = self.session.main_view.center_of_rotation
for model in models:
if isinstance(vector, dict):
if model not in vector.keys():
continue
else:
v = vector[model]
else:
v = vector
if isinstance(center, dict):
if model not in center.keys():
continue
else:
c = center[model]
else:
c = center
if self.vector_option.currentText(
) == "centroid of atoms" and self.cor_button.currentText(
) != "automatic":
v = v - c
v = v / np.linalg.norm(v)
q = np.hstack(([np.cos(angle / 2)], v * np.sin(angle / 2)))
q /= np.linalg.norm(q)
qs = q[0]
qv = q[1:]
xyz = np.array([a.coord for a in models[model]])
xyz -= c
xprod = np.cross(qv, xyz)
qs_xprod = 2 * qs * xprod
qv_xprod = 2 * np.cross(qv, xprod)
xyz += qs_xprod + qv_xprod + c
for t, coord in zip(models[model], xyz):
t.coord = coord
def show_rot_vec(self, *args):
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
if self.display_rot_vec.checkState() == Qt.Unchecked:
return
selection = selected_atoms(self.session)
if len(selection) == 0:
return
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
if len(models.keys()) == 0:
return
if self.vector_option.currentText() == "axis":
if self.axis.currentText() == "z":
vector = np.array([0., 0., 1.])
elif self.axis.currentText() == "y":
vector = np.array([0., 1., 0.])
elif self.axis.currentText() == "x":
vector = np.array([1., 0., 0.])
elif self.vector_option.currentText() == "view axis":
if self.view_axis.currentText() == "z":
vector = self.session.view.camera.get_position().axes()[2]
elif self.view_axis.currentText() == "y":
vector = self.session.view.camera.get_position().axes()[1]
elif self.view_axis.currentText() == "x":
vector = self.session.view.camera.get_position().axes()[0]
elif self.vector_option.currentText() == "bond":
vector = self.bonds
elif self.vector_option.currentText() == "perpendicular to plane":
vector = self.perpendiculars
elif self.vector_option.currentText() == "centroid of atoms":
vector = self.groups
elif self.vector_option.currentText() == "custom":
x = self.vector_x.value()
y = self.vector_y.value()
z = self.vector_z.value()
vector = np.array([x, y, z])
center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
center[model] = np.mean(coords, axis=0)
if self.cor_button.currentText() == "automatic":
if self.vector_option.currentText() == "perpendicular to plane":
center = self.perp_centers
elif self.vector_option.currentText() == "bond":
center = self.bond_centers
elif self.cor_button.currentText() == "select atoms":
center = self.manual_center
else:
center = self.session.main_view.center_of_rotation
for model in models:
if isinstance(vector, dict):
if model not in vector.keys():
continue
else:
v = vector[model]
else:
v = vector
if isinstance(center, dict):
if model not in center.keys():
continue
else:
c = center[model]
else:
c = center
if self.vector_option.currentText(
) == "centroid of atoms" and self.cor_button.currentText(
) != "automatic":
v = v - c
if np.linalg.norm(v) == 0:
continue
residues = []
for atom in models[model]:
if atom.residue not in residues:
residues.append(atom.residue)
v_c = c + v
s = ".color red\n"
s += ".arrow %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f 0.2 0.4 0.7\n" % (
*c, *v_c)
stream = BytesIO(bytes(s, 'utf-8'))
bild_obj, status = read_bild(self.session, stream,
"rotation vector")
self.session.models.add(bild_obj, parent=model)
def delete(self):
self.session.triggers.remove_handler(self._show_rot_vec)
global_triggers = get_triggers()
global_triggers.remove_handler(self._changes)
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
return super().delete()
def close(self):
self.session.triggers.remove_handler(self._show_rot_vec)
global_triggers = get_triggers()
global_triggers.remove_handler(self._changes)
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
return super().close()
