R/sysdata.R
In Chebuu/fastalign:
#' #' @title Dataset `Z18_CBDAS`
#' #' @details Fig. 6B (Zirpel et al., 2018)
#' #' #' @format (Names: dact = "Percent change Kcat compared to WT", res1a = "WT residue", pos1 = "Homologous position in WT", res1b = "Mutant residue").
#' #' @source https://doi.org/10.1016/j.jbiotec.2018.07.031
#' Z18_CBDAS <- data.frame(
#' actv =
#' c(2.84,1.33,-0.99,-1.00,3.37,-0.75,-0.80,-0.84,-0.45,-0.35,4.14,3.63,2.17),
#'
#' res1a = c( 'S', 'S', 'S', 'S', 'A', 'A', 'L', 'A', 'I', 'I', 'A', 'S', 'S'),
#' pos1 = c( 116, 118, 116, 116, 414, 414, 414, 414, 445, 445, 414, 116, 116),
#' res1b = c( 'A', 'G', 'V', 'L', 'V', 'T', 'L', 'I', 'T', 'T', 'V', 'A', 'A'),
#'
#'
#' res2a = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , 'C', 'A', 'A', 'A'),
#' pos2 = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , 446, 46, 46, 414),
#' res2b = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , 'A', 'V', 'V', 'V'),
#'
#' res3a = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , 'T', 'T', NA ),
#' pos3 = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , 47, 47, NA ),
#' res3b = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , 'A', 'A', NA )
#' )
#'
#' usethis::use_data(Z18_CBDAS, overwrite = TRUE)
#'
#' #' @title Dataset `Z18_THCAS`
#' #' @details Fig. 6C Zirpel et al., 2018
#' #' @format (Names: dact = "Percent change Kcat compared to WT", res1a = "WT residue", pos1 = "Homologous position in WT", res1b = "Mutant residue").
#' #' @source https://doi.org/10.1016/j.jbiotec.2018.07.031
#' Z18_THCAS <- data.frame(
#' actv =
#' c(-1.00,-0.12,0.17 ,-0.70,-0.90,-0.91,-0.96,-0.31,-0.46,-0.55,-1.00,-0.93,-0.69,-0.97,-1.00,-1.00,-0.15,-0.58,-1.00,-0.95,-0.90,-0.87),
#'
#' res1a = c( NA, 'K', 'Q', 'T', 'S', 'I', 'V', 'V', 'V', 'V', 'V', 'A', 'A', 'A', 'A', 'A', 'E', 'Y', 'Y', 'H', 'R', 'R'),
#' pos1 = c( 12, 377, 69 , 446, 382, 257, 415, 415, 415, 415, 415, 116, 116, 116, 116, 116, 442, 417, 484, 292, 110, 108),
#' res1b = c( NA, 'Q', 'H', 'I', 'K', 'M', 'A', 'I', 'L', 'T', 'N', 'S', 'G', 'V', 'T', 'Y', 'Q', 'F', 'F', 'A', 'A', 'A'),
#'
#' res2a = c( NA, 'K', NA , 'A', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' pos2 = c( NA, 378, NA , 447, NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' res2b = c( NA, 'N', NA , 'C', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#'
#' res3a = c( NA, 'T', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' pos3 = c( NA, 379, NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' res3b = c( NA, 'G', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA )
#' )
#'
#' usethis::use_data(Z18_THCAS, overwrite = TRUE)
#'
#' Z18 <- list(
#' THCAS = Z18_THCAS,
#' CBDAS = Z18_CBDAS
#' )
#'
#' usethis::use_data(Z18, internal = T, overwrite = TRUE)
#'
#' #' @name ANNOTATIONS_Q8GTB6
