schrodinger.application.jaguar.gui.input_tab_widgets_pka module¶

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka(row=None)¶

Bases: schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry

PKA_ATOM_PROP = 's_m_pKa_atom'¶

PKA_VALID = 0¶

PKA_INVALID = 1¶

PKA_MISSING = 2¶

update(row)¶

Update this entry with information from the provided row

Parameters:	row (`schrodinger.project.ProjectRow`) – The project row

getStructureWithJagNames()¶

Return the entry structure with jaguar atom naming applied

Returns:	The structure with jaguar atom naming applied
Return type:	`schrodinger.structure.Structure`

reset()¶: Reset any user-specified settings

checkPkaAtom()¶

Make sure that a valid pKa atom(s) is specified

Returns:	PKA_VALID if all valid pKa atoms are specified, PKA_INVALID if any invalid pKa atom is specified, and PKA_MISSING is no pKa atom is specified.
Return type:	int

getPkaAtom()¶

Get the currently selected pKa atom(s)

Returns:	If the currently selected pKa atom(s) is valid, returns the list of atoms itself. Otherwise, returns None.
Return type:	list or NoneType

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka(entry_id, struc, charge, spin_mult, pka_atom)¶

Bases: tuple

charge¶: Alias for field number 2

entry_id¶: Alias for field number 0

pka_atom¶: Alias for field number 4

spin_mult¶: Alias for field number 3

struc¶: Alias for field number 1

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka¶

Bases: object

Column constants for the pKa selected entries table

HEADERS = ['ID', 'In', 'Entry Title', 'Charge', 'Spin Mult.', 'pKa Atom']¶

NUM_COLS = 6¶

ID = 0¶

INCLUSION = 1¶

TITLE = 2¶

CHARGE = 3¶

SPIN_MULT = 4¶

PKA_ATOM = 5¶

BASIS = -1¶

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.PickingModes¶

Bases: enum.Enum

An enumeration.

MANUAL = 1¶

AUTO = 2¶

SMARTS = 3¶

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka(parent)¶

Bases: schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel

The data model for the pKa selected entries table

Variables:	set_pka_marker (`PyQt5.QtCore.pyqtSignal`) – A signal emitted when a new pKa atom should be marked in the workspace. Emitted with two arguments: The entry id of the structure to be marked (str) The atom to be marked (`schrodinger.structure._StructureAtom`) projUpdated – A signal emitted when the project changes which should trigger a SMARTS search again if picking mode is SMARTS

COLUMN¶: alias of InputEntriesColumnsPka

set_pka_marker¶

projUpdated¶

ROW_CLASS¶: alias of ProjEntryPka

setPickingMode(mode)¶

Set the picking mode. This impacts what is shown in the pKa atom column.

Parameters:	mode (PickingModes) – the new picking mode

data(self, QModelIndex, role: int = Qt.DisplayRole) → Any¶

flags(index)¶

Enable or disable the pka column depending on whether manual editing is enabled or not

Parameters:	index (`QtCore.QModelIndex`) – The model index to get flags for.

setData(index, value, role=2)¶

Set data for the specified index. The spin multiplicity tool tip will be shown if an invalid spin multiplicity is set, or if a charge is set that renders the spin multiplicity invalid. (The tool tip explains that the default spin multiplicity is being used because the user-specifed value is invalid.)

Parameters:	index (`PyQt5.QtCore.QModelIndex`) – The index to modify value – The value to set role (int) – The role to set data for. Must be Qt.EditRole or setting will fail.
Returns:	True if setting succeeded. False if it failed.
Return type:	bool

updatePkaAtomsFromSmarts(smarts_models)¶

Update pKa atoms of entry rows based on patterns given by a list of SMARTS patterns and atom positions.

Parameters:	smarts_models (list(SmartsPageModel)) – a list of smarts patterns to search for in each structure. The list may be empty.

projectUpdated()¶: Update the table when the project is updated

getStructures()¶

Get a list of all structures loaded into the table (i.e. all structures selected in the project table) and the associated settings.

Returns:	A list of ProjEntryTuple objects
Return type:	list

checkPkaAtoms()¶

Make sure that all structure have a valid pKa atom selected

Returns:	A tuple of - A list of structures with invalid pKa atoms - A list of structures with no pKa atom
Return type:	tuple

addPkaMarkers(index, start_row, end_row)¶

Add pKa workspace atom markers for the specified rows

Parameters:	index – Not used, but present for Qt compatability start_row (int) – The first row to add a pKa marker to end_row (int) – The last row to add a pKa marker to

removePkaMarkers(index, start_row, end_row)¶

Remove the pKa workspace atom markers for the specified rows

Parameters:	index – Not used, but present for Qt compatibility start_row (int) – The first row to add a pKa marker to end_row (int) – The last row to add a pKa marker to

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka(parent)¶

Bases: schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView

The view for the pKa selected entries table

Variables:

set_pka_marker (PyQt5.QtCore.pyqtSignal) –

A signal emitted when a new pKa atom should be marked in the workspace. Emitted with two arguments:

