class Variables(QWidget):
changed = Signal(object)
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.setMinimumWidth(500)
self.table = QTableWidget()
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.itemChanged.connect(self._item_changed)
self.table.currentItemChanged.connect(self._current_item_changed)
self.table.horizontalHeader().hide()
self.table.verticalHeader().hide()
self.table.setColumnCount(3)
self.table.horizontalHeader().resizeSection(0, 200)
self.table.horizontalHeader().resizeSection(1, 200)
self.table.horizontalHeader().resizeSection(2, 20)
self.new = QPushButton('New variable')
self.new.clicked.connect(self._new)
self.color = Color()
self.color.changed.connect(self._color_changed)
layout = QGridLayout(self)
layout.addWidget(self.table)
layout.addWidget(self.color)
layout.addWidget(self.new)
@property
def variables(self):
variables = dict()
for row_index in range(self.table.rowCount()):
name = self.table.item(row_index, 0).text()
value = self.table.item(row_index, 1).text()
if value.startswith('[') and value.endswith(']'):
value = eval(value) # OULA LA
variables[name] = value
return variables
@variables.setter
def variables(self, variables):
self.table.blockSignals(True)
self.table.clear()
for name, value in variables.items():
self._add_row(name, value)
self.table.blockSignals(False)
self.changed.emit(variables)
def _item_changed(self, item):
self.changed.emit(self.variables)
self._current_item_changed(item)
def _current_item_changed(self, item):
self.color.setEnabled(False)
if item is None or item.column() != 1:
return
text = item.text().strip()
if not (text.startswith('[') and text.endswith(']')):
return
r, g, b = [int(channel.strip()) for channel in text[1:-1].split(',')]
self.color.blockSignals(True)
self.color.set_rgb(r, g, b)
self.color.setEnabled(True)
self.color.blockSignals(False)
def _color_changed(self, r, g, b):
self.table.blockSignals(True)
self.table.currentItem().setText('[{}, {}, {}]'.format(r, g, b))
self.table.blockSignals(False)
self.changed.emit(self.variables)
def _add_row(self, name, value):
row = self.table.rowCount()
self.table.setRowCount(row + 1)
name = QTableWidgetItem(name)
value = QTableWidgetItem(str(value))
delete = QPushButton("X")
delete.name_item = name
delete.clicked.connect(self._delete)
self.table.blockSignals(True)
self.table.setItem(row, 0, name)
self.table.setItem(row, 1, value)
self.table.setCellWidget(row, 2, delete)
self.table.blockSignals(False)
def _new(self):
self._add_row('new_variable', '[255, 255, 255]')
self.changed.emit(self.variables)
def _delete(self):
name_item = self.sender().name_item
self.table.removeRow(name_item.row())
self.changed.emit(self.variables)
class LigandTable(QWidget):
def __init__(
self,
parent=None,
singleSelect=False,
maxDenticity=None,
include_substituents=False,
):
super().__init__(parent)
self._include_substituents = include_substituents
layout = QGridLayout(self)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(
['name', 'denticity', 'coordinating elements'])
self.add_ligands(maxDenticity)
for i in range(0, 3):
self.table.resizeColumnToContents(i)
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.setSortingEnabled(True)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
if singleSelect:
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.filterEdit = QLineEdit()
self.filterEdit.textChanged.connect(self.apply_filter)
self.filterEdit.setClearButtonEnabled(True)
self.filter_columns = QComboBox()
self.filter_columns.addItem("name")
self.filter_columns.addItem("denticity")
self.filter_columns.addItem("coordinating elements")
self.filter_columns.currentTextChanged.connect(
self.change_filter_method)
self.name_regex_option = QComboBox()
self.name_regex_option.addItem("case-insensitive")
self.name_regex_option.addItem("case-sensitive")
self.name_regex_option.currentTextChanged.connect(self.apply_filter)
self.name_regex_option.setVisible(
self.filter_columns.currentText() == "name")
self.coordinating_elements_method = QComboBox()
