def __init__(self, settings, *args, **kwargs):
super().__init__(*args, **kwargs)
layout = QGridLayout(self)
#layout.setContentsMargins(0, 0, 0, 0)
settings_tabs = QTabWidget()
layout.addWidget(settings_tabs)
form = 'Gaussian'
self.method = MethodOption(settings, form)
settings_tabs.addTab(self.method, "Method")
self.basis = BasisWidget(settings, form)
settings_tabs.addTab(self.basis, "Basis Sets")
#menu stuff
menu = QMenuBar()
self.presets_menu = menu.addMenu("Presets")
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.settings = settings
self.presets = {}
self.presets['Gaussian'] = loads(self.settings.gaussian_presets)
self.presets['ORCA'] = loads(self.settings.orca_presets)
self.presets['Psi4'] = loads(self.settings.psi4_presets)
self.refresh_presets()
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)
class Thermochem(ToolInstance):
"""tool for calculating free energy corrections based on frequencies and energies
associated with FileReaders
there are two tabs: absolute and relative
the absolute tab can be used to combine the thermo corrections from one
FileReader with the energy of another
the relative tab can do the same, but it prints the energies relative to
those of another FileReader
multiple molecule groups can be added (i.e. for reactions with multiple
reactants and products)
each molecule group can have multiple conformers
the energies of these conformers are boltzmann weighted, and the boltzmann-weighted
energy is used to calculate the energy of either the reference group or the 'other' group"""
SESSION_ENDURING = False
SESSION_SAVE = False
help = "https://github.com/QChASM/SEQCROW/wiki/Process-Thermochemistry-Tool"
theory_helper = {
"Grimme's Quasi-RRHO": "https://doi.org/10.1002/chem.201200497",
"Truhlar's Quasi-Harmonic": "https://doi.org/10.1021/jp205508z"
}
def __init__(self, session, name):
super().__init__(session, name)
self.display_name = "Thermochemistry"
self.tool_window = MainToolWindow(self)
self.settings = _ComputeThermoSettings(self.session, name)
self.nrg_fr = {}
self.thermo_fr = {}
self.thermo_co = {}
self._headers = []
self._data = []
self._build_ui()
self.set_sp()
self.set_thermo_mdl()
self.calc_relative_thermo()
def _build_ui(self):
#each group has an empty widget at the bottom so they resize the way I want while also having the
#labels where I want them
layout = QGridLayout()
self.tab_widget = QTabWidget()
layout.addWidget(self.tab_widget)
#layout for absolute thermo stuff
absolute_widget = QWidget()
absolute_layout = QGridLayout(absolute_widget)
#box for sp
sp_area_widget = QGroupBox("Single-point")
sp_layout = QFormLayout(sp_area_widget)
self.sp_selector = FilereaderComboBox(self.session,
otherItems=['energy'])
self.sp_selector.currentIndexChanged.connect(self.set_sp)
sp_layout.addRow(self.sp_selector)
self.sp_table = QTableWidget()
self.sp_table.setColumnCount(3)
self.sp_table.setShowGrid(False)
self.sp_table.horizontalHeader().hide()
self.sp_table.verticalHeader().hide()
self.sp_table.setFrameShape(QTableWidget.NoFrame)
self.sp_table.setSelectionMode(QTableWidget.NoSelection)
self.sp_table.insertRow(0)
sp_layout.addRow(self.sp_table)
#box for thermo
therm_area_widget = QGroupBox("Thermal corrections")
thermo_layout = QFormLayout(therm_area_widget)
self.thermo_selector = FilereaderComboBox(self.session,
otherItems=['frequency'])
self.thermo_selector.currentIndexChanged.connect(self.set_thermo_mdl)
thermo_layout.addRow(self.thermo_selector)
self.temperature_line = QDoubleSpinBox()
self.temperature_line.setMaximum(2**31 - 1)
self.temperature_line.setValue(298.15)
self.temperature_line.setSingleStep(10)
self.temperature_line.setSuffix(" K")
self.temperature_line.setMinimum(0)
self.temperature_line.valueChanged.connect(self.set_thermo)
thermo_layout.addRow("T =", self.temperature_line)
self.v0_edit = QDoubleSpinBox()
self.v0_edit.setMaximum(4000)
self.v0_edit.setValue(self.settings.w0)
self.v0_edit.setSingleStep(25)
self.v0_edit.setSuffix(" cm\u207b\u00b9")
self.v0_edit.valueChanged.connect(self.set_thermo)
self.v0_edit.setMinimum(0)
self.v0_edit.setToolTip(
"frequency parameter for quasi treatments of entropy")
thermo_layout.addRow("𝜔<sub>0</sub> =", self.v0_edit)
self.thermo_table = QTableWidget()
self.thermo_table.setColumnCount(3)
self.thermo_table.setShowGrid(False)
self.thermo_table.horizontalHeader().hide()
self.thermo_table.verticalHeader().hide()
self.thermo_table.setFrameShape(QTableWidget.NoFrame)
self.thermo_table.setSelectionMode(QTableWidget.NoSelection)
thermo_layout.addRow(self.thermo_table)
# for for total
sum_area_widget = QGroupBox("Thermochemistry")
sum_layout = QFormLayout(sum_area_widget)
self.sum_table = QTableWidget()
self.sum_table.setColumnCount(3)
self.sum_table.setShowGrid(False)
self.sum_table.horizontalHeader().hide()
self.sum_table.verticalHeader().hide()
self.sum_table.setFrameShape(QTableWidget.NoFrame)
self.sum_table.setSelectionMode(QTableWidget.NoSelection)
sum_layout.addRow(self.sum_table)
splitter = QSplitter(Qt.Horizontal)
splitter.setChildrenCollapsible(False)
splitter.addWidget(sp_area_widget)
splitter.addWidget(therm_area_widget)
splitter.addWidget(sum_area_widget)
absolute_layout.addWidget(splitter)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
self.status.setStyleSheet("color: red")
absolute_layout.addWidget(self.status, 1, 0, 1, 1, Qt.AlignTop)
self.tab_widget.addTab(absolute_widget, "absolute")
relative_widget = QWidget()
relative_layout = QGridLayout(relative_widget)
size = [self.settings.ref_col_1, self.settings.ref_col_2]
self.ref_group = ThermoGroup("reference group", self.session,
self.nrg_fr, self.thermo_co, size)
self.ref_group.changes.connect(self.calc_relative_thermo)
relative_layout.addWidget(self.ref_group, 0, 0, 1, 3, Qt.AlignTop)
size = [self.settings.other_col_1, self.settings.other_col_2]
self.other_group = ThermoGroup("other group", self.session,
self.nrg_fr, self.thermo_co, size)
self.other_group.changes.connect(self.calc_relative_thermo)
relative_layout.addWidget(self.other_group, 0, 3, 1, 3, Qt.AlignTop)
self.relative_temperature = QDoubleSpinBox()
self.relative_temperature.setMaximum(2**31 - 1)
self.relative_temperature.setValue(self.settings.rel_temp)
self.relative_temperature.setSingleStep(10)
self.relative_temperature.setSuffix(" K")
