schrodinger.application.matsci.clusterstructgui module¶

GUI elements to aid in pulling dimers or clusters of nearest neighbors from a larger structure.

class schrodinger.application.matsci.clusterstructgui.SpeciesCombo(label=None, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SLabeledComboBox

Combobox for showing species

__init__(label=None, **kwargs)¶

Create a SpeciesCombo instance

Parameters: label (str) – The label for the combobox

setCurrentSpecies(species)¶

Fill the combo with the list of current species

Parameters: species (dict) – Keys are unique SMILES strings, values are SpeciesData objects for the species with that SMILES string.

currentSpecies()¶

Return the currently selected species

Return type: clusterstruct.SpeciesData
Returns: The currently selected species

getSampleMolNumber()¶

Get a sample molecule number for the current species

Return type: int
Returns: a sample molecule number for the current species

class schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector(label='Limit active molecules to those of type:', command=None, find_species_fn=None, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SCheckBoxWithSubWidget

Checkbox and combo that allows the user to select a species. The enabled state of the combobox is controlled by the checkbox.

species_changed¶

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__(label='Limit active molecules to those of type:', command=None, find_species_fn=None, **kwargs)¶

Create a Monomer SpeciesSelector instance

Parameters

label (str) – The text between the checkbox and combobox
command (callable) – The slot to connect to the species_changed signal
find_species_fn (function) – Function that is used to create species

All other keyword args are passed to the SCheckBoxWithSubWidget class

createSubWidgets()¶

Create the subwidgets the checkbox controls

For this class, it is only the species type combobox

currentSpecies()¶

Return the currently selected species

Return type: clusterstruct.SpeciesData
Returns: The currently selected species

speciesChanged()¶: React to a new species being selected

hasSpecies()¶

Check if any species have been loaded

Return type: bool
Returns: True of any species has been loaded, False if not

clear()¶: Clear out the species combo

loadSpecies(structs)¶

Find all the species in the given structures and load them into the species type combobox

Parameters: structs (list(structure.Structure)) – The structures to find the species in
Return type: list(clusterstruct.SpeciesData)
Returns: Each item of the list is the data for a species found

setCurrentSpecies(species)¶

Fill the species combo with the list of current species

Parameters: species (dict) – Keys are unique SMILES strings, values are SpeciesData objects for the species with that SMILES string.

reset()¶: Reset the widget, including clearing the species type combo

getNumberOfType()¶

Get the number of members of the current species

Return type: int
Returns: The number of members of the current species

class schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector(label='Limit dimers to only those that contain:', command=None, **kwargs)¶

Bases: schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector

Checkbox and combo that allows the user to select a species for the purpose of selecting dimers with or without the given species. The enabled state of the combobox is controlled by the checkbox.

criterion_changed¶

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__(label='Limit dimers to only those that contain:', command=None, **kwargs)¶

Create a DimerSpeciesSelector instance

Parameters

label (str) – The text between the checkbox and combobox
command (callable) – The slot to connect to the species_changed and criterion_changed signals

See parent class for additional documentation

createSubWidgets()¶

Create the subwidgets the checkbox controls

For this class, it is an amount criterion combobox and the species type combobox

currentCriterion()¶

Return the current amount criterion

Return type: str
Returns: The desired amount of the species. Will be one of the items from the CRITERIA list

criterionChanged()¶: React to a change in the amount criterion

reset()¶: Reset the widgets

applyToDimers(dimers)¶

Apply the current settings to a list of dimers, marking them as meeting the criteria or not. If the controlling checkbox is unchecked, all dimers will be marked as meeting the criteria.

Parameters: dimers (list) – A list of Dimer objects. Each dimer will have its meets_species_criterion property set based on the results of the Dimer.evaluateSpeciesCriterion method.

schrodinger.application.matsci.clusterstructgui.count_species_in_cms(model, *, sanitize=True, include_stereo=True)¶

Enumerates and counts the species in a Desmond system.

Parameters

model (cms.Cms) – The model you want to count the species for
sanitize (bool) – Whether RDKit sanitization should be performed when identifying unique species. This option is not applicable for coarsegrained structures.
include_stereo (bool) – Whether the stereochemistry of the structure should be considered when identifying unique species. Setting to False can speed this up substantially.

Return type

dict

Returns

Dictionary whose keys are the display formulae of the species and whose values are the number of molecules of that species present in the system.

schrodinger.application.matsci.clusterstructgui.get_species_display_names_from_cms(model, *, sanitize=True, include_stereo=True)¶

Gets formatted chemical formulae for each species from a Desmond system. They are formatted for printing in a GUI.

Parameters

model (cms.Cms) – The model you want to get the formulae for
sanitize (bool) – Whether RDKit sanitization should be performed when identifying unique species to get chemical formulae for. This option is not applicable for coarsegrained structures.
include_stereo (bool) – Whether the stereochemistry of the structure should be considered when identifying unique species to analyze. Setting to False can speed this up substantially.

Return type

dict(str=clusterstruct.SpeciesData)

Returns

Keys are the names of each species found in the system, and values are their corresponding SpeciesData objects.