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. |