class LigandSterimol(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Ligand-Sterimol-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.settings = _SterimolSettings(self.session, name)
self._build_ui()
def _build_ui(self):
layout = QFormLayout()
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
layout.addRow("radii:", self.radii_option)
self.L_option = QComboBox()
self.L_option.addItems([
"to centroid of coordinating atoms",
"bisect angle between coordinating atoms"
])
ndx = self.L_option.findText(self.settings.L_option, Qt.MatchExactly)
self.L_option.setCurrentIndex(ndx)
layout.addRow("L axis:", self.L_option)
self.sterimol2vec = QGroupBox("Sterimol2Vec")
sterimol2vec_layout = QFormLayout(self.sterimol2vec)
self.at_L = QDoubleSpinBox()
self.at_L.setRange(-10, 30)
self.at_L.setDecimals(2)
self.at_L.setSingleStep(0.25)
self.at_L.setValue(self.settings.at_L)
sterimol2vec_layout.addRow("L value:", self.at_L)
layout.addRow(self.sterimol2vec)
self.sterimol2vec.setCheckable(True)
self.sterimol2vec.toggled.connect(lambda x: self.at_L.setEnabled(x))
self.sterimol2vec.setChecked(self.settings.sterimol2vec)
self.display_vectors = QCheckBox()
self.display_vectors.setChecked(self.settings.display_vectors)
layout.addRow("show vectors:", self.display_vectors)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
calc_sterimol_button = QPushButton(
"calculate parameters for selected ligands")
calc_sterimol_button.clicked.connect(self.calc_sterimol)
layout.addRow(calc_sterimol_button)
self.calc_sterimol_button = calc_sterimol_button
remove_sterimol_button = QPushButton("remove Sterimol visualizations")
remove_sterimol_button.clicked.connect(self.del_sterimol)
layout.addRow(remove_sterimol_button)
self.remove_sterimol_button = remove_sterimol_button
self.table = QTableWidget()
self.table.setColumnCount(8)
self.table.setHorizontalHeaderLabels([
'model',
'coord. atoms',
'B\u2081',
'B\u2082',
'B\u2083',
'B\u2084',
'B\u2085',
'L',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.resizeColumnToContents(3)
self.table.resizeColumnToContents(4)
self.table.resizeColumnToContents(5)
self.table.resizeColumnToContents(6)
self.table.resizeColumnToContents(7)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
4, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
5, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
6, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
7, QHeaderView.Stretch)
layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def clear_table(self):
are_you_sure = QMessageBox.question(
None,
"Clear table?",
"Are you sure you want to clear the data table?",
)
if are_you_sure != QMessageBox.Yes:
return
self.table.setRowCount(0)
def calc_sterimol(self, *args):
self.settings.radii = self.radii_option.currentText()
self.settings.display_radii = self.display_radii.checkState(
) == Qt.Checked
self.settings.display_vectors = self.display_vectors.checkState(
) == Qt.Checked
self.settings.at_L = self.at_L.value()
self.settings.sterimol2vec = self.sterimol2vec.isChecked()
self.settings.L_option = self.L_option.currentText()
targets, neighbors, datas = sterimol_cmd(
self.session,
selected_atoms(self.session),
radii=self.radii_option.currentText(),
showVectors=self.display_vectors.checkState() == Qt.Checked,
showRadii=self.display_radii.checkState() == Qt.Checked,
return_values=True,
at_L=self.at_L.value() if self.sterimol2vec.isChecked() else None,
bisect_L=self.L_option.currentText() ==
"bisect angle between coordinating atoms",
)
if len(targets) == 0:
return
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
# self.table.setRowCount(0)
for t, b, data in zip(targets, neighbors, datas):
row = self.table.rowCount()
self.table.insertRow(row)
targ = QTableWidgetItem()
targ.setData(Qt.DisplayRole, t)
self.table.setItem(row, 0, targ)
neigh = QTableWidgetItem()
