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

DesignFrame

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.