self.relative_temperature.setMinimum(0)
self.relative_temperature.valueChanged.connect(
self.calc_relative_thermo)
relative_layout.addWidget(QLabel("T ="), 1, 0, 1, 1,
Qt.AlignRight | Qt.AlignVCenter)
relative_layout.addWidget(self.relative_temperature, 1, 1, 1, 5,
Qt.AlignLeft | Qt.AlignVCenter)
self.relative_v0 = QDoubleSpinBox()
self.relative_v0.setMaximum(2**31 - 1)
self.relative_v0.setValue(self.settings.w0)
self.relative_v0.setSingleStep(25)
self.relative_v0.setSuffix(" cm\u207b\u00b9")
self.relative_v0.setMinimum(0)
self.relative_v0.setToolTip(
"frequency parameter for quasi treatments of entropy")
self.relative_v0.valueChanged.connect(self.calc_relative_thermo)
relative_layout.addWidget(QLabel("𝜔<sub>0</sub> ="), 2, 0, 1, 1,
Qt.AlignRight | Qt.AlignVCenter)
relative_layout.addWidget(self.relative_v0, 2, 1, 1, 5,
Qt.AlignLeft | Qt.AlignVCenter)
relative_layout.addWidget(
QLabel("Boltzmann-weighted relative energies in kcal/mol:"), 3, 0,
1, 6, Qt.AlignVCenter | Qt.AlignLeft)
self.relative_table = QTextBrowser()
self.relative_table.setMaximumHeight(
4 * self.relative_table.fontMetrics().boundingRect("Q").height())
relative_layout.addWidget(self.relative_table, 4, 0, 1, 6, Qt.AlignTop)
relative_layout.setRowStretch(0, 1)
relative_layout.setRowStretch(1, 0)
relative_layout.setRowStretch(2, 0)
relative_layout.setRowStretch(3, 0)
relative_layout.setRowStretch(4, 0)
self.tab_widget.addTab(relative_widget, "relative")
#menu stuff
menu = QMenuBar()
export = menu.addMenu("&Export")
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 calc_relative_thermo(self, *args):
"""changes the values on the 'relative' tab
called when the tool is opened and whenever something changes on the relative tab"""
def calc_free_energies(nrg_list, co_list, T, w0):
"""returns lists for ZPVE, H, RRHO G, QRRHO G, and QHARM G
for the items in nrg_list and co_list at temperature T
and frequency parameter w0"""
ZPVEs = []
if all(co.frequency.anharm_data for co_group in co_list
for co in co_group):
anharm_ZVPEs = []
else:
anharm_ZVPEs = None
Hs = []
Gs = []
RRHOG = []
QHARMG = []
for i in range(0, len(nrg_list)):
ZPVEs.append([])
if anharm_ZVPEs is not None:
anharm_ZVPEs.append([])
Hs.append([])
Gs.append([])
RRHOG.append([])
QHARMG.append([])
for nrg, co in zip(nrg_list[i], co_list[i]):
ZPVE = co.ZPVE
ZPVEs[-1].append(nrg + ZPVE)
if anharm_ZVPEs is not None:
zpve_anharm = co.calc_zpe(anharmonic=True)
anharm_ZVPEs[-1].append(nrg + zpve_anharm)
dH = co.therm_corr(T, w0, CompOutput.RRHO)[1]
Hs[-1].append(nrg + dH)
dG = co.calc_G_corr(temperature=T,
v0=w0,
method=CompOutput.RRHO)
Gs[-1].append(nrg + dG)
dQRRHOG = co.calc_G_corr(temperature=T,
v0=w0,
method=CompOutput.QUASI_RRHO)
RRHOG[-1].append(nrg + dQRRHOG)
dQHARMG = co.calc_G_corr(temperature=T,
v0=w0,
method=CompOutput.QUASI_HARMONIC)
QHARMG[-1].append(nrg + dQHARMG)
return ZPVEs, anharm_ZVPEs, Hs, Gs, RRHOG, QHARMG
def boltzmann_weight(energies1, energies2, T):
"""
energies - list of lists
list axis 0 - molecule groups
axis 1 - energies of conformers
boltzmann weight energies for conformers
combine energies for molecule groups
return the difference"""
totals1 = []
totals2 = []
beta = UNIT.HART_TO_JOULE / (PHYSICAL.KB * T)
for energy_group in energies1:
if len(energy_group) == 0:
continue
rezero = min(energy_group)
rel_nrgs = [(x - rezero) for x in energy_group]
weights = [np.exp(-beta * nrg) for nrg in rel_nrgs]
totals1.append(-PHYSICAL.BOLTZMANN * T * np.log(sum(weights)) +
rezero * UNIT.HART_TO_KCAL)
for energy_group in energies2:
if len(energy_group) == 0:
continue
rezero = min(energy_group)
rel_nrgs = [(x - rezero) for x in energy_group]
weights = [np.exp(-beta * nrg) for nrg in rel_nrgs]
totals2.append(-PHYSICAL.BOLTZMANN * T * np.log(sum(weights)) +
rezero * UNIT.HART_TO_KCAL)
return sum(totals2) - sum(totals1)
ref_Es = self.ref_group.energies()
ref_cos = self.ref_group.compOutputs()
other_Es = self.other_group.energies()
other_cos = self.other_group.compOutputs()
if any(
len(x) == 0 or all(len(y) == 0 for y in x)
for x in [ref_Es, other_Es]):
self.relative_table.setText("not enough data")
return
T = self.relative_temperature.value()
self.settings.rel_temp = T
w0 = self.relative_v0.value()
if w0 != self.settings.w0:
self.settings.w0 = w0
rel_E = boltzmann_weight(ref_Es, other_Es, T)
headers = ["ΔE"]
data = [rel_E]
empty_groups = []
for i, group in enumerate(ref_cos):
if len(group) == 0:
empty_groups.append(i)
for ndx in empty_groups[::-1]:
ref_Es.pop(ndx)
ref_cos.pop(ndx)
empty_groups = []
for i, group in enumerate(other_cos):
if len(group) == 0:
empty_groups.append(i)
for ndx in empty_groups[::-1]:
other_Es.pop(ndx)
other_cos.pop(ndx)
if not any(
len(x) == 0 or all(len(y) == 0 for y in x)
for x in [ref_cos, other_cos]):
rel_E = boltzmann_weight(ref_Es, other_Es, T)
data = [rel_E]
ref_ZPVEs, ref_anharm_zpve, ref_Hs, ref_Gs, ref_QRRHOGs, ref_QHARMGs = calc_free_energies(
ref_Es, ref_cos, T, w0)
other_ZPVEs, other_anharm_zpve, other_Hs, other_Gs, other_QRRHOGs, other_QHARMGs = calc_free_energies(
other_Es, other_cos, T, w0)
rel_ZPVE = boltzmann_weight(ref_ZPVEs, other_ZPVEs, T)
rel_H = boltzmann_weight(ref_Hs, other_Hs, T)
rel_G = boltzmann_weight(ref_Gs, other_Gs, T)
rel_QRRHOG = boltzmann_weight(ref_QRRHOGs, other_QRRHOGs, T)
rel_QHARMG = boltzmann_weight(ref_QHARMGs, other_QHARMGs, T)
if ref_anharm_zpve and other_anharm_zpve:
rel_anharm_ZPVE = boltzmann_weight(ref_anharm_zpve,
other_anharm_zpve, T)
headers.extend([
"ΔZPE",
"ΔZPE<sub>anh</sub>",
"ΔH<sub>RRHO</sub>",
"ΔG<sub>RRHO</sub>",
"ΔG<sub>Quasi-RRHO</sub>",
"ΔG<sub>Quasi-Harmonic</sub>",
])
data.extend([
rel_ZPVE,
rel_anharm_ZPVE,
rel_H,
rel_G,
rel_QRRHOG,
rel_QHARMG,
])
else:
headers.extend([
"ΔZPE",
"ΔH<sub>RRHO</sub>",
"ΔG<sub>RRHO</sub>",
"ΔG<sub>Quasi-RRHO</sub>",
"ΔG<sub>Quasi-Harmonic</sub>",
])
data.extend([
rel_ZPVE,
rel_H,
rel_G,
rel_QRRHOG,
rel_QHARMG,
])
self._headers = headers
self._data = data
s = "<table style=\"border: 1px solid ghostwhite;\">\n"
s += "\t<tr>\n"
for header in headers:
s += "\t\t<th style=\"text-align: center; border: 1px solid ghostwhite; padding-left: 5px; padding-right: 5px\">%s</th>\n" % header
s += "\t</tr>\n"
s += "\t<tr>\n"
for val in data:
s += "\t\t<td style=\"text-align: center; border: 1px solid ghostwhite; padding-left: 5px; padding-right: 5px\">%.1f</td>\n" % val
