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¶

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¶: A pyqtSignal emitted by instances of the class.

__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