self.coordinating_elements_method.addItem("exactly")
self.coordinating_elements_method.addItem("at least")
self.coordinating_elements_method.currentTextChanged.connect(
self.apply_filter)
self.coordinating_elements_method.setVisible(
self.filter_columns.currentText() == "coordinating elements")
layout.addWidget(self.table, 0, 0, 1, 4)
layout.addWidget(QLabel("filter based on"), 1, 0)
layout.addWidget(self.filter_columns, 1, 1)
layout.addWidget(self.coordinating_elements_method, 1, 2)
layout.addWidget(self.name_regex_option, 1, 2)
layout.addWidget(self.filterEdit, 1, 3)
self.change_filter_method("name")
def add_ligands(self, maxDenticity=None):
from AaronTools.component import Component
names = []
for lib in [Component.AARON_LIBS, Component.BUILTIN]:
if not os.path.exists(lib):
continue
for lig in os.listdir(lib):
name, ext = os.path.splitext(lig)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
geom = Geometry(
os.path.join(lib, lig),
refresh_connected=False,
refresh_ranks=False,
)
key_atoms = [geom.atoms[i] for i in geom.other["key_atoms"]]
if maxDenticity and len(key_atoms) > maxDenticity:
continue
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
#this is an integer, so I need to initialize it then set the data
denticity = QTableWidgetItem()
denticity.setData(Qt.DisplayRole, len(key_atoms))
self.table.setItem(row, 1, denticity)
self.table.setItem(
row, 2,
QTableWidgetItem(", ".join(
sorted([atom.element for atom in key_atoms]))))
if self._include_substituents:
from AaronTools.substituent import Substituent
for lib in [Substituent.AARON_LIBS, Substituent.BUILTIN]:
if not os.path.exists(lib):
continue
for sub in os.listdir(lib):
name, ext = os.path.splitext(sub)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
geom = Geometry(
os.path.join(lib, sub),
refresh_connected=False,
refresh_ranks=False,
)
key_atoms = [geom.atoms[0]]
if maxDenticity and len(key_atoms) > maxDenticity:
continue
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
#this is an integer, so I need to initialize it then set the data
denticity = QTableWidgetItem()
denticity.setData(Qt.DisplayRole, len(key_atoms))
self.table.setItem(row, 1, denticity)
self.table.setItem(
row, 2,
QTableWidgetItem(", ".join(
sorted([atom.element for atom in key_atoms]))))
self.ligand_list = names
def change_filter_method(self, text):
if text == "coordinating elements":
self.filterEdit.setToolTip("comma and/or space delimited elements")
self.coordinating_elements_method.setVisible(True)
self.name_regex_option.setVisible(False)
elif text == "name":
self.filterEdit.setToolTip("name regex")
self.coordinating_elements_method.setVisible(False)
self.name_regex_option.setVisible(True)
elif text == "denticity":
self.filterEdit.setToolTip("number of key atoms")
self.coordinating_elements_method.setVisible(False)
self.name_regex_option.setVisible(False)
self.apply_filter()
def apply_filter(self, *args):
text = self.filterEdit.text()
if text:
if self.filter_columns.currentText() == "name":
m = QRegularExpression(text)
if m.isValid():
if self.name_regex_option.currentText(
) == "case-insensitive":
m.setPatternOptions(
QRegularExpression.CaseInsensitiveOption)
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
elif self.filter_columns.currentText() == "denticity":
if text.isdigit():
filter = lambda row_num: int(
self.table.item(row_num, 1).text()) == int(text)
else:
filter = lambda row: True
elif self.filter_columns.currentText() == "coordinating elements":
method = self.coordinating_elements_method.currentText()
def filter(row_num):
row_key_atoms = [
item.strip() for item in self.table.item(
row_num, 2).text().split(',')
]
search_atoms = []
for item in text.split():
for ele in item.split(','):
if ele.strip() != "":
search_atoms.append(ele)
if method == "exactly":
if all([row_key_atoms.count(element) == search_atoms.count(element) for element in set(search_atoms)]) and \
all([row_key_atoms.count(element) == search_atoms.count(element) for element in set(row_key_atoms)]):
