pwem.wizards.wizards module

This module is for Actual wizards to be able to be discovered from the Domain. wizard.py is left for wizard models and base classes.

class pwem.wizards.wizards.ChangeOriginSamplingWizard[source]

Bases: Wizard

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.ColorScaleWizardRMSD[source]: Bases: ColorScaleWizardBase

class pwem.wizards.wizards.GetStructureChainsWizard[source]

Bases: Wizard

Load an atomic structure, parse chain related information as name, number of residues, list of aminoacids (or other residues)

editionListOfChains(listOfChains)[source]

classmethod getModelsChainsStep(protocol)[source]: Returns (1) list with the information {“model”: %d, “chain”: “%s”, “residues”: %d} (modelsLength) (2) list with residues, position and chain (modelsFirstResidue)

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.ImportAcquisitionWizard[source]

Bases: EmWizard

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.ImportCoordinatesBoxSizeWizard[source]

Bases: Wizard

classmethod show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.ImportOriginVolumeWizard[source]

Bases: Wizard

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.PythonFormulaWizardX1[source]

Bases: Wizard

Assist in the creation of python formula to be evaluated. In Steps

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.PythonFormulaWizardX2[source]

Bases: Wizard

Assist in the creation of python formula to be evaluated. In Steps

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.PythonFormulaeWizard[source]

Bases: Wizard

Assist in the creation of python formula to be evaluated. In Steps

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.PythonTopRankWizard[source]

Bases: Wizard

Assist in the creation of python formula to be evaluated. In Steps

class pwem.wizards.wizards.SelectAttributeWizard[source]

Bases: VariableWizard

Wizard to select attributes stored in a scipion object or set

getFirstItem(form, inputParam)[source]

getInputAttributes(form, inputParam)[source]

getInputSet(form, inputParam)[source]

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.SelectChainWizard[source]

Bases: VariableWizard

Opens the input AtomStruct and allows you to select one of the present chains

editionListOfChains(listOfChains)[source]

classmethod getModelsChainsStep(protocol, inputObj)[source]: Returns (1) list with the information {“model”: %d, “chain”: “%s”, “residues”: %d} (modelsLength) (2) list with residues, position and chain (modelsFirstResidue)

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.

class pwem.wizards.wizards.SelectResidueWizard[source]

Bases: SelectChainWizard

editionListOfResidues(modelsFirstResidue, model, chain)[source]

getResidues(form, inputObj, chainStr)[source]

getSequence(finalResiduesList, idxs)[source]

show(form, *params)[source]

EMPTY METHOD. Needs to be implemented in your class. This will be called to show the wizard.

Parameters

form – the protocol form, given access to to all parameters. Some times the same wizard will modify several elements in the form.
params – a list of params to modify. Sometimes the wizard can be generic and can be used for different parameters in the same form.