RNADiscrepancy.measures

Module Contents

Functions

c1prime_distance_difference

Returns the difference in distance between the C1’ atoms (connecting sugar to residue) in the two pairs always positive

c1prime_translation

Here we have to do things in regards to the _left and _right side symmetricaly

isodiscrepancy

Return IDI between pairs (nt1_left, nt1_right) and (nt2_left, nt2_right) it assumes the orientation is to align nt1_left with nt2_left / nt1_right with nt2_right

discrepancy

Compute the discrepancy between set of nucleotides between the two modules.

API

RNADiscrepancy.measures.c1prime_distance_difference(pair1, pair2)

Returns the difference in distance between the C1’ atoms (connecting sugar to residue) in the two pairs always positive

RNADiscrepancy.measures.c1prime_translation(pair1, pair2)

Here we have to do things in regards to the _left and _right side symmetricaly

1’. Use N1/N9 of their reference as (0, 0) 2’. Rotate to align the first base to the reference (and apply rotation to the pair)

RNADiscrepancy.measures.isodiscrepancy(pair1, pair2)

Return IDI between pairs (nt1_left, nt1_right) and (nt2_left, nt2_right) it assumes the orientation is to align nt1_left with nt2_left / nt1_right with nt2_right

we follow https://doi.org/10.1093/nar/gkp011

  1. delta c1’ distances

  2. align on one N1/N9 and see other C1’ translation distance

  3. rotation in plane to orient same second base in relation to first

RNADiscrepancy.measures.discrepancy(module1: collections.abc.Sequence[RNADiscrepancy.rna.Nucleotide], module2: collections.abc.Sequence[RNADiscrepancy.rna.Nucleotide]) → float

Compute the discrepancy between set of nucleotides between the two modules.

We follow the steps in https://doi.org/10.1007/s00285-007-0110-x

Args:

module1 (Sequence[Nucleotide]): List of nucleotides of the first module module2 (Sequence[Nucleotide]): List of nucleotides of the second module

Returns:

The discrepancy value (float) when aligning pairwise atoms between the modules