Module matrix 

This module contains some constants/matrices for curvature calculation.

Enums

MatrixLookupError

Why a matrix lookup could not be performed.

RollType

Which ROLL matrix a curvature calculation should use.

Constants

ROLL_ACTIVE

The “activated” version of the ROLL matrix is used to calculate the roll angle in three nucleotides of DNA. This matrix differs from the simple matrix in that the angle values represent a more activated state of the nucleosomes bound to the DNA.

ROLL_SIMPLE

The simple version of the ROLL matrix is used to calculate the roll angle in three nucleotides of DNA.

TILT

The TILT matrix is not really used in the current implementation, but is included here for completeness. The values are all 0.0 for all combinations of nucleotide triplets.

TRIPLET_SIZE

The number of nucleotides in a triplet, which is also the number of dimensions in the nucleotide matrices used for triplet -> value lookup.

TWIST

The TWIST matrix is used to calculate the twist angle in three nucleotides of DNA. The values are all 0.598647428 for all combinations of nucleotide triplets.

Functions

lookup_by_index

Reads a value out of a matrix using indices already decoded by triplet_indices.

matrix_lookup

Looks up a value in a nucleotide matrix based on a triplet of nucleotides.

nuc_index

Maps a nucleotide to its index in a NucMatrix, in either case.

triplet_indices

Decodes a triplet into its three NucMatrix indices.

Type Aliases

NucMatrix

A type alias for a 3D matrix sized 4x4x4 of f64 values. The first dimension is the first nucleotide in a triplet, the second dimension is the second nucleotide in a triplet, and the third dimension is the third nucleotide in a triplet.