s += "\t</tr>\n"
s += "</table>"
self.relative_table.setText(s)
def open_link(self, theory):
"""open the oft-cited QRRHO or QHARM reference"""
link = self.theory_helper[theory]
run(self.session, "open %s" % link)
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 copy_csv(self):
"""put CSV data for current tab on the clipboard"""
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def get_csv(self):
"""get CSV data for the current tab"""
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.tab_widget.currentIndex() == 0:
s = ""
if self.settings.include_header:
link_re = QRegularExpression("<a[\d\D]*>(𝛿?Δ?[\d\D]*)</a>")
# get header labels from the tables
for table in [
self.sp_table, self.thermo_table, self.sum_table
]:
for row in range(0, table.rowCount()):
item = table.cellWidget(row, 0)
text = item.text()
text = text.replace(" =", "")
text = text.replace("<sub>", "(")
text = text.replace("</sub>", ")")
# if there's a link like for QRRHO G, remove the link
if "href=" in text:
match = link_re.match(text)
text = match.captured(1)
text = text.replace("𝛿", "d")
s += "%s%s" % (text, delim)
s += "SP_File%sThermo_File\n" % delim
# get values from tables
for table in [self.sp_table, self.thermo_table, self.sum_table]:
for row in range(0, table.rowCount()):
item = table.cellWidget(row, 1)
s += "%s%s" % (item.text(), delim)
sp_mdl = self.sp_selector.currentData()
sp_name = sp_mdl.name
therm_mdl = self.thermo_selector.currentData()
s += "%s" % sp_name
if therm_mdl:
therm_name = therm_mdl.name
s += "%s%s" % (delim, therm_name)
s += "\n"
elif self.tab_widget.currentIndex() == 1:
s = ""
if self.settings.include_header:
link_re = QRegularExpression("<a[\d\D]*>(𝛿?Δ?[\d\D]*)</a>")
# get header labels from the tables
for text in self._headers:
text = text.replace(" =", "")
text = text.replace("<sub>", "(")
text = text.replace("</sub>", ")")
# if there's a link like for QRRHO G, remove the link
if "href=" in text:
match = link_re.match(text)
text = match.captured(1)
text = text.replace("𝛿", "d")
s += "%s%s" % (text, delim)
s = s.rstrip(delim)
s += "\n"
s += delim.join(["%.1f" % val for val in self._data])
return s
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 set_sp(self):
"""set energy entry for when sp model changes"""
self.sp_table.setRowCount(0)
if self.sp_selector.currentIndex() >= 0:
fr = self.sp_selector.currentData()
self.check_geometry_rmsd("SP")
self.sp_table.insertRow(0)
nrg_label = QLabel("E =")
nrg_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
self.sp_table.setCellWidget(0, 0, nrg_label)
unit_label = ReadOnlyTableItem()
unit_label.setData(Qt.DisplayRole, "E\u2095")
unit_label.setTextAlignment(Qt.AlignLeft | Qt.AlignVCenter)
self.sp_table.setItem(0, 2, unit_label)
sp_nrg = SmallLineEdit("%.6f" % fr.other['energy'])
sp_nrg.setReadOnly(True)
sp_nrg.setFrame(False)
self.sp_table.setCellWidget(0, 1, sp_nrg)
self.sp_table.resizeRowToContents(0)
self.sp_table.resizeColumnToContents(0)
self.sp_table.resizeColumnToContents(1)
self.sp_table.resizeColumnToContents(2)
self.update_sum()
def set_thermo_mdl(self):
"""
frequencies filereader has changed on the absolute tab
also changes the temperature option (on the absolute tab only)
"""
if self.thermo_selector.currentIndex() >= 0:
fr = self.thermo_selector.currentData()
self.check_geometry_rmsd("THERM")
if 'temperature' in fr.other:
self.temperature_line.setValue(fr.other['temperature'])
self.set_thermo()
def check_geometry_rmsd(self, *args):
"""check RMSD between energy and frequency filereader on the absolute tab
if the RMSD is > 10^-5 or the number of atoms is different, put a warning in the
status bar"""
if self.thermo_selector.currentIndex(
) >= 0 and self.sp_selector.currentIndex() >= 0:
fr = self.sp_selector.currentData()
fr2 = self.thermo_selector.currentData()
if len(fr.atoms) != len(fr2.atoms):
self.status.showMessage(
"structures are not the same: different number of atoms")
return
geom = Geometry(fr)
geom2 = Geometry(fr2)
rmsd = geom.RMSD(geom2)
if not isclose(rmsd, 0, atol=10**-5):
rmsd = geom.RMSD(geom2, sort=True)
if not isclose(rmsd, 0, atol=10**-5):
self.status.showMessage(
"structures might not be the same - RMSD = %.4f" % rmsd)
else:
self.status.showMessage("")
def set_thermo(self):
"""computes thermo corrections and sets thermo entries for when thermo model changes"""
#index of combobox is -1 when combobox has no entries
self.thermo_table.setRowCount(0)
if self.thermo_selector.currentIndex() >= 0:
fr = self.thermo_selector.currentData()
if fr not in self.thermo_co:
self.thermo_co[fr] = CompOutput(fr)
co = self.thermo_co[fr]
v0 = self.v0_edit.value()
if v0 != self.settings.w0:
self.settings.w0 = v0
T = self.temperature_line.value()
if not T:
return
dZPE = co.ZPVE
#compute enthalpy and entropy at this temperature
#AaronTools uses Grimme's Quasi-RRHO, but this is the same as RRHO when w0=0
dE, dH, s = co.therm_corr(temperature=T, v0=0, method="RRHO")
rrho_dg = dH - T * s
#compute G with quasi entropy treatments
qrrho_dg = co.calc_G_corr(v0=v0, temperature=T, method="QRRHO")
qharm_dg = co.calc_G_corr(v0=v0, temperature=T, method="QHARM")
items = [(
"𝛿ZPE =",
dZPE,
None,
"lowest energy the molecule can have\n"
"no rotational or vibrational modes populated\n"
"equal to enthalpy at 0 K",
)]
if fr.other["frequency"].anharm_data:
dZPE_anh = co.calc_zpe(anharmonic=True)
items.append((
"𝛿ZPE<sub>anh</sub> =",
dZPE_anh,
None,
"lowest energy the molecule can have\n"
"no rotational or vibrational modes populated\n"
"includes corrections for anharmonic vibrations",
))
items.extend([
(
"𝛿H<sub>RRHO</sub> =",
dH,
None,
"enthalpy of formation",
),
(
"𝛿G<sub>RRHO</sub> =",
rrho_dg,
None,
"energy after taking into account the average\n"
"population of vibrational, rotational, and translational\n"
"degrees of freedom",
),
(
"𝛿G<sub>Quasi-RRHO</sub> =",
qrrho_dg,
"Grimme's Quasi-RRHO",
"vibrational entropy of each real mode is damped and complemented\n"
"with rotational entropy, with the damping function being stronger for\n"
"frequencies < 𝜔\u2080\n"
"can mitigate error from inaccuracies in the harmonic oscillator\n"
"approximation for low-frequency vibrations",
),
(
"𝛿G<sub>Quasi-Harmonic</sub> =",
qharm_dg,
"Truhlar's Quasi-Harmonic",