#' #' @title Dataset: \code{ANNOTATIONS_Q8GTB6}
#' #' @description
#' #' @format A list
#' #' @source
#' #'\url{https://pfam.xfam.org/structure/3vte#tabview=tab0}
#' ANNOTATIONS_Q8GTB6 <- list(
#' 'Sites' = list(
#' 'FAD-binding' = list(
#' 'H292' = list(
#' type = 'Covalent',
#' label = 'C-N linkage',
#' description = 'FAD-binding site',
#' ranges = IRanges::IRangesList(
#' coordinates = IRanges(292)
#' )
#' ),
#' 'C417' = list(
#' type = 'Covalent',
#' label = 'C-S linkage',
#' description = 'FAD-binding site',
#' ranges = IRanges::IRangesList(
#' coordinates = IRanges(417)
#' )
#' )
#' ),
#' 'Active' = list(
#' 'Y484' = list(
#' type = 'Catalytic',
#' label = 'Active site',
#' description = 'Catalytic base Tyr484',
#' ranges = IRanges::IRangesList(
#' 'Y484' = IRanges::IRanges(484)
#' )
#' )
#' ),
#' 'Glycosylation' = list(
#' GlNAc = list(
#' type = 'Covalent',
#' label = 'GlcNAc',
#' description = 'N-Acetyl Glucosamine',
#' ranges = IRanges::IRangesList(
#' IRanges::IRanges(65)
#' IRanges::IRanges(89)
#' IRanges::IRanges(168)
#' IRanges::IRanges(297)
#' IRanges::IRanges(305)
#' IRanges::IRanges(329)
#' IRanges::IRanges(467)
#' IRanges::IRanges(499)
#' )
#' )
#' )
#' ),
#' 'Tertiary' = list(
#' 'Disulfide' = list(
#' S99 = list(
#' type = 'Covalent',
#' description = 'Disulfide bond S37-S99',
#' label = 'Disulfide bond',
#' ranges = IRanges::IRanges(37, 99, 2)
#' )
#' ),
#' 'Crosslink' = list(
#' H114 = list(
#' type = 'Covalent',
#' label = 'H114-[FAD]-C176',
#' description = 'Crosslink H114-[FAD]-C176',
#' ranges = IRanges::IRanges(114, 176, 2)
#' )
#' )
#' ),
#' 'Domains' = list(
#' 'FAD-binding' = list(
#' type = 'Covalent',
#' label = 'FAD-binding 80-219',
#' desciption = 'FAD-binding domain',
#' ranges = IRanges::IRanges(81, 219)
#' ),
#' 'BBE-domain' = list(
#' type = 'Covalent',
#' label = 'BBE-domain 480-438',
#' description = 'Berberine bidge-like domain',
#' ranges = IRanges::IRanges(480, 438)
#' ),
#' 'Signal-peptide' = list(
#' type = 'Covalent',
#' label = 'Signal peptide 1-28',
#' description = 'Signal peptide',
#' ranges = IRanges::IRanges(1, 28)
#' ),
#' ),
#' 'Families' = list(
#' 'FAD-binding' = list(
#' type = 'PCMH-type',
#' label = 'FAD-binding',
#' description = 'FAD-binding (PCMH family)',
#' ranges = IRanges::IRanges(77, 251)
#' )
#' ),
#' # 'Composition' = list(
#' # 'Bias' = list(
#' # type = 'Bias',
#' # label = 'Compositional bias 77-251',
#' # description = 'Compositional bias 77-251',
#' # ranges = IRanges::IRanges(77, 251)
#' # )
#' # ),
#' # 'Chains' = list(
#' # 'A' = list(
#' # type = 'Main',
#' # label = 'Chain-A',
#' # dscription = NULL,
#' # ranges = IRanges::IRanges(29, 545)
#' # )
#' # ),
#' 'Mutations' = list(
#' H92A = list(
#' effect = FALSE,
#' magnitude = '0',
#' desciption = 'No effect',
#' ranges = IRanges::IRanges(92)
#' ),