neigh.setData(Qt.DisplayRole, delim.join(b))
self.table.setItem(row, 1, neigh)
l = np.linalg.norm(data["L"][1] - data["L"][0])
b1 = np.linalg.norm(data["B1"][1] - data["B1"][0])
b2 = np.linalg.norm(data["B2"][1] - data["B2"][0])
b3 = np.linalg.norm(data["B3"][1] - data["B3"][0])
b4 = np.linalg.norm(data["B4"][1] - data["B4"][0])
b5 = np.linalg.norm(data["B5"][1] - data["B5"][0])
li = QTableWidgetItem()
li.setData(Qt.DisplayRole, "%.2f" % l)
self.table.setItem(row, 7, li)
b1i = QTableWidgetItem()
b1i.setData(Qt.DisplayRole, "%.2f" % b1)
self.table.setItem(row, 2, b1i)
b2i = QTableWidgetItem()
b2i.setData(Qt.DisplayRole, "%.2f" % b2)
self.table.setItem(row, 3, b2i)
b3i = QTableWidgetItem()
b3i.setData(Qt.DisplayRole, "%.2f" % b3)
self.table.setItem(row, 4, b3i)
b4i = QTableWidgetItem()
b4i.setData(Qt.DisplayRole, "%.2f" % b4)
self.table.setItem(row, 5, b4i)
b5i = QTableWidgetItem()
b5i.setData(Qt.DisplayRole, "%.2f" % b5)
self.table.setItem(row, 6, b5i)
for i in range(0, 7):
if i == 1:
continue
self.table.resizeColumnToContents(i)
def header_check(self, state):
"""user has [un]checked the 'include header' option on the menu"""
if state:
self.settings.include_header = True
else:
self.settings.include_header = False
def get_csv(self):
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
if self.settings.include_header:
s = delim.join([
"substituent_atom", "bonded_atom", "B1", "B2", "B3", "B4",
"B5", "L"
])
s += "\n"
else:
s = ""
for i in range(0, self.table.rowCount()):
s += delim.join([
item.data(Qt.DisplayRole)
for item in [self.table.item(i, j) for j in range(0, 8)]
])
s += "\n"
return s
def copy_csv(self):
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def save_csv(self):
"""save data on current tab to CSV file"""
filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)")
if filename:
s = self.get_csv()
with open(filename, 'w') as f:
f.write(s.strip())
self.session.logger.status("saved to %s" % filename)
def del_sterimol(self):
for model in self.session.models.list(type=Generic3DModel):
if model.name.startswith("Sterimol"):
model.delete()
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 "")
class PercentVolumeBuried(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Buried-Volume-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _VburSettings(self.session, name)
self.ligand_atoms = []
self._build_ui()
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
calc_widget = QWidget()
calc_layout = QFormLayout(calc_widget)
settings_widget = QWidget()
settings_layout = QFormLayout(settings_widget)
steric_map_widget = QWidget()
steric_layout = QFormLayout(steric_map_widget)
cutout_widget = QWidget()
vol_cutout_layout = QFormLayout(cutout_widget)
layout.addWidget(tabs)
tabs.addTab(calc_widget, "calculation")
tabs.addTab(settings_widget, "settings")
tabs.addTab(steric_map_widget, "steric map")
tabs.addTab(cutout_widget, "volume cutout")
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
settings_layout.addRow("radii:", self.radii_option)
self.scale = QDoubleSpinBox()
self.scale.setValue(self.settings.vdw_scale)
self.scale.setSingleStep(0.01)
self.scale.setRange(1., 1.5)
settings_layout.addRow("VDW scale:", self.scale)
set_ligand_atoms = QPushButton("set ligands to current selection")
set_ligand_atoms.clicked.connect(self.set_ligand_atoms)
set_ligand_atoms.setToolTip(
"specify atoms to use in calculation\n" +
"by default, all atoms will be used unless a single center is specified\n"
+
"in the case of a single center, all atoms except the center is used"
)
calc_layout.addRow(set_ligand_atoms)
self.set_ligand_atoms = set_ligand_atoms
self.radius = QDoubleSpinBox()
self.radius.setValue(self.settings.center_radius)
self.radius.setSuffix(" \u212B")
self.radius.setDecimals(1)
self.radius.setSingleStep(0.1)
self.radius.setRange(1., 15.)