"real vibrational frequencies below 𝜔\u2080 are treated as 𝜔\u2080\n"
"can mitigate error from inaccuracies in the harmonic oscillator\n"
"approximation for low-frequency vibrations",
),
])
for i, (label_text, val, link, tooltip) in enumerate(items):
self.thermo_table.insertRow(i)
label = QLabel(label_text)
if link:
label = QLabel()
label.setText(
"<a href=\"%s\" style=\"text-decoration: none;\">%s</a>"
% (link, label_text))
label.setTextFormat(Qt.RichText)
label.setTextInteractionFlags(Qt.TextBrowserInteraction)
label.linkActivated.connect(self.open_link)
label.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
label.setToolTip(tooltip)
self.thermo_table.setCellWidget(i, 0, label)
unit_label = ReadOnlyTableItem()
unit_label.setData(Qt.DisplayRole, "E\u2095")
unit_label.setTextAlignment(Qt.AlignLeft | Qt.AlignVCenter)
unit_label.setToolTip(tooltip)
self.thermo_table.setItem(i, 2, unit_label)
d_nrg = SmallLineEdit("%.6f" % val)
d_nrg.setReadOnly(True)
d_nrg.setFrame(False)
d_nrg.setToolTip(tooltip)
self.thermo_table.setCellWidget(i, 1, d_nrg)
self.thermo_table.resizeRowToContents(i)
self.thermo_table.resizeColumnToContents(0)
self.thermo_table.resizeColumnToContents(1)
self.thermo_table.resizeColumnToContents(2)
self.update_sum()
def update_sum(self):
"""updates the sum of energy and thermo corrections"""
self.sum_table.setRowCount(0)
if not self.sp_table.rowCount():
return
sp_nrg = float(self.sp_table.cellWidget(0, 1).text())
for row in range(0, self.thermo_table.rowCount()):
self.sum_table.insertRow(row)
label = self.thermo_table.cellWidget(row, 0)
tooltip = label.toolTip()
text = label.text().replace("𝛿", "")
sum_label = QLabel(text)
if "href=" in text:
sum_label = QLabel()
sum_label.setText(text)
sum_label.setTextFormat(Qt.RichText)
sum_label.setTextInteractionFlags(Qt.TextBrowserInteraction)
sum_label.linkActivated.connect(self.open_link)
sum_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
sum_label.setToolTip(tooltip)
self.sum_table.setCellWidget(row, 0, sum_label)
thermo = float(self.thermo_table.cellWidget(row, 1).text())
total = sp_nrg + thermo
total_nrg = SmallLineEdit("%.6f" % total)
total_nrg.setFrame(False)
total_nrg.setReadOnly(True)
total_nrg.setToolTip(tooltip)
self.sum_table.setCellWidget(row, 1, total_nrg)
unit_label = ReadOnlyTableItem()
unit_label.setData(Qt.DisplayRole, "E\u2095")
unit_label.setTextAlignment(Qt.AlignLeft | Qt.AlignVCenter)
unit_label.setToolTip(tooltip)
self.sum_table.setItem(row, 2, unit_label)
self.sum_table.resizeRowToContents(row)
self.sum_table.resizeColumnToContents(0)
self.sum_table.resizeColumnToContents(1)
self.sum_table.resizeColumnToContents(2)
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 delete(self):
#overload because closing a tool window doesn't destroy any widgets on it
self.settings.ref_col_1 = self.ref_group.tree.columnWidth(0)
self.settings.ref_col_2 = self.ref_group.tree.columnWidth(1)
self.settings.other_col_1 = self.other_group.tree.columnWidth(0)
self.settings.other_col_2 = self.other_group.tree.columnWidth(1)
self.sp_selector.deleteLater()
self.thermo_selector.deleteLater()
self.ref_group.deleteLater()
self.other_group.deleteLater()
return super().delete()
def close(self):
#overload because closing a tool window doesn't destroy any widgets on it
self.settings.ref_col_1 = self.ref_group.tree.columnWidth(0)
self.settings.ref_col_2 = self.ref_group.tree.columnWidth(1)
self.settings.other_col_1 = self.other_group.tree.columnWidth(0)
self.settings.other_col_2 = self.other_group.tree.columnWidth(1)
self.sp_selector.deleteLater()
self.thermo_selector.deleteLater()
self.ref_group.deleteLater()
self.other_group.deleteLater()
return super().close()
def _build_ui(self):
layout = QGridLayout()
tab_widget = QTabWidget()
layout.addWidget(tab_widget)
structure_widget = QWidget()
structure_layout = QGridLayout(structure_widget)
tab_widget.addTab(structure_widget, "structure")
self.structure_source = QComboBox()
self.structure_source.addItems(
["AARON template", "file", "coordination complexes", "SMILES"])
structure_layout.addWidget(QLabel("structure source:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
structure_layout.addWidget(
self.structure_source,
0,
1,
1,
1,
)
open_button = QPushButton("open")
open_button.clicked.connect(self.open_template)
structure_layout.addWidget(
open_button,
0,
2,
1,
1,
)
# SMILES options
self.smiles_options = QGroupBox("SMILES options")
smiles_layout = QFormLayout(self.smiles_options)
structure_layout.addWidget(self.smiles_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
self.smiles_line = QLineEdit()
smiles_layout.addRow("SMILES string:", self.smiles_line)
self.smiles_options.setVisible(
self.structure_source.currentText() == "SMILES")
self.structure_source.currentTextChanged.connect(
lambda text: self.smiles_options.setVisible(text == "SMILES"))
# coordination complexes options
self.coord_comp_options = QGroupBox("Coordination Complex Options")
coord_layout = QFormLayout(self.coord_comp_options)
structure_layout.addWidget(self.coord_comp_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
create_coord_items(self,
coord_layout,
allow_minimization=False,
default_ele="Pd")
self.coord_comp_options.setVisible(
self.structure_source.currentText() == "coordination complexes")
self.structure_source.currentTextChanged.connect(
lambda text: self.coord_comp_options.setVisible(
text == "coordination complexes"))
# aaron template options
self.aaron_options = QGroupBox("AARON template structures")
aaron_layout = QFormLayout(self.aaron_options)
structure_layout.addWidget(self.aaron_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
self.aaron_options.setVisible(
self.structure_source.currentText() == "AARON template")
self.structure_source.currentTextChanged.connect(
lambda text: self.aaron_options.setVisible(text == "AARON template"
))
# file options
self.file_options = QGroupBox("single file options")
file_layout = QFormLayout(self.file_options)
structure_layout.addWidget(self.file_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
file_widget = QWidget()
file_browse_layout = QGridLayout(file_widget)
self.template_file = QLineEdit()
file_browse_layout.addWidget(self.template_file, 0, 0, 1, 1,
Qt.AlignCenter)
browse_button = QPushButton("browse...")