#' R108A = list(
#' effect = 'Kcat',
#' magnitude = '---',
#' desciption = 'Strongly reduced catalytic activity',
#' ranges = IRanges::IRanges(108)
#' ),
#' R110A = list(
#' effect = 'Kcat',
#' magnitude = '----',
#' desciption = 'Strongly reduced catalytic activity',
#' ranges = IRanges::IRanges(110)
#' ),
#' H114A = list(
#' effect = 'FAD',
#' magnitude = '-----',
#' desciption = 'Loss of FAD binding and loss of catalytic activity. 2 Publications',
#' ranges = IRanges::IRanges(114)
#' ),
#' H208A = list(
#' effect = FALSE,
#' magnitude = '0',
#' desciption = 'No effect',
#' ranges = IRanges::IRanges(208)
#' ),
#' H292A = list(
#' effect = 'Kcat',
#' magnitude = '----',
#' desciption = 'Strongly reduced catalytic activity',
#' ranges = IRanges::IRanges(292)
#' ),
#' Y417F = list(
#' effect = 'Kcat',
#' magnitude = '---',
#' desciption = 'Reduced catalytic activity',
#' ranges = IRanges::IRanges(417)
#' ),
#' E442Q = list(
#' effect = 'Kcat',
#' magnitude = '-',
#' desciption = 'Slightly reduced catalytic activity',
#' ranges = IRanges::IRanges(442)
#' ),
#' Y484F = list(
#' effect = 'Kcat',
#' magnitude = '-----',
#' desciption = 'Loss of catalytic activity',
#' ranges = IRanges::IRanges(484)
#' )
#' )
#' )
#' usethis::use_data(ANNOTATIONS_Q8GTB6, overwrite = TRUE)
#'
#' #' @name KINETICS
#' #' @title Dataset: \code{KINETICS_Q8GTB6}
#' #' @description
#' #' @format A list
#' #' @source
#' #'\url{https://pfam.xfam.org/structure/3vte#tabview=tab0}
#' KINETICS_Q8GTB6 <- list(
#' Kcat = list(
#' CBGA = list(
#' value = '0.30',
#' units = '1/sec',
#' label = 'Kcat[CBGA] = 0.30 sec(-1)',
#' description = 'Kcat value for CBGA substrate 0.30 sec(-1)',
#' references = c(NULL)
#' )
#' ),
#' Km = list(
#' CBGA = list(
#' value = c('134', '254'),
#' units = 'µM',
#' label = 'Km[CBGA] = (134 µM, 254 µM)',
#' description = 'Km values for CBGA (134 µM, 254 µM)',
#' references = c(
#' 'https://doi.org/10.1074/jbc.M403693200',
#' 'https://doi.org/10.1021/ja00143a024'
#' )
#' )
#' ),
#' Vmax = list(
#' CBGA = list(
#' value = c('0.36', '2.68'),
#' units = 'nmol/sec/mg',
#' label = 'Vmax[CBGA] = 2.68 nmol/sec/mg',
#' desciption = 'Vmax values for CBGA substrate (0.36 nmol/sec/mg, 2.68 nmol/sec/mg)',
#' references = c(
#' 'https://doi.org/10.1074/jbc.M403693200',
#' 'https://doi.org/10.1021/ja00143a024'
#' )
#' ),
#' ),
#' pH = list(
#' CBGA = list(
#' value = c('5.5', '6.0'),
#' units = 'pH',
#' label = 'Optimum pH 5.5-6.0',
#' desciption = 'Optimum catalytic pH for CBGA substrate between 5.5-6.0',
#' references = c(
#' 'https://doi.org/10.1074/jbc.M403693200',
#' 'https://doi.org/10.1021/ja00143a024'
#' )
#' )
#' ),
#' )
#' usethis::use_data(KINETICS_Q8GTB6, overwrite = TRUE)
#'
#' #' @title Dataset AA86BTB6
#' #' @desciption Amino acid sequence of active THCAS