settings_layout.addRow("radius around center:", self.radius)
self.method = QComboBox()
self.method.addItems(["Lebedev", "Monte-Carlo"])
self.method.setToolTip("Lebedev: deterministic method\n" +
"Monte-Carlo: non-deterministic method")
ndx = self.method.findText(self.settings.method, Qt.MatchExactly)
self.method.setCurrentIndex(ndx)
settings_layout.addRow("integration method:", self.method)
leb_widget = QWidget()
leb_layout = QFormLayout(leb_widget)
leb_layout.setContentsMargins(0, 0, 0, 0)
self.radial_points = QComboBox()
self.radial_points.addItems(["20", "32", "64", "75", "99", "127"])
self.radial_points.setToolTip(
"more radial points will give more accurate results, but integration will take longer"
)
ndx = self.radial_points.findText(self.settings.radial_points,
Qt.MatchExactly)
self.radial_points.setCurrentIndex(ndx)
leb_layout.addRow("radial points:", self.radial_points)
self.angular_points = QComboBox()
self.angular_points.addItems([
"110", "194", "302", "590", "974", "1454", "2030", "2702", "5810"
])
self.angular_points.setToolTip(
"more angular points will give more accurate results, but integration will take longer"
)
ndx = self.angular_points.findText(self.settings.angular_points,
Qt.MatchExactly)
self.angular_points.setCurrentIndex(ndx)
leb_layout.addRow("angular points:", self.angular_points)
settings_layout.addRow(leb_widget)
mc_widget = QWidget()
mc_layout = QFormLayout(mc_widget)
mc_layout.setContentsMargins(0, 0, 0, 0)
self.min_iter = QSpinBox()
self.min_iter.setValue(self.settings.minimum_iterations)
self.min_iter.setRange(0, 10000)
self.min_iter.setToolTip(
"each iteration is 3000 points\n" +
"iterations continue until convergence criteria are met")
mc_layout.addRow("minimum interations:", self.min_iter)
settings_layout.addRow(mc_widget)
if self.settings.method == "Lebedev":
mc_widget.setVisible(False)
elif self.settings.method == "Monte-Carlo":
leb_widget.setVisible(False)
self.report_component = QComboBox()
self.report_component.addItems(["total", "quadrants", "octants"])
ndx = self.report_component.findText(self.settings.report_component,
Qt.MatchExactly)
self.report_component.setCurrentIndex(ndx)
settings_layout.addRow("report volume:", self.report_component)
self.use_scene = QCheckBox()
self.use_scene.setChecked(self.settings.use_scene)
self.use_scene.setToolTip(
"quadrants/octants will use the orientation the molecule is displayed in"
)
settings_layout.addRow("use display orientation:", self.use_scene)
self.method.currentTextChanged.connect(
lambda text, widget=leb_widget: widget.setVisible(text == "Lebedev"
))
self.method.currentTextChanged.connect(
lambda text, widget=mc_widget: widget.setVisible(text ==
"Monte-Carlo"))
self.use_centroid = QCheckBox()
self.use_centroid.setChecked(self.settings.use_centroid)
self.use_centroid.setToolTip(
"place the center between selected atoms\n" +
"might be useful for polydentate ligands")
calc_layout.addRow("use centroid of centers:", self.use_centroid)
self.steric_map = QCheckBox()
self.steric_map.setChecked(self.settings.steric_map)
self.steric_map.setToolTip(
"produce a 2D projection of steric bulk\ncauses buried volume to be reported for individual quadrants"
)
steric_layout.addRow("create steric map:", self.steric_map)
self.num_pts = QSpinBox()
self.num_pts.setRange(25, 250)
self.num_pts.setValue(self.settings.num_pts)
self.num_pts.setToolTip("number of points along x and y axes")
steric_layout.addRow("number of points:", self.num_pts)
self.include_vbur = QCheckBox()
self.include_vbur.setChecked(self.settings.include_vbur)
steric_layout.addRow("label quadrants with %V<sub>bur</sub>",
self.include_vbur)
self.map_shape = QComboBox()
self.map_shape.addItems(["circle", "square"])
ndx = self.map_shape.findText(self.settings.map_shape, Qt.MatchExactly)
self.map_shape.setCurrentIndex(ndx)
steric_layout.addRow("map shape:", self.map_shape)
self.auto_minmax = QCheckBox()
self.auto_minmax.setChecked(self.settings.auto_minmax)
steric_layout.addRow("automatic min. and max.:", self.auto_minmax)
self.map_min = QDoubleSpinBox()
self.map_min.setRange(-15., 0.)
