fuzzy2ct: Convert hydrogen bond data from RSIM 3D RNA structure into 2D...

In jpbida/RRNA: Secondary Structure Plotting for RNA

Convert hydrogen bond data from RSIM 3D RNA structure into 2D secondary structures

Description

Given hydrogen bond data generated from a pdb file using the RSIM 3D structure prediction program, generate a bracket notation that does not contain pseudoknots that can be used as input for the RNAPlot function.

Usage

fuzzy2ct(dat)

Arguments

dat

Dataframe with columns containing the data pdb - name of pdb file model - model number in the file pos1 - nucleotide 1 position in hydrogen bonded pair pos2 - nucleotide 2 position in hydrogen bonded pair face1 - face of NT 1 participating in the bond face2 - face of NT 2 participating in the bond h-bonds - probility assigned to number of hydrogen bonds

Value

returns secondary structure in bracket notation for the 3D structure

Author(s)

JP Bida

jpbida/RRNA documentation built on April 28, 2024, 1:27 p.m.