get_structures_idx: Get IDs of structure(s) elements from aligned sequences (MSA)
In BALCONY: Better ALignment CONsensus analYsis

Description Usage Arguments Details Value Author(s) Examples

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.

1	get_structures_idx(structure)

structure

The output of create_structure_seq() function

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

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

Alicja Pluciennik & Michal Stolarczyk

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)