# browse_button.clicked.connect(self.browse_file_template)
file_browse_layout.addWidget(browse_button, 0, 1, 1, 1, Qt.AlignCenter)
file_browse_layout.setColumnStretch(0, 1)
file_browse_layout.setColumnStretch(1, 0)
margins = file_browse_layout.contentsMargins()
file_browse_layout.setContentsMargins(margins.left(), 0,
margins.right(), 0)
file_layout.addRow("file:", file_widget)
self.file_options.setVisible(
self.structure_source.currentText() == "file")
self.structure_source.currentTextChanged.connect(
lambda text: self.file_options.setVisible(text == "file"))
self.optimize_template = QCheckBox()
self.optimize_template.setCheckState(Qt.Checked)
structure_layout.addWidget(
QLabel("optimize template:"),
2,
0,
1,
1,
Qt.AlignLeft | Qt.AlignVCenter,
)
structure_layout.addWidget(
self.optimize_template,
2,
1,
1,
2,
Qt.AlignLeft | Qt.AlignVCenter,
)
structure_layout.setColumnStretch(0, 0)
structure_layout.setColumnStretch(1, 1)
structure_layout.setColumnStretch(2, 0)
# structure changes
changes_widget = QWidget()
changes_layout = QGridLayout(changes_widget)
tab_widget.addTab(changes_widget, "changes")
# HPC settings
hpc_widget = QWidget()
hpc_layout = QGridLayout(hpc_widget)
tab_widget.addTab(hpc_widget, "HPC")
# theory settings
theory_widget = QWidget()
theory_layout = QGridLayout(theory_widget)
tab_widget.addTab(theory_widget, "theory")
# results
results_widget = QWidget()
results_layout = QGridLayout(results_widget)
tab_widget.addTab(results_widget, "results")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QVBoxLayout()
self.file_selector = FilereaderComboBox(self.session)
self.file_selector.currentIndexChanged.connect(self.fill_table)
layout.insertWidget(0, self.file_selector, 0)
tabs = QTabWidget()
self.tabs = tabs
layout.insertWidget(1, self.tabs, 1)
general_info = QWidget()
general_layout = QVBoxLayout(general_info)
tabs.addTab(general_info, "general")
self.table = QTableWidget()
self.table.setColumnCount(2)
self.table.setHorizontalHeaderLabels(['Data', 'Value'])
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Interactive)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Stretch)
self.table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
general_layout.insertWidget(1, self.table, 1)
self.filter = QLineEdit()
self.filter.setPlaceholderText("filter data")
self.filter.textChanged.connect(self.apply_filter)
self.filter.setClearButtonEnabled(True)
general_layout.insertWidget(2, self.filter, 0)
freq_info = QWidget()
freq_layout = QVBoxLayout(freq_info)
tabs.addTab(freq_info, "harmonic frequencies")
self.freq_table = QTableWidget()
self.freq_table.setColumnCount(4)
self.freq_table.setHorizontalHeaderLabels([
"Frequency (cm\u207b\u00b9)",
"symmetry",
"IR intensity",
"force constant (mDyne/\u212B)",
])
self.freq_table.setSortingEnabled(True)
self.freq_table.setEditTriggers(QTableWidget.NoEditTriggers)
for i in range(0, 4):
self.freq_table.resizeColumnToContents(i)
self.freq_table.horizontalHeader().setStretchLastSection(False)
self.freq_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.freq_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.freq_table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Fixed)
self.freq_table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.freq_table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
freq_layout.insertWidget(1, self.freq_table, 1)
anharm_info = QWidget()
anharm_layout = QVBoxLayout(anharm_info)
tabs.addTab(anharm_info, "anharmonic frequencies")
anharm_layout.insertWidget(0, QLabel("fundamentals:"), 0)
self.fundamental_table = QTableWidget()
self.fundamental_table.setColumnCount(3)
self.fundamental_table.setHorizontalHeaderLabels([
"Fundamental (cm\u207b\u00b9)",
"Δ\u2090\u2099\u2095 (cm\u207b\u00b9)",
"IR intensity",
])
self.fundamental_table.setSortingEnabled(True)
self.fundamental_table.setEditTriggers(QTableWidget.NoEditTriggers)
for i in range(0, 3):
self.fundamental_table.resizeColumnToContents(i)
self.fundamental_table.horizontalHeader().setStretchLastSection(False)
self.fundamental_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.fundamental_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.fundamental_table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.fundamental_table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
anharm_layout.insertWidget(1, self.fundamental_table, 1)
# self.overtone_table = QTableWidget()
# self.overtone_table.setColumnCount(3)
# self.overtone_table.setHorizontalHeaderLabels(
# [
# "Fundamental (cm\u207b\u00b9)",
# "Overtone (cm\u207b\u00b9)",
# "IR intensity",
# ]
# )
# self.overtone_table.setSortingEnabled(True)
# self.overtone_table.setEditTriggers(QTableWidget.NoEditTriggers)
# for i in range(0, 3):
# self.overtone_table.resizeColumnToContents(i)
#
# self.overtone_table.horizontalHeader().setStretchLastSection(False)
# self.overtone_table.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
# self.overtone_table.horizontalHeader().setSectionResizeMode(1, QHeaderView.Fixed)
# self.overtone_table.horizontalHeader().setSectionResizeMode(2, QHeaderView.Stretch)
#
# self.overtone_table.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding)
# anharm_layout.insertWidget(2, self.overtone_table, 1)
anharm_layout.insertWidget(2, QLabel("combinations and overtones:"), 0)
self.combo_table = QTableWidget()
self.combo_table.setColumnCount(4)
self.combo_table.setHorizontalHeaderLabels([
"Fundamental (cm\u207b\u00b9)",
"Fundamental (cm\u207b\u00b9)",
"Combination (cm\u207b\u00b9)",
"IR intensity",
])
self.combo_table.setSortingEnabled(True)
self.combo_table.setEditTriggers(QTableWidget.NoEditTriggers)
for i in range(0, 3):
self.combo_table.resizeColumnToContents(i)
self.combo_table.horizontalHeader().setStretchLastSection(False)
self.combo_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.combo_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.combo_table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Fixed)
self.combo_table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.combo_table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
anharm_layout.insertWidget(3, self.combo_table, 1)
menu = QMenuBar()
export = menu.addMenu("&Export")
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)
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)
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
archive = QAction("Include archive if present",
self.tool_window.ui_area,
checkable=True)
archive.triggered.connect(
lambda checked: setattr(self.settings, "archive", checked))
archive.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
archive.setChecked(self.settings.archive)
export.addAction(archive)
unit = menu.addMenu("&Units")
energy = unit.addMenu("energy")
hartree = QAction("Hartree", self.tool_window.ui_area, checkable=True)
hartree.setChecked(self.settings.energy == "Hartree")
kcal = QAction("kcal/mol", self.tool_window.ui_area, checkable=True)
kcal.setChecked(self.settings.energy == "kcal/mol")
kjoule = QAction("kJ/mol", self.tool_window.ui_area, checkable=True)
kjoule.setChecked(self.settings.energy == "kJ/mol")
energy.addAction(hartree)
energy.addAction(kcal)
energy.addAction(kjoule)
hartree.triggered.connect(
lambda *args, val="Hartree": setattr(self.settings, "energy", val))
hartree.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
hartree.triggered.connect(
lambda *args, action=kcal: action.setChecked(False))
hartree.triggered.connect(
lambda *args, action=kjoule: action.setChecked(False))
kcal.triggered.connect(lambda *args, val="kcal/mol": setattr(
self.settings, "energy", val))
kcal.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
kcal.triggered.connect(
lambda *args, action=hartree: action.setChecked(False))
kcal.triggered.connect(
lambda *args, action=kjoule: action.setChecked(False))
kjoule.triggered.connect(
lambda *args, val="kJ/mol": setattr(self.settings, "energy", val))
kjoule.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
kjoule.triggered.connect(
lambda *args, action=hartree: action.setChecked(False))
kjoule.triggered.connect(
lambda *args, action=kcal: action.setChecked(False))
mass = unit.addMenu("mass")
kg = QAction("kg", self.tool_window.ui_area, checkable=True)
kg.setChecked(self.settings.mass == "kg")
amu = QAction("Da", self.tool_window.ui_area, checkable=True)
amu.setChecked(self.settings.mass == "Da")
mass.addAction(kg)
mass.addAction(amu)
kg.triggered.connect(
lambda *args, val="kg": setattr(self.settings, "mass", val))
kg.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
kg.triggered.connect(
lambda *args, action=amu: action.setChecked(False))
amu.triggered.connect(
lambda *args, val="Da": setattr(self.settings, "mass", val))
amu.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
amu.triggered.connect(
lambda *args, action=kg: action.setChecked(False))
rot_const = unit.addMenu("rotational constants")
temperature = QAction("K", self.tool_window.ui_area, checkable=True)
temperature.setChecked(self.settings.rot_const == "K")
hertz = QAction("GHz", self.tool_window.ui_area, checkable=True)
hertz.setChecked(self.settings.rot_const == "GHz")
rot_const.addAction(temperature)
rot_const.addAction(hertz)
temperature.triggered.connect(
lambda *args, val="K": setattr(self.settings, "rot_const", val))
temperature.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
temperature.triggered.connect(
lambda *args, action=hertz: action.setChecked(False))
hertz.triggered.connect(
