rstoolbox.components.DesignFrame.structure_frequencies¶

DesignFrame.structure_frequencies(seqID, seqType='protein', cleanExtra=True, cleanUnused=-1)¶

Create a frequency-based SequenceFrame for secondary structure assignation.

Generates a SequenceFrame for the frequencies of the secondary structure in the designFrame with seqID identifier. If there is a reference_structure for this seqID, it will also be attached to the SequenceFrame.

All letters in the secondary structure will be capitalized. All symbols that do not belong to string.ascii_uppercase will be transformed to “*” as this is the symbol recognized by the substitution matrices.

Parameters:

Parameters:	seqID (str) – Identifier of the sequence of interest. seqType (str) – Type of sequence: `protein`, `dna`, `rna`. cleanExtra (bool) – Remove from the class:.SequenceFrame the non-regular amino/nucleic acids if they are empty for all positions. cleanUnused (int) – Remove from the class:.SequenceFrame the regular amino/nucleic acids if they frequency is equal or under the value . Default is -1, so nothing is deleted.
Returns:	`SequenceFrame`

seqID (str) – Identifier of the sequence of interest.
seqType (str) – Type of sequence: protein, dna, rna.
cleanExtra (bool) – Remove from the class:.SequenceFrame the non-regular amino/nucleic acids if they are empty for all positions.
cleanUnused (int) – Remove from the class:.SequenceFrame the regular amino/nucleic acids if they frequency is equal or under the value . Default is -1, so nothing is deleted.

Returns:

SequenceFrame