get_structures_entropy: Get entropy of amino acids (for region of interest) in given...

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function allows to get values of entropy/conservation for amino acids dispersed in sequence of given protein. It works well with a list of dispersed amino acids in one protein.

Usage

get_structures_entropy(structure_index, score_list)

Arguments

structure_index	A is a list of indices in alignment of protein and structures. Output output of get_structures_idx function
score_list	A list of entropies for whole alignment

Details

This function allows to obtain entropy (calculated on MSA) for dispersed amino acids in protein e.g. surface, binding site, tunnels etc. The input is a list of few structure indices in given protein sequence. Function calculates position of those in aligned sequence and returns a vector/matrix or a list of matrices with entropy values.

Value

A list of matrices. Rows are entropy scores, columns are

Examples

data("structure")
data("alignment")

#creating library uniprot - PDB
uniprot="P34914"
tunnel=create_structure_seq(structure,uniprot,alignment)
indices=get_structures_idx(structure)
protein_index = indices$proteinIndices
structure_index = indices$structureIndices
entropy_scores_list=list(Schneider_entropy = schneider_conservativity(alignment),
                                   Escore_entropy = Escore_conservativity(alignment))
structure_entropy=get_structures_entropy(structure_index, entropy_scores_list)

michalstolarczyk/BALCONY documentation built on May 7, 2019, 6:08 a.m.