Currently Available Plugins

Basic Management and Visualization

class nomenclator(tag, subnames)

Alters the configuration.name of a Case by adding subnames.

This affects on the creation of the subfolders where the rest of the Pipeline will be executed.

Note

On execution, the plugin will not append new subnames when those already exist. For example, if configuration.name is 1QYS_experiment1_naive and subnames=['experiment1', 'naive'], the final configuration.name will still be 1QYS_experiment1_naive and not 1QYS_experiment1_naive_experiment1_naive. This is to avoid folder recursion generation when re-running a previous Pipeline.

Caution

There are some keywords that cannot be used as a subname due to them generating their own first level subfolders. These keywords are architecture, connectivity, images and summary. Trying to add one of those terms as subname will generate a NodeDataError on check time.

To Developers

When developing a new plugin, if it is expected to create new first level subfolders, they should be listed in the class attribute nomenclator.RESERVED_KEYWORDS. See more on how to develop your own plugins.

Parameters:

subnames (Union[List[str], str]) – Subnames that will be added to the Case initial name.

Raises:

NodeOptionsError:  On initialization. If a reserved key is provided as a subname. NodeDataError:On check. If the required fields to be executed are not there.

FORM and Parametric

class corrector(tag, corrections=None)

Applies corrections to the placements of the secondary structures in a FORM.

This affects on the creation of the subfolders where the rest of the Pipeline will be executed.

Note

On execution, the plugin will not append new subnames when those already exist. For example, if configuration.name is 1QYS_experiment1_naive and subnames=['experiment1', 'naive'], the final configuration.name will still be 1QYS_experiment1_naive and not 1QYS_experiment1_naive_experiment1_naive. This is to avoid folder recursion generation when re-running a previous Pipeline.

Caution

There are some keywords that cannot be used as a subname due to them generating their own first level subfolders. These keywords are architecture, connectivity, images and summary. Trying to add one of those terms as subname will generate a NodeDataError on check time.

To Developers

When developing a new plugin, if it is expected to create new first level subfolders, they should be listed in the class attribute nomenclator.RESERVED_KEYWORDS. See more on how to develop your own plugins.

Parameters:

subnames – Subnames that will be added to the Case initial name.

Raises:

NodeOptionsError:  On initialization. If a reserved key is provided as a subname. NodeDataError:On check. If the required fields to be executed are not there.

Loop Building and Identification

Protein Backbone

Sequence Design

Analytics