lambda *args, val="GHz": setattr(self.settings, "rot_const", val))
hertz.triggered.connect(
lambda *args: self.fill_table(self.file_selector.count() - 1))
hertz.triggered.connect(
lambda *args, action=temperature: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
if len(self.session.filereader_manager.list()) > 0:
self.fill_table(0)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
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 _build_ui(self):
layout = QGridLayout()
library_tabs = QTabWidget()
#ligand tab
ligand_tab = QWidget()
ligand_layout = QFormLayout(ligand_tab)
self.ligand_name = QLineEdit()
self.ligand_name.setText("")
self.ligand_name.setPlaceholderText("leave blank to preview")
self.ligand_name.setToolTip(
"name of ligand you are adding to your ligand library\nleave blank to open a new model with just the ligand"
)
ligand_layout.addRow("ligand name:", self.ligand_name)
ligand_key_atoms = QPushButton("set key atoms to current selection")
ligand_key_atoms.clicked.connect(self.update_key_atoms)
ligand_key_atoms.setToolTip(
"the current selection will be the key atoms for the ligand\nleave blank to automatically determine key atoms"
)
ligand_layout.addRow(ligand_key_atoms)
libadd_ligand = QPushButton("add current selection to library")
libadd_ligand.clicked.connect(self.libadd_ligand)
ligand_layout.addRow(libadd_ligand)
#substituent tab
sub_tab = QWidget()
sub_layout = QFormLayout(sub_tab)
self.sub_name = QLineEdit()
self.sub_name.setText("")
self.sub_name.setPlaceholderText("leave blank to preview")
self.sub_name.setToolTip(
"name of substituent you are adding to your substituent library\nleave blank to open a new model with just the substituent"
)
sub_layout.addRow("substituent name:", self.sub_name)
self.sub_confs = QSpinBox()
self.sub_confs.setMinimum(1)
sub_layout.addRow("number of conformers:", self.sub_confs)
self.sub_angle = QSpinBox()
self.sub_angle.setRange(0, 180)
self.sub_angle.setSingleStep(30)
sub_layout.addRow("angle between conformers:", self.sub_angle)
libadd_sub = QPushButton("add current selection to library")
libadd_sub.clicked.connect(self.libadd_substituent)
sub_layout.addRow(libadd_sub)
#ring tab
ring_tab = QWidget()
ring_layout = QFormLayout(ring_tab)
self.ring_name = QLineEdit()
self.ring_name.setText("")
self.ring_name.setPlaceholderText("leave blank to preview")
self.ring_name.setToolTip(
"name of ring you are adding to your ring library\nleave blank to open a new model with just the ring"
)
ring_layout.addRow("ring name:", self.ring_name)
libadd_ring = QPushButton("add ring with selected walk to library")
libadd_ring.clicked.connect(self.libadd_ring)
ring_layout.addRow(libadd_ring)
library_tabs.addTab(sub_tab, "substituent")
library_tabs.addTab(ring_tab, "ring")
library_tabs.addTab(ligand_tab, "ligand")
self.library_tabs = library_tabs
layout.addWidget(library_tabs)
whats_this = QLabel()
whats_this.setText(
"<a href=\"req\" style=\"text-decoration: none;\">what's this?</a>"
)
whats_this.setTextFormat(Qt.RichText)
whats_this.setTextInteractionFlags(Qt.TextBrowserInteraction)
whats_this.linkActivated.connect(self.open_link)
whats_this.setToolTip(
"click for more information about AaronTools libraries")
layout.addWidget(whats_this)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
class EditStructure(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Structure-Modification-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.settings = _EditStructureSettings(session, "Structure Modification")
self.tool_window = MainToolWindow(self)
self.close_previous_bool = self.settings.modify
self._build_ui()
def _build_ui(self):
layout = QGridLayout()
self.alchemy_tabs = QTabWidget()
#substitute
substitute_tab = QWidget()
substitute_layout = QGridLayout(substitute_tab)
sublabel = QLabel("substituent name:")
substitute_layout.addWidget(sublabel, 0, 0, Qt.AlignVCenter)
self.subname = QLineEdit()
# self.subname.setText("Et")
sub_completer = NameCompleter(Substituent.list(), self.subname)
self.subname.setCompleter(sub_completer)
self.subname.setToolTip("name of substituent in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
substitute_layout.addWidget(self.subname, 0, 1, Qt.AlignVCenter)
open_sub_lib = QPushButton("from library...")
open_sub_lib.clicked.connect(self.open_sub_selector)
substitute_layout.addWidget(open_sub_lib, 0, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_sub = QCheckBox()
self.close_previous_sub.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_sub.setChecked(self.settings.modify)
self.close_previous_sub.stateChanged.connect(self.close_previous_change)
substitute_layout.addWidget(self.close_previous_sub, 1, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("relax substituent:"), 2, 0, 1, 1, Qt.AlignVCenter)
self.minimize = QCheckBox()
self.minimize.setToolTip("spin the added substituents to try to minimize the LJ potential energy")
self.minimize.setChecked(self.settings.minimize)
substitute_layout.addWidget(self.minimize, 2, 1, 1, 1, Qt.AlignTop)
substitute_layout.addWidget(QLabel("guess previous substituent:"), 3, 0, 1, 1, Qt.AlignVCenter)
self.guess_old = QCheckBox()
self.guess_old.setToolTip("checked: leave the longest connected fragment in the residue\nunchecked: previous substituent must be selected")
self.guess_old.setChecked(self.settings.guess)
self.guess_old.stateChanged.connect(lambda state, settings=self.settings: settings.__setattr__("guess", True if state == Qt.Checked else False))
substitute_layout.addWidget(self.guess_old, 3, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("new residue:"), 5, 0, 1, 1, Qt.AlignVCenter)
self.new_residue = QCheckBox()
self.new_residue.setToolTip("put the new substituent in its own residue instead\nof adding it to the residue of the old substituent")
self.new_residue.setChecked(self.settings.new_residue)
self.new_residue.stateChanged.connect(lambda state, settings=self.settings: settings.__setattr__("new_residue", True if state == Qt.Checked else False))
substitute_layout.addWidget(self.new_residue, 5, 1, 1, 2, Qt.AlignTop)
substitute_layout.addWidget(QLabel("use distance names:"), 4, 0, 1, 1, Qt.AlignVCenter)
self.use_greek = QCheckBox()
self.use_greek.setChecked(self.settings.use_greek)
self.use_greek.setToolTip("indicate distance from point of attachment with atom name")
substitute_layout.addWidget(self.use_greek, 4, 1, 1, 1, Qt.AlignTop)
substitute_layout.addWidget(QLabel("change residue name:"), 6, 0, 1, 1, Qt.AlignVCenter)
self.new_sub_name = QLineEdit()
self.new_sub_name.setToolTip("change name of modified residues")
self.new_sub_name.setPlaceholderText("leave blank to keep current")
substitute_layout.addWidget(self.new_sub_name, 6, 1, 1, 2, Qt.AlignTop)
substitute_button = QPushButton("substitute current selection")
substitute_button.clicked.connect(self.do_substitute)
substitute_layout.addWidget(substitute_button, 7, 0, 1, 3, Qt.AlignTop)
self.substitute_button = substitute_button
substitute_layout.setRowStretch(0, 0)
substitute_layout.setRowStretch(1, 0)
substitute_layout.setRowStretch(2, 0)
substitute_layout.setRowStretch(3, 0)
substitute_layout.setRowStretch(4, 0)
substitute_layout.setRowStretch(5, 0)
substitute_layout.setRowStretch(6, 0)
substitute_layout.setRowStretch(7, 1)
#map ligand
maplig_tab = QWidget()
maplig_layout = QGridLayout(maplig_tab)
liglabel = QLabel("ligand name:")
maplig_layout.addWidget(liglabel, 0, 0, Qt.AlignVCenter)
self.ligname = QLineEdit()
lig_completer = NameCompleter(Component.list(), self.ligname)
self.ligname.setCompleter(lig_completer)
self.ligname.setToolTip("name of ligand in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
maplig_layout.addWidget(self.ligname, 0, 1, Qt.AlignVCenter)
open_lig_lib = QPushButton("from library...")
open_lig_lib.clicked.connect(self.open_lig_selector)
maplig_layout.addWidget(open_lig_lib, 0, 2, Qt.AlignTop)
maplig_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_lig = QCheckBox()
self.close_previous_lig.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_lig.setChecked(self.settings.modify)
self.close_previous_lig.stateChanged.connect(self.close_previous_change)
maplig_layout.addWidget(self.close_previous_lig, 1, 1, 1, 2, Qt.AlignTop)
maplig_button = QPushButton("swap ligand with selected coordinating atoms")
maplig_button.clicked.connect(self.do_maplig)
maplig_layout.addWidget(maplig_button, 2, 0, 1, 3, Qt.AlignTop)
self.maplig_button = maplig_button
start_structure_button = QPushButton("place in:")
self.lig_model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_lig)
maplig_layout.addWidget(start_structure_button, 3, 0, 1, 1, Qt.AlignTop)
maplig_layout.addWidget(self.lig_model_selector, 3, 1, 1, 2, Qt.AlignTop)
maplig_layout.setRowStretch(0, 0)
maplig_layout.setRowStretch(1, 0)
maplig_layout.setRowStretch(2, 0)
maplig_layout.setRowStretch(3, 1)
#close ring
closering_tab = QWidget()
closering_layout = QGridLayout(closering_tab)
ringlabel = QLabel("ring name:")
closering_layout.addWidget(ringlabel, 0, 0, Qt.AlignVCenter)
self.ringname = QLineEdit()
ring_completer = NameCompleter(Ring.list(), self.ringname)
self.ringname.setCompleter(ring_completer)
self.ringname.setToolTip("name of ring in the AaronTools library or your personal library\nseparate names with commas and uncheck 'modify selected structure' to create several structures")
closering_layout.addWidget(self.ringname, 0, 1, Qt.AlignVCenter)
open_ring_lib = QPushButton("from library...")
