Description Usage Arguments Details Value Author(s) Examples
This function allows to obtain vector of entropies for one complete protein sequence from MSA (gaps introduced in alignment are omitted)
1 | get_prot_entropy(protein_index, score_list)
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protein_index |
Indices of given protein aminoacids in aligned sequence |
score_list |
A list of entropy scores calculated for MSA |
This function can be used on list of entropies or list with one element for one entropy score.
entropy |
A list where each element is a vector of entropy values provided in entropy_scores_list |
Alicja Pluciennik & Michal Stolarczyk
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data("structure")
data("alignment")
pdb_name = "1CQZ" #A string with path to PDB file
uniprot="P43914"
chain_identifier = "B"
structure_index=get_structures_idx(structure)
entropy_scores_list=list(Schneider_entropy = schneider_conservativity(alignment),
Escore_entropy = Escore_conservativity(alignment))
prot_entropy=get_prot_entropy(structure_index$proteinIndices, entropy_scores_list)
# In case of one entropy score
entropy_scores_list = list()
entropy_scores_list[[1]] = Schneider_entropy = schneider_conservativity(alignment)
prot_entropy=get_prot_entropy(structure_index$proteinIndices, entropy_scores_list)
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