self.map_min.setSuffix(" \u212B")
self.map_min.setSingleStep(0.1)
self.map_min.setValue(self.settings.map_min)
steric_layout.addRow("minimum value:", self.map_min)
self.map_max = QDoubleSpinBox()
self.map_max.setRange(0., 15.)
self.map_max.setSuffix(" \u212B")
self.map_max.setSingleStep(0.1)
self.map_max.setValue(self.settings.map_max)
steric_layout.addRow("maximum value:", self.map_max)
self.num_pts.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.num_pts: widget.setEnabled(state == Qt.
Checked))
self.include_vbur.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.include_vbur: widget.setEnabled(
state == Qt.Checked))
self.map_shape.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_shape: widget.setEnabled(state == Qt.
Checked))
self.auto_minmax.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.auto_minmax: widget.setEnabled(
state == Qt.Checked))
self.map_min.setEnabled(not self.settings.auto_minmax
and self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_min, widget2=self.auto_minmax: widget
.setEnabled(state == Qt.Checked and not widget2.isChecked()))
self.auto_minmax.stateChanged.connect(
lambda state, widget=self.map_min, widget2=self.steric_map: widget.
setEnabled(not state == Qt.Checked and widget2.isChecked()))
self.map_max.setEnabled(not self.settings.auto_minmax
and self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_max, widget2=self.auto_minmax: widget
.setEnabled(state == Qt.Checked and not widget2.isChecked()))
self.auto_minmax.stateChanged.connect(
lambda state, widget=self.map_max, widget2=self.steric_map: widget.
setEnabled(not state == Qt.Checked and widget2.isChecked()))
self.display_cutout = QComboBox()
self.display_cutout.addItems(["no", "free", "buried"])
ndx = self.display_cutout.findText(self.settings.display_cutout,
Qt.MatchExactly)
self.display_cutout.setCurrentIndex(ndx)
self.display_cutout.setToolTip("show free or buried volume")
vol_cutout_layout.addRow("display volume:", self.display_cutout)
self.point_spacing = QDoubleSpinBox()
self.point_spacing.setDecimals(3)
self.point_spacing.setRange(0.01, 0.5)
self.point_spacing.setSingleStep(0.005)
self.point_spacing.setSuffix(" \u212B")
self.point_spacing.setValue(self.settings.point_spacing)
self.point_spacing.setToolTip(
"distance between points on cutout\n" +
"smaller spacing will narrow gaps, but increase time to create the cutout"
)
vol_cutout_layout.addRow("point spacing:", self.point_spacing)
self.intersection_scale = QDoubleSpinBox()
self.intersection_scale.setDecimals(2)
self.intersection_scale.setRange(1., 10.)