The entry id of the structure to be marked (str)

List of atoms (schrodinger.structure._StructureAtom) to be marked

COLUMN¶: alias of InputEntriesColumnsPka

set_pka_marker¶

setEditablePkaAtomDelegate(editable)¶

Add the delegates to the pKa column

Parameters:	editable – Whether to set the editable default message delegate or to set the Qt default delegate

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel(default_value=None, **kwargs)¶

Bases: schrodinger.models.parameters.ParamModel

Model for a single page which contains the a single smarts string and single atom position index.

atom_pos¶

smarts¶

atom_posChanged¶

atom_posReplaced¶

smartsChanged¶

smartsReplaced¶

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage(*args, **kwargs)¶

Bases: schrodinger.models.mappers.MapperMixin, schrodinger.ui.qt.basewidgets.BaseWidget

model_class¶: alias of SmartsPageModel

initSetOptions()¶: Suggested subclass use: set instance variables, excluding layouts and subwidgets.

initSetUp()¶

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

updateSpinBoxLimits()¶: Update limits of atom position spin box to reflect the number of atoms in the SMARTS string

defineMappings()¶

Override this in the subclass to define mappings. Should return a list of tuples [(<target>, <param>)]. Most commonly, targets will be a basic widget, like QLineEdit or QComboBox, or a custom widget that inherits from MapperMixin or DefaultTargetMixin.

For more fine-grain custom control, instantiate a Target object, which allows custom setters, getters, and signals to be specified.

The param is an abstract param reference, e.g. MyModel.my_param.

Example:

def defineMappings(self):
    combo = self.style_combo
    return [(self.name_le, MyModel.name),
            (Target(combo,
                    getter=combo.currentText,
                    setter=combo.setCurrentText), MyModel.style),
            (self.coord_widget, MyModel.coord)]

getFromSelection()¶: Get smarts from selected atoms in workspace and add it to the current page

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector(*args, **kwargs)¶

Bases: schrodinger.ui.qt.basewidgets.BaseWidget

A popup widget that allows users to specify any number of SMARTS strings to specify pka atoms as well as an atom position which specifies the atom in the SMARTS

Variables:	smartsChanged – a signal emitted when the popup is closed. This signal passes the list of models for the SMARTS pages
Vartype:	schrodinger.Qt.QtCore.pyqtSignal

closed¶

initSetOptions()¶: Suggested subclass use: set instance variables, excluding layouts and subwidgets.

initSetUp()¶

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

addPage()¶: Add an additional page for specifying SMARTS

removeCurrentPage()¶: Remove the current page. If there was only one page before removing, add another after so there is always one page.

next()¶: Show next page of stacked widget

back()¶: Show previous page of stacked widget

updatePagination()¶: Enable or disable forward and back button based on current page index and number of pages and update label indicating current page

getModels()¶

Get the models for the Smarts Pages

Returns:	A list of the models
Return type:	list(SmartsPageModel)

closeEvent(ev)¶: Ensures proper handling of OK, Cancel, and [X] button clicks

class schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate(parent)¶

Bases: schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate, schrodinger.ui.qt.delegates.DefaultMessageDelegate

A delegate for selecting a pKa atom. The atom name can either be typed into the line edit or selected from the workspace. A tool tip containing instructions will appear when the editor is first open and any time the user hovers their mouse over the editor. If the user clicks on an atom from the wrong structure, the atom will be ignored and a tool tip warning will appear. Clicking on an atom does not close the editor so that the user can immediately pick a different atom if desired.

Variables:

set_pka_marker (PyQt5.QtCore.pyqtSignal) –

A signal emitted when a new pKa atom should be marked in the workspace. Emitted with two arguments:

The entry id of the structure to be marked (str)

List of atoms (schrodinger.structure._StructureAtom) to be marked

MAESTRO_STATUS_MESSAGE = 'Pick an atom to be treated as the pKa atom'¶

TOOL_TIP_INSTRUCTIONS = 'Click an atom in the workspace to\nset it as the pKa atom or type the\natom name here.'¶

TOOL_TIP_WRONG_EID = 'The atom you selected is not\npart of this structure.'¶

set_pka_marker¶

createEditor(self, QWidget, QStyleOptionViewItem, QModelIndex) → QWidget¶

setEditorData(self, QWidget, QModelIndex)¶

setModelData(self, QWidget, QAbstractItemModel, QModelIndex)¶

eventFilter(editor, event)¶

Make sure that the editor doesn’t close when the user clicks on another window since that will prevent the user from being able to click on an atom.

Parameters:	editor (`PyQt5.QtWidgets.QWidget`) – The pKa atom line edit event – A Qt event event – `PyQt5.QtCore.QEvent`
Note:	We don’t need to worry about the case where the user clicks on a different widget in the pKa panel after selecting an atom. Since the editor was the last widget with focus in the pKa panel, it will receive another FocusOut event when the other widget receives focus, and that FocusOut event will cause the editor to close.

schrodinger.application.jaguar.gui.input_tab_widgets_pka module¶

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