open_ring_lib.clicked.connect(self.open_ring_selector)
closering_layout.addWidget(open_ring_lib, 0, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("modify selected structure:"), 1, 0, 1, 1, Qt.AlignVCenter)
self.close_previous_ring = QCheckBox()
self.close_previous_ring.setToolTip("checked: selected structure will be modified\nunchecked: new model will be created for the modified structure")
self.close_previous_ring.setChecked(self.settings.modify)
self.close_previous_ring.stateChanged.connect(self.close_previous_change)
closering_layout.addWidget(self.close_previous_ring, 1, 1, 1, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("try multiple:"), 2, 0, 1, 1, Qt.AlignVCenter)
self.minimize_ring = QCheckBox()
self.minimize_ring.setToolTip("try to use other versions of this ring in the library to find the one that fits best")
self.minimize_ring.setChecked(self.settings.minimize_ring)
closering_layout.addWidget(self.minimize_ring, 2, 1, 1, 2, Qt.AlignTop)
closering_layout.addWidget(QLabel("new residue name:"), 3, 0, 1, 1, Qt.AlignVCenter)
self.new_ring_name = QLineEdit()
self.new_ring_name.setToolTip("change name of modified residues")
self.new_ring_name.setPlaceholderText("leave blank to keep current")
closering_layout.addWidget(self.new_ring_name, 3, 1, 1, 2, Qt.AlignTop)
closering_button = QPushButton("put a ring on current selection")
closering_button.clicked.connect(self.do_fusering)
closering_layout.addWidget(closering_button, 4, 0, 1, 3, Qt.AlignTop)
self.closering_button = closering_button
start_structure_button = QPushButton("place in:")
self.ring_model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_ring)
closering_layout.addWidget(start_structure_button, 5, 0, 1, 1, Qt.AlignTop)
closering_layout.addWidget(self.ring_model_selector, 5, 1, 1, 2, Qt.AlignTop)
closering_layout.setRowStretch(0, 0)
closering_layout.setRowStretch(1, 0)
closering_layout.setRowStretch(2, 0)
closering_layout.setRowStretch(3, 0)
closering_layout.setRowStretch(4, 0)
closering_layout.setRowStretch(5, 1)
#change element
changeelement_tab = QWidget()
changeelement_layout = QFormLayout(changeelement_tab)
self.element = ElementButton("C", single_state=True)
self.element.clicked.connect(self.open_ptable)
changeelement_layout.addRow("element:", self.element)
self.vsepr = QComboBox()
self.vsepr.addItems([
"do not change", # 0
"linear (1 bond)", # 1
"linear (2 bonds)", # 2
"trigonal planar (2 bonds)", # 3
"tetrahedral (2 bonds)", # 4
"trigonal planar", # 5
"tetrahedral (3 bonds)", # 6
"T-shaped", # 7
"trigonal pyramidal", # 8
"tetrahedral", # 9
"sawhorse", #10
"seesaw", #11
"square planar", #12
"trigonal bipyramidal", #13
"square pyramidal", #14
"pentagonal", #15
"octahedral", #16
"hexagonal", #17
"trigonal prismatic", #18
"pentagonal pyramidal", #19
"capped octahedral", #20
"capped trigonal prismatic", #21
"heptagonal", #22
"hexagonal pyramidal", #23
"pentagonal bipyramidal", #24
"biaugmented trigonal prismatic", #25
"cubic", #26
"elongated trigonal bipyramidal", #27
"hexagonal bipyramidal", #28
"heptagonal pyramidal", #29
"octagonal", #30
"square antiprismatic", #31
"trigonal dodecahedral", #32
"capped cube", #33
"capped square antiprismatic", #34
"enneagonal", #35
"heptagonal bipyramidal", #36
"hula-hoop", #37
"triangular cupola", #38
"tridiminished icosahedral", #39
"muffin", #40
"octagonal pyramidal", #41
"tricapped trigonal prismatic", #42
])
self.vsepr.setCurrentIndex(9)
self.vsepr.insertSeparator(33)
self.vsepr.insertSeparator(25)
self.vsepr.insertSeparator(20)
self.vsepr.insertSeparator(16)
self.vsepr.insertSeparator(13)
self.vsepr.insertSeparator(8)
self.vsepr.insertSeparator(5)
self.vsepr.insertSeparator(2)
self.vsepr.insertSeparator(1)
self.vsepr.insertSeparator(0)
changeelement_layout.addRow("geometry:", self.vsepr)
self.change_bonds = QCheckBox()
self.change_bonds.setChecked(self.settings.change_bonds)
changeelement_layout.addRow("adjust bond lengths:", self.change_bonds)
change_element_button = QPushButton("change selected elements")
change_element_button.clicked.connect(self.do_change_element)
changeelement_layout.addRow(change_element_button)
self.change_element_button = change_element_button
start_structure_button = QPushButton("place in:")
self.model_selector = ModelComboBox(self.session, addNew=True)
start_structure_button.clicked.connect(self.do_new_atom)
changeelement_layout.addRow(start_structure_button, self.model_selector)
delete_atoms_button = QPushButton("delete selected atoms")
delete_atoms_button.clicked.connect(self.delete_atoms)
changeelement_layout.addRow(delete_atoms_button)
self.alchemy_tabs.addTab(substitute_tab, "substitute")
self.alchemy_tabs.addTab(maplig_tab, "swap ligand")
self.alchemy_tabs.addTab(closering_tab, "fuse ring")
self.alchemy_tabs.addTab(changeelement_tab, "change element")
layout.addWidget(self.alchemy_tabs)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def close_previous_change(self, state):
if state == Qt.Checked:
self.settings.modify = True
for checkbox in [self.close_previous_lig, self.close_previous_sub, self.close_previous_ring]:
checkbox.setChecked(True)
self.close_previous_bool = True
else:
self.settings.modify = False
for checkbox in [self.close_previous_lig, self.close_previous_sub, self.close_previous_ring]:
checkbox.setChecked(False)
self.close_previous_bool = False
def do_substitute(self):
subnames = self.subname.text()
new_name = self.new_sub_name.text()
use_attached = not self.guess_old.isChecked()
minimize = self.minimize.isChecked()
new_residue = self.new_residue.isChecked()
use_greek = self.use_greek.isChecked()
self.settings.minimize = minimize
self.settings.use_greek = use_greek
if len(new_name.strip()) > 0:
run(
self.session,
"substitute sel substituents %s newName %s guessAttachment %s modify %s minimize %s useRemoteness %s newResidue %s" %
(
subnames,
new_name,
not use_attached,
self.close_previous_bool,
minimize,
use_greek,
new_residue,
)
)
else:
run(
self.session,
"substitute sel substituents %s guessAttachment %s modify %s minimize %s useRemoteness %s newResidue %s" %
(
subnames,
not use_attached,
self.close_previous_bool,
minimize,
use_greek,
new_residue,
)
)
def open_sub_selector(self):
self.tool_window.create_child_window("select substituents", window_class=SubstituentSelection, textBox=self.subname)
def do_maplig(self):
lignames = self.ligname.text()
selection = selected_atoms(self.session)
if len(selection) < 1:
raise RuntimeWarning("nothing selected")
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [AtomSpec(atom.atomspec)]
else:
models[atom.structure].append(AtomSpec(atom.atomspec))
first_pass = True
new_structures = []
for ligname in lignames.split(','):
ligname = ligname.strip()
lig = Component(ligname)
for model in models:
if self.close_previous_bool and first_pass:
rescol = ResidueCollection(model)
elif self.close_previous_bool and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
rescol = ResidueCollection(model_copy)
