Description Usage Arguments Value Examples
This function facilitates the exclusion of low probability structural data from the downstream conservativity analysis, which helps to reduce the effect of non-consistent structural amino acids on the conservativity analysis of the structure of interest
1 | excl_low_prob_strcts(structure, threshold)
|
structure |
A structure object generated with |
threshold |
The threshold for the structural data exclusion |
structure_matrix |
A matrix of characters "S" and "N" marking on sequence the structural element; "S" - amino acid forms the analyzed structure, "N" - amino acid which does not form the structure. Number of rows of the matrix corresponds to the number of structures analyzed |
structure_numbers |
A vector containing the numbers of the amino acids in the sequence of interest (no gaps) |
structure_probabilities |
A matrix of numeric values: probabilities of corresponding to the structural information from first element of the output |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data("alignment")
structure_files = c(system.file("extdata", "T1_4JNC.structure", package = "BALCONY"),
system.file("extdata", "T2_4JNC.structure", package = "BALCONY"),
system.file("extdata", "T3_4JNC.structure", package = "BALCONY")
)
structure_list = read_structure(structure_files)
#creating library uniprot - PDB
lib=list(c("Q84HB8","4I19","4QA9"),
c("P34913","4JNC"),
c("P34914","1EK2","1CR6","1EK1","1CQZ"))
pdb_name = "4JNC"
uniprot=find_seqid(pdb_name,lib)
tunnel=create_structure_seq(structure_list,uniprot,alignment)
tunnel_excluded = excl_low_prob_strcts(tunnel, 0.5)
|
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