rstoolbox.components.DesignFrame.structure_bits¶

DesignFrame.structure_bits(seqID, seqType='protein', cleanExtra=True, cleanUnused=False)¶

Create a bit-based SequenceFrame for secondary structure assignation.

Generates a SequenceFrame for the bits 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.

Bit calculation is performed as explained in http://www.genome.org/cgi/doi/10.1101/gr.849004 such as:

Rseq = Smax - Sobs = log2 N - (-sum(n=1,N):pn * log2 pn)

Where:

N is the total number of options (4: DNA/RNA; 20: PROTEIN).
pn is the observed frequency of the symbol n.

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