for i, atom in enumerate(model.atoms):
rescol.atoms[i].atomspec = atom.atomspec
rescol.atoms[i].add_tag(atom.atomspec)
rescol.atoms[i].chix_atom = atom
target = rescol.find(models[model])
if len(target) % len(lig.key_atoms) == 0:
k = 0
ligands = []
while k != len(target):
res_lig = ResidueCollection(lig.copy(), comment=lig.comment)
res_lig.parse_comment()
res_lig = Component(res_lig, key_atoms = ",".join([str(k + 1) for k in res_lig.other["key_atoms"]]))
ligands.append(res_lig)
k += len(lig.key_atoms)
else:
raise RuntimeError("number of key atoms no not match: %i now, new ligand has %i" % (len(target), len(lig.key_atoms)))
rescol.map_ligand(ligands, target)
for center_atom in rescol.center:
center_atom.connected = set([])
for atom in rescol.atoms:
if atom not in rescol.center:
if center_atom.is_connected(atom):
atom.connected.add(center_atom)
center_atom.connected.add(atom)
if self.close_previous_bool:
rescol.update_chix(model)
else:
struc = rescol.get_chimera(self.session)
new_structures.append(struc)
first_pass = False
if not self.close_previous_bool:
self.session.models.add(new_structures)
def open_lig_selector(self):
self.tool_window.create_child_window("select ligands", window_class=LigandSelection, textBox=self.ligname)
def do_fusering(self):
ring_names = self.ringname.text()
new_name = self.new_ring_name.text()
minimize_ring = self.minimize_ring.isChecked()
self.settings.minimize_ring = minimize_ring
if len(new_name.strip()) > 0:
run(
self.session,
"fuseRing sel rings %s newName %s modify %s minimize %s" % (
ring_names,
new_name,
self.close_previous_bool,
minimize_ring,
)
)
else:
run(
self.session,
"fuseRing sel rings %s modify %s minimize %s" % (
ring_names,
self.close_previous_bool,
minimize_ring,
)
)
def open_ring_selector(self):
self.tool_window.create_child_window("select rings", window_class=RingSelection, textBox=self.ringname)
def open_ptable(self):
self.tool_window.create_child_window("select element", window_class=_PTable, button=self.element)
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 do_change_element(self):
element = self.element.text()
adjust_bonds = self.change_bonds.isChecked()
self.settings.change_bonds = adjust_bonds
vsepr = self.vsepr.currentText()
if vsepr == "do not change":
vsepr = False
elif vsepr == "linear (1 bond)":
vsepr = "linear 1"
goal = 1
elif vsepr == "linear (2 bonds)":
vsepr = "linear 2"
goal = 2
elif vsepr == "trigonal planar (2 bonds)":
vsepr = "bent 2 planar"
goal = 2
elif vsepr == "tetrahedral (2 bonds)":
vsepr = "bent 2 tetrahedral"
goal = 2
elif vsepr == "trigonal planar":
goal = 3
elif vsepr == "tetrahedral (3 bonds)":
vsepr = "bent 3 tetrahedral"
goal = 3
else:
goal = len(Atom.get_shape(vsepr)) - 1
sel = selected_atoms(self.session)
models, _ = guessAttachmentTargets(sel, self.session, allow_adjacent=False)
for model in models:
conv_res = list(models[model].keys())
for res in models[model]:
for target in models[model][res]:
for neighbor in target.neighbors:
if neighbor.residue not in conv_res:
conv_res.append(neighbor.residue)
for pbg in self.session.models.list(type=PseudobondGroup):
for pbond in pbg.pseudobonds:
if target in pbond.atoms and all(atom.structure is model for atom in pbond.atoms):
other_atom = pbond.other_atom(target)
if other_atom.residue not in conv_res:
conv_res.append(other_atom.residue)
rescol = ResidueCollection(model, convert_residues=conv_res)
for res in models[model]:
residue = [resi for resi in rescol.residues if resi.chix_residue is res][0]
for target in models[model][res]:
targ = rescol.find_exact(AtomSpec(target.atomspec))[0]
adjust_hydrogens = vsepr
if vsepr is not False:
cur_bonds = len(targ.connected)
change_Hs = goal - cur_bonds
adjust_hydrogens = (change_Hs, vsepr)
residue.change_element(targ,
element,
adjust_bonds=adjust_bonds,
adjust_hydrogens=adjust_hydrogens,
)
residue.update_chix(res)
def do_new_ring(self):
rings = self.ringname.text()
for ring in rings.split(","):
ring = ring.strip()
rescol = ResidueCollection(Ring(ring))
model = self.ring_model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
self.ring_model_selector.setCurrentIndex(self.ring_model_selector.count()-1)
else:
res = model.new_residue("new", "a", len(model.residues)+1)
rescol.residues[0].update_chix(res)
run(self.session, "select add %s" % " ".join([atom.atomspec for atom in res.atoms]))
def do_new_lig(self):
ligands = self.ligname.text()
for lig in ligands.split(","):
lig = lig.strip()
rescol = ResidueCollection(Component(lig))
model = self.lig_model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
self.lig_model_selector.setCurrentIndex(self.lig_model_selector.count()-1)
else:
res = model.new_residue("new", "a", len(model.residues)+1)
rescol.residues[0].update_chix(res)
run(self.session, "select add %s" % " ".join([atom.atomspec for atom in res.atoms]))
def do_new_atom(self):
element = self.element.text()
adjust_bonds = self.change_bonds.isChecked()
self.settings.change_bonds = adjust_bonds
vsepr = self.vsepr.currentText()
if vsepr == "do not change":
vsepr = False
elif vsepr == "linear (1 bond)":
vsepr = "linear 1"
elif vsepr == "linear (2 bonds)":
vsepr = "linear 2"
elif vsepr == "trigonal planar (2 bonds)":
vsepr = "bent 2 planar"
elif vsepr == "tetrahedral (2 bonds)":
vsepr = "bent 2 tetrahedral"
elif vsepr == "tetrahedral (3 bonds)":
vsepr = "bent 3 tetrahedral"
if vsepr:
atoms = Atom.get_shape(vsepr)
atoms[0].element = element
for atom in atoms[1:]:
atom.element = "H"
if adjust_bonds:
# this works b/c all atoms are 1 angstrom from the center
# just multiply by the distance we want
expected_dist = RADII[element] + RADII["H"]
for atom in atoms[1:]:
atom.coords *= expected_dist
for atom in atoms[1:]:
atoms[0].connected.add(atom)
atom.connected.add(atoms[0])
else:
atoms = [Atom(element=element, coords=np.zeros(3))]
rescol = ResidueCollection(atoms, name="new", refresh_connected=False)
model = self.model_selector.currentData()
if model is None:
chix = rescol.get_chimera(self.session)
self.session.models.add([chix])
apply_seqcrow_preset(chix, fallback="Ball-Stick-Endcap")
self.model_selector.setCurrentIndex(self.model_selector.count()-1)
else:
res = model.new_residue("new", "a", len(model.residues)+1)
rescol.residues[0].update_chix(res)
run(self.session, "select add %s" % " ".join([atom.atomspec for atom in res.atoms]))
def delete_atoms(self, *args):
atoms = selected_atoms(self.session)
for atom in atoms:
atom.delete()
def delete(self):
self.ring_model_selector.deleteLater()
self.lig_model_selector.deleteLater()
self.model_selector.deleteLater()
return super().delete()
def close(self):
self.ring_model_selector.deleteLater()
self.lig_model_selector.deleteLater()
self.model_selector.deleteLater()
return super().close()
class AaronTools_Library(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Browse-AaronTools-Libraries-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 = _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 "")