self.intersection_scale.setSingleStep(0.5)
self.intersection_scale.setSuffix("x")
self.intersection_scale.setToolTip(
"relative density of points where VDW radii intersect\n" +
"higher density will narrow gaps, but increase time to create cutout"
)
self.intersection_scale.setValue(self.settings.intersection_scale)
vol_cutout_layout.addRow("intersection density:",
self.intersection_scale)
self.cutout_labels = QComboBox()
self.cutout_labels.addItems(["none", "quadrants", "octants"])
ndx = self.cutout_labels.findText(self.settings.cutout_labels,
Qt.MatchExactly)
self.cutout_labels.setCurrentIndex(ndx)
vol_cutout_layout.addRow("label sections:", self.cutout_labels)
self.point_spacing.setEnabled(self.settings.display_cutout != "no")
self.intersection_scale.setEnabled(
self.settings.display_cutout != "no")
self.cutout_labels.setEnabled(self.settings.display_cutout != "no")
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.point_spacing: widget.setEnabled(text !=
"no"))
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.intersection_scale: widget.setEnabled(
text != "no"))
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.cutout_labels: widget.setEnabled(text !=
"no"))
calc_vbur_button = QPushButton(
"calculate % buried volume for selected centers")
calc_vbur_button.clicked.connect(self.calc_vbur)
calc_layout.addRow(calc_vbur_button)
self.calc_vbur_button = calc_vbur_button
remove_vbur_button = QPushButton(
"remove % buried volume visualizations")
remove_vbur_button.clicked.connect(self.del_vbur)
vol_cutout_layout.addRow(remove_vbur_button)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(['model', 'center', '%Vbur'])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Interactive)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Interactive)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
calc_layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
self.copy = copy
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def clear_table(self):
are_you_sure = QMessageBox.question(
None,
"Clear table?",
"Are you sure you want to clear the data table?",
)
if are_you_sure != QMessageBox.Yes:
return
self.table.setRowCount(0)
def set_ligand_atoms(self):
self.ligand_atoms = selected_atoms(self.session)
self.session.logger.status("set ligand to current selection")
def calc_vbur(self):
args = dict()
cur_sel = selected_atoms(self.session)
if len(cur_sel) == 0:
return
models = []
for atom in cur_sel:
if atom.structure not in models:
models.append(atom.structure)
center = []
for atom in cur_sel:
center.append(atom)
args["center"] = center
radii = self.radii_option.currentText()
self.settings.radii = radii
args["radii"] = radii
scale = self.scale.value()
self.settings.vdw_scale = scale
args["scale"] = scale
radius = self.radius.value()
self.settings.center_radius = radius
args["radius"] = radius
steric_map = self.steric_map.checkState() == Qt.Checked
self.settings.steric_map = steric_map
args["steric_map"] = steric_map
use_scene = self.use_scene.checkState() == Qt.Checked
self.settings.use_scene = use_scene
args["useScene"] = use_scene
num_pts = self.num_pts.value()
self.settings.num_pts = num_pts
args["num_pts"] = num_pts
include_vbur = self.include_vbur.checkState() == Qt.Checked
self.settings.include_vbur = include_vbur
use_centroid = self.use_centroid.checkState() == Qt.Checked
self.settings.use_centroid = use_centroid
args["useCentroid"] = use_centroid
shape = self.map_shape.currentText()
self.settings.map_shape = shape
args["shape"] = shape
report_component = self.report_component.currentText()
self.settings.report_component = report_component
args["reportComponent"] = report_component
method = self.method.currentText()
self.settings.method = method
if method == "Lebedev":
args["method"] = "lebedev"
rad_pts = self.radial_points.currentText()
self.settings.radial_points = rad_pts
args["radialPoints"] = rad_pts
ang_pts = self.angular_points.currentText()
self.settings.angular_points = ang_pts
args["angularPoints"] = ang_pts
elif method == "Monte-Carlo":
args["method"] = "mc"
min_iter = self.min_iter.value()
self.settings.minimum_iterations = min_iter
