get_structures_idx {BALCONY}R Documentation

Get IDs of structure(s) elements from aligned sequences (MSA)

Description

This function allows to obtain positions in aligned sequences for analyzed structure (e.g. functionally related amino acids dispersed in sequence) based on sequence corresponding to the crystal structure.

Usage

get_structures_idx(structure)

Arguments

structure

The output of create_structure_seq() function

Details

It facilitates the management and oparation on the entropy values calculated for given MSA.

Value

Output is a list of two elements:

proteinIndices

A sorted vector of amino acids of analyzed sequence in MSA

strucureIndices

A list of sorted vectors of amino acids indices in aligned sequence for each structure

Author(s)

Alicja Pluciennik & Michal Stolarczyk

Examples

data("structure")

#creating library uniprot - PDB
lib=list(c("Q84HB8","4I19","4QA9"),
        c("P34913","4JNC"),
        c("P34914","1EK2","1CR6","1EK1","1CQZ"))
pdb_name = "1CQZ" #A string with path to PDB file
uniprot=find_seqid(pdb_name,lib)
tunnel=create_structure_seq(structure,uniprot,alignment)
structure_index=get_structures_idx(tunnel)

[Package BALCONY version 0.2.10 Index]