rstoolbox.components.DesignSeries¶

class rstoolbox.components.DesignSeries(*args, **kwargs)¶

The DesignSeries extends the Series adding some functionalities in order to improve its usability in the analysis of a single design decoys.

It is generated as the reduced dimensionality version of the DesignFrame.

See also

Getters

`get_id`()	Return identifier data for the design(s).
`get_available_sequences`()	List which sequence identifiers are available in the data container
`get_sequence`(seqID[, key_residues])	Return the sequence data for `seqID` available in the container.
`get_available_structures`()	List which structure identifiers are available in the data container
`get_structure`(seqID[, key_residues])	Return the structure data for `seqID` available in the container.
`get_available_structure_predictions`()	List which structure prediction identifiers are available in the data container.
`get_structure_prediction`(seqID[, key_residues])	Return the structure prediction(s) data.
`get_sequential_data`(query, seqID)	Provides data on the requested query.
`get_dihedrals`(seqID[, key_residues])	Return the dihedrals data for `phi-psi` available in the container.
`get_phi`(seqID[, key_residues])	Return the phi angle for `seqID` available in the container.
`get_psi`(seqID[, key_residues])	Return the psi angle for `seqID` available in the container.
`get_available_labels`()	List which slabels are available in the data container.
`get_label`(label[, seqID])	Return the content(s) of the labels of interest as a `Selection` for a given sequece.

Reference Data

`has_reference_sequence`(seqID)	Checks if there is a `reference_sequence` for `sequID`.
`add_reference_sequence`(seqID, sequence)	Add a `reference_sequence` attached to chain `seqID`.
`get_reference_sequence`(seqID[, key_residues])	Get the `reference_sequence` attached to chain `seqID`.
`has_reference_structure`(seqID)	Checks if there is a `reference_structure` for `seqID`.
`add_reference_structure`(seqID, structure)	Add a `reference_structure` attached to chain `seqID`.
`get_reference_structure`(seqID[, key_residues])	Get the `reference_structure` attached to chain `seqID`.
`add_reference_shift`(seqID, shift[, shift_labels])	Add a `reference_shift` attached to a chain `seqID`.
`get_reference_shift`(seqID)	Get a `reference_shift` attached to a particular `seqID`.
`get_available_references`()	List which decoy chain identifiers have some kind of reference data.
`add_reference`(seqID[, sequence, structure, …])	Single access to `add_reference_sequence()`, `add_reference_structure()` and `add_reference_shift()`.
`transfer_reference`(df)	Transfer reference data from one container to another.
`delete_reference`(seqID[, shift_labels])	Remove all reference data regarding a particular seqID.

Source Files

`add_source_file`(file)	Adds a `source_file` to the `DesignFrame`.
`add_source_files`(files)	Adds `source_file` to the `DesignFrame`.
`get_source_files`()	Get `source_file` stored in the data container.
`has_source_files`()	Checks if there are source files added.
`replace_source_files`(files)	Replaces `source_file` of the `DesignFrame`.

Mutation Methods

`identify_mutants`(seqID)	Assess mutations of each decoy for sequence `seqID` againt the `reference_sequence`.
`get_identified_mutants`()	List for which sequence identifiers mutants have been calculated.
`get_mutation_count`(seqID)	Return the number of mutantion positions data for seqID available in the container.
`get_mutation_positions`(seqID)	Return the mutantion positions data for seqID available in the container.
`get_mutations`(seqID)	Return the mutantions data for `seqID` available in the container.
`generate_mutant_variants`(seqID, mutations[, …])	Expands selected decoy sequences generating all the provided mutant combinations.
`generate_mutants_from_matrix`(seqID, matrix, …)	From a provided positional frequency matrix, generates `count` random variants.
`generate_wt_reversions`(seqID[, key_residues])	Generate all variant that revert decoy sequences to the `reference_sequence`.
`make_resfile`(seqID, header, filename[, write])	Generate a Rosetta resfile to match the design’s sequence assuming the `reference_sequence` as the starting point.
`apply_resfile`(seqID, filename[, rscript, …])	Apply a generated Rosetta resfile to the decoy.
`score_by_pssm`(seqID, matrix)	Score sequences according to a provided PSSM matrix.
`view_mutants_alignment`(seqID[, …])	Generates a pretty representation alignment of the mutations in Jupyter Notebooks.