return True
else:
return False
elif method == "at least":
if all([
row_key_atoms.count(element) >=
search_atoms.count(element)
for element in set(search_atoms)
]):
return True
else:
return False
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
class SubstituentTable(QWidget):
def __init__(self, parent=None, singleSelect=False):
super().__init__(parent)
layout = QGridLayout(self)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(
['name', 'conformers', 'conf. angle'])
self.add_subs()
for i in range(0, 3):
self.table.resizeColumnToContents(i)
self.table.horizontalHeader().setStretchLastSection(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Fixed)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.setSortingEnabled(True)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
if singleSelect:
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.filterEdit = QLineEdit()
self.filterEdit.textChanged.connect(self.apply_filter)
self.filterEdit.setClearButtonEnabled(True)
self.filter_columns = QComboBox()
self.filter_columns.addItem("name")
self.filter_columns.addItem("conformers")
self.filter_columns.addItem("conf. angle")
self.filter_columns.currentTextChanged.connect(
self.change_filter_method)
self.name_regex_option = QComboBox()
self.name_regex_option.addItem("case-insensitive")
self.name_regex_option.addItem("case-sensitive")
self.name_regex_option.currentTextChanged.connect(self.apply_filter)
self.name_regex_option.setVisible(
self.filter_columns.currentText() == "name")
layout.addWidget(self.table, 0, 0, 1, 4)
layout.addWidget(QLabel("filter based on"), 1, 0)
layout.addWidget(self.filter_columns, 1, 1)
layout.addWidget(self.name_regex_option, 1, 2)
layout.addWidget(self.filterEdit, 1, 3)
self.change_filter_method("name")
def change_filter_method(self, text):
if text == "name":
self.filterEdit.setToolTip("name regex")
self.name_regex_option.setVisible(True)
elif text == "conformers":
self.filterEdit.setToolTip("number of conformers")
self.name_regex_option.setVisible(False)
elif text == "conf. angle":
self.filterEdit.setToolTip("angle between conformers")
self.name_regex_option.setVisible(False)
self.apply_filter()
def apply_filter(self, *args):
text = self.filterEdit.text()
if text:
if self.filter_columns.currentText() == "name":
m = QRegularExpression(text)
if m.isValid():
if self.name_regex_option.currentText(
) == "case-insensitive":
m.setPatternOptions(
QRegularExpression.CaseInsensitiveOption)
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
elif self.filter_columns.currentText() == "conformers":
if text.isdigit():
filter = lambda row_num: int(
self.table.item(row_num, 1).text()) == int(text)
else:
filter = lambda row: True
elif self.filter_columns.currentText() == "conf. angle":
if text.isdigit():
filter = lambda row_num: int(
self.table.item(row_num, 2).text()) == int(text)
else:
filter = lambda row: True
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
def add_subs(self):
from AaronTools.substituent import Substituent
names = []
for lib in [Substituent.AARON_LIBS, Substituent.BUILTIN]:
if not os.path.exists(lib):
continue
for ring in os.listdir(lib):
name, ext = os.path.splitext(ring)
if not any(".%s" % x == ext for x in read_types):
continue
if name in names:
continue
names.append(name)
geom = Geometry(
os.path.join(lib, ring),
refresh_connected=False,
refresh_ranks=False,
)
conf_info = re.search(r"CF:(\d+),(\d+)", geom.comment)
row = self.table.rowCount()
self.table.insertRow(row)
self.table.setItem(row, 0, QTableWidgetItem(name))
#the next two items are integers - need to initialize then setData so they sort and display correctly
conf_num = QTableWidgetItem()
conf_num.setData(Qt.DisplayRole, conf_info.group(1))
self.table.setItem(row, 1, conf_num)
conf_angle = QTableWidgetItem()
conf_angle.setData(Qt.DisplayRole, conf_info.group(2))
self.table.setItem(row, 2, conf_angle)
self.substituent_list = names
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()