args["minimumIterations"] = min_iter
display_cutout = self.display_cutout.currentText()
self.settings.display_cutout = display_cutout
if display_cutout != "no":
args["displaySphere"] = display_cutout
if display_cutout != "no":
point_spacing = self.point_spacing.value()
self.settings.point_spacing = point_spacing
args["pointSpacing"] = point_spacing
intersection_scale = self.intersection_scale.value()
self.settings.intersection_scale = intersection_scale
args["intersectionScale"] = intersection_scale
cutout_labels = self.cutout_labels.currentText()
self.settings.cutout_labels = cutout_labels
args["labels"] = cutout_labels
if len(self.ligand_atoms) > 0:
args["onlyAtoms"] = [a for a in self.ligand_atoms if not a.deleted]
if len(args["onlyAtoms"]) == 0:
args["onlyAtoms"] = None
auto_minmax = self.auto_minmax.checkState() == Qt.Checked
self.settings.auto_minmax = auto_minmax
if not auto_minmax:
map_max = self.map_max.value()
self.settings.map_max = map_max
map_min = self.settings.map_min
self.settings.map_min = map_min
info = percent_vbur_cmd(self.session,
models,
return_values=True,
**args)
# self.table.setRowCount(0)
if steric_map:
for mdl, cent, vbur, map_info in info:
row = self.table.rowCount()
self.table.insertRow(row)
m = QTableWidgetItem()
m.setData(Qt.DisplayRole, mdl.name)
self.table.setItem(row, 0, m)
c = QTableWidgetItem()
c.setData(Qt.DisplayRole, cent)
self.table.setItem(row, 1, c)
v = QTableWidgetItem()
if report_component == "octants":
v.setData(Qt.DisplayRole,
",".join(["%.1f" % x for x in vbur]))
elif report_component == "quadrants":
v.setData(
Qt.DisplayRole, ",".join("%.1f" % x for x in [
vbur[0] + vbur[7],
vbur[1] + vbur[6],
vbur[2] + vbur[5],
vbur[3] + vbur[4],
]))
else:
if hasattr(vbur, "__iter__"):
v.setData(Qt.DisplayRole, "%.1f" % sum(vbur))
else:
v.setData(Qt.DisplayRole, "%.1f" % vbur)
v.setTextAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.table.setItem(row, 2, v)
x, y, z, min_alt, max_alt = map_info
plot = self.tool_window.create_child_window(
"steric map of %s" % mdl.name, window_class=StericMap)
if auto_minmax:
plot.set_data(x, y, z, min_alt, max_alt, vbur, radius,
include_vbur)
else:
plot.set_data(x, y, z, map_min, map_max, vbur, radius,
include_vbur)
else:
for mdl, cent, vbur in info:
row = self.table.rowCount()
self.table.insertRow(row)
m = QTableWidgetItem()
m.setData(Qt.DisplayRole, mdl.name)
self.table.setItem(row, 0, m)
c = QTableWidgetItem()
c.setData(Qt.DisplayRole, cent)
self.table.setItem(row, 1, c)
v = QTableWidgetItem()
if report_component == "octants":
v.setData(Qt.DisplayRole,
",".join(["%.1f" % x for x in vbur]))
elif report_component == "quadrants":
v.setData(
Qt.DisplayRole, ",".join("%.1f" % x for x in [
vbur[0] + vbur[7],
vbur[1] + vbur[6],
vbur[2] + vbur[5],
vbur[3] + vbur[4],
]))
else:
if hasattr(vbur, "__iter__"):
v.setData(Qt.DisplayRole, "%.1f" % sum(vbur))
else:
v.setData(Qt.DisplayRole, "%.1f" % vbur)
v.setTextAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.table.setItem(row, 2, v)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
def header_check(self, state):
"""user has [un]checked the 'include header' option on the menu"""
if state:
self.settings.include_header = True
else:
self.settings.include_header = False
def get_csv(self):
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
if self.settings.include_header:
s = delim.join(["model", "center", "%Vbur"])
s += "\n"
else:
s = ""
for i in range(0, self.table.rowCount()):
s += delim.join([
item.data(Qt.DisplayRole)
for item in [self.table.item(i, j) for j in range(0, 3)]
])
s += "\n"
return s
def copy_csv(self):
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def save_csv(self):
"""save data on current tab to CSV file"""
filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)")
if filename:
s = self.get_csv()
with open(filename, 'w') as f:
f.write(s.strip())
self.session.logger.status("saved to %s" % filename)
def del_vbur(self):
for model in self.session.models.list(type=Surface):
if model.name.startswith("%Vbur") or model.name.startswith(
"%Vfree"):
model.delete()
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 "")