schrodinger.application.phase.phase_widgets module

class schrodinger.application.phase.phase_widgets.FeatureOptionsCombo(parent)

Bases: schrodinger.ui.qt.multi_combo_box.MultiComboBox

MultiComboBox containing feature presets. This currently includes feature equivalencies and use of alternate feature definitions.

FEATURE_EQUIV_PRESETS = {'Make acceptor and negative equivalent': 'AN', 'Make donor and positive equivalent': 'DP', 'Make hydrophobic and aromatic rings equivalent': 'HR'}

FEATURE_DEFINITION_PRESETS = ['Replace vectors with projected points (acceptors and donors)']

__init__(parent)

Parameters

• parent (PyQt5.QtWidgets.QWidget) – The Qt parent widget

• include_all_and_none (bool) – Whether “All” and “None” options should be added to the top of the item list.

• delimiter (str) – The delimiter to use when listing all selected items

addFeatureDefinitionPresets()

Adds the optional feature definition presets.

getSelectedFeatureEquivalencies()

Return a list of feature equivalencies that were checked/selected in the menu.

Returns

list of equivalencies to pass to PhpProject.saveFeatureEquiv

Return type

list of str

setADProjectedPointsChecked(checked)

Sets the selected state of the Replace acceptor/donor projected points preset item.

Parameters

checked (bool) – whether to select the projected point feature preset

useADProjectedPointsChecked()

Whether the Replace acceptor/donor projected points item is checked.

Returns

string indicating the number of selected feature presets

Return type

str

currentText(self) → str

class schrodinger.application.phase.phase_widgets.FeatureMatchCombo(parent)

Bases: schrodinger.ui.qt.multi_combo_box.MultiComboBox

This class defines special variant of a combo box used in Edit Feature dialog to define features that are allowed and forbidden to match. This combo box would contain a list of Phase features, which should be checkable. Line edit would show comma checked features as a string, which contains comma separated one letter feature names. In addition some items could be disabled.

__init__(parent)

Parameters

• parent (PyQt5.QtWidgets.QWidget) – The Qt parent widget

• include_all_and_none (bool) – Whether “All” and “None” options should be added to the top of the item list.

• delimiter (str) – The delimiter to use when listing all selected items

currentText()

Text to show in the combo menu, depending on the current selection. Over-rides the standard method of MultiComboBox.

setSelectedFeatures(features)

Select the given features in the combo menu.

Parameters

features (list of str) – List of one-letter feature types.

setChecked(feature, select)

This function sets feature item ‘checked’ state.

Parameters

• feature_type (str) – one letter feature type. ‘Enabled’ and ‘checked’ states will be set for this feature type.

• checked (bool) – boolean indicating whether item should be checked

setEnabled(feature_type, enabled)

This function sets feature item ‘enabled’ state.

Parameters

• feature_type (str) – one letter feature type. ‘Enabled’ and ‘checked’ states will be set for this feature type.

• enabled (bool) – boolean indicating whether item should be enabled

enableAllFeatures()

Set all items to be enabled. Except the features that were “forced” to be selected (they are selected and disabled).

resetAllFeatures()

Resets all item states to enabled and unchecked.

checkedFeatures()

This function returns a list that contains one letter types of checked features. Feature that is checked and disabled is the ‘current’ feature type. It should be the first item in the list.

Returns

list of checked features

Return type

list

class schrodinger.application.phase.phase_widgets.HypothesisRow(entry_id, hypo)

Bases: object

Data class that contains information about entry ids for a given Phase hypothesis.

__init__(entry_id, hypo)

Hypothesis data class.

Parameters

• entry_id (int) – hypothesis entry ID

• hypo (hypothesis.PhaseHypothesis) – hypothesis data object

class schrodinger.application.phase.phase_widgets.HypothesisColumns(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.TableColumns

HypoName = Column 0 (Hypothesis)

MinSites = Column 1 (Matches)

ExclVols = Column 2 (Excluded Volumes)

class schrodinger.application.phase.phase_widgets.HypothesisModel(parent=None)

Bases: schrodinger.ui.qt.table_helper.RowBasedTableModel

Hypotheses Model.

Column

alias of schrodinger.application.phase.phase_widgets.HypothesisColumns

ROW_CLASS

alias of schrodinger.application.phase.phase_widgets.HypothesisRow

getAllHypotheses()

Returns a list of all PhaseHypothesis objects in this model.

Returns

All hypotheses

Return type

list of hypothesis.PhaseHypothesis

getAllHypoIDs()

Return a list of entry IDs of all hypotheses in the table.

class schrodinger.application.phase.phase_widgets.HypothesesListWidget(parent)

Bases: PyQt6.QtWidgets.QWidget

Widget that shows list of Project Table hypotheses. It has a control that allows to select hypotheses for ‘included’ and ‘selected’ entries.

Variables

modelChanged (QtCore.pyqtSignal) – signal emitted when hypotheses are added to this widget or deleted.

ADD_HYPO_WS = 0

ADD_HYPO_PT = 1

COMBO_TEXT = 'Add Hypothesis...'

modelChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(parent)

Initialize hypotheses widget.

reset()

Reset hypotheses list model.

setDefaults()

Sets default widget options.

addHypoFromWorkspace()

Adds hypotheses from Workspace (included Project Table entries).

addHypoFromPT()

Adds hypotheses from the selected Project Table entries.

addHypothesisFromEntry(entry_id)

Adds a PT hypothesis to the list, given it’s entry ID.

Parameters

entry_id (int or str) – Project Table entry ID

updateHypothesisFromEntry(entry_id)

Updates hypothesis in the model (if it is found) from the PT hypothesis with a given entry ID.

getHypotheses()

Returns a list of all hypotheses in the table.

Returns

list of PhaseHypothesis objects.

Return type

list