#' #' @source https://www.uniprot.org/uniprot/Q8GTB6
#' # usethis::use_data(AA_Q8GTB6)
#' # usethis::use_data(AA_Q8GTB6, internal = T, overwrite = T)
#'
#' #' @title Dataset AA_Q33DQ2
#' #' @desciption Amino acid sequence of inactive THCAS
#' #' @source https://www.uniprot.org/uniprot/Q33DQ2
#' # usethis::use_data(AA_Q33DQ2)
#' # usethis::use_data(AA_Q33DQ2, internal = T, overwrite = T)
#'
#'
#' #' @name CANSAT_CODONS_DNA
#' #' @title Dataset: \code{CANSAT_CODONS}
#' #' @description Cannabis sativa codons and codon usage table
#' #' @format A list
#' #' \describe{
#' #' \item{TABLE}{DNA/RNA triplets and their translations}
#' #' \item{FREQS}{DNA/RNA codon usage as pecent frequency}
#' #' }
#' #' @source
#' #' \url{https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3483}
#' # CANSAT_CODONS_DNA <- list(
#' # 'A' = c('GCT', 'GCC', 'GCA', 'GCG'),
#' # 'R' = c('CGT', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'),
#' # 'N' = c('AAT', 'AAC'),
#' # 'D' = c('GAT', 'GAC'),
#' # 'C' = c('TGT', 'TGC'),
#' # 'Q' = c('CAA', 'CAG'),
#' # 'E' = c('GAA', 'GAG'),
#' # 'G' = c('GGT', 'GGC', 'GGA', 'GGG'),
#' # 'H' = c('CAT', 'CAC'),
#' # 'I' = c('ATT', 'ATC', 'ATA'),
#' # 'L' = c('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'),
#' # 'K' = c('AAA', 'AAG'),
#' # 'M' = c('ATG'),
#' # 'F' = c('TTT', 'TTC'),
#' # 'P' = c('CCT', 'CCC', 'CCA', 'CCG'),
#' # 'S' = c('TCT', 'TCC', 'TCA', 'TCG', 'AGT', 'AGC'),
#' # 'T' = c('ACT', 'ACC', 'ACA', 'ACG'),
#' # 'W' = c('TGG'),
#' # 'Y' = c('TAT', 'TAC'),
#' # 'V' = c('GTT', 'GTC', 'GTA', 'GTG'),
#' # 'START' = c('ATG'),
#' # 'STOP' = c('TAG', 'TGA', 'TAA')
#' # )
#' #
#' # CANSAT_CODON_USAGE_RNA <- list(
#' # UUU = 33.5, UCU = 15.0, UAU = 30.7, UGU = 5.9,
#' # UUC = 22.7, UCC = 9.3, UAC = 13.9, UGC = 8.3,
#' # UUA = 20.6, UCA = 18.8, UAA = 1.5, UGA = 0.3,
#' # UUG = 23.7, UCG = 6.2, UAG = 0.3, UGG = 17.8,
#' #
#' # CUU = 20.9, CCU = 17.8, CAU = 19.6, CGU = 6.5,
#' # CUC = 9.3, CCC = 4.6, CAC = 8.0, CGC = 2.3,
#' # CUA = 7.2, CCA = 16.0, CAA = 27.1, CGA = 7.2,
#' # CUG = 3.1, CCG = 1.3, CAG = 4.1, CGG = 1.5,
#' #
#' # AUU = 37.7, ACU = 22.7, AAU = 46.7, AGU = 15.5,
#' # AUC = 14.7, ACC = 9.8, AAC = 17.5, AGC = 5.7,
#' # AUA = 24.3, ACA = 18.1, AAA = 43.1, AGA = 16.5,
#' # AUG = 26.3, ACG = 2.6, AAG = 28.1, AGG = 6.7,
#' #
#' # GUU = 28.6, GCU = 24.5, GAU = 37.7, GGU = 21.2,
#' # GUC = 10.8, GCC = 5.2, GAC = 9.5, GGC = 9.0,
#' # GUA = 11.6, GCA = 14.2, GAA = 37.9, GGA = 24.0,
#' # GUG = 8.0, GCG = 6.5, GAG = 22.7, GGG = 7.2
#' # )
#' #
#' # CANSAT_CODON_USAGE_DNA <- setNames(CANSAT_CODON_USAGE_RNA, lapply(names(CANSAT_CODON_USAGE_RNA), function(rna) {
#' # stringr::str_replace_all(rna, 'U', 'T')
#' # }))
#' #
#' # CANSAT_CODONS_RNA <- lapply(CANSAT_CODONS_DNA, function(dna){
#' # stringr::str_replace_all(dna, 'T', 'U')
#' # })
#' #
#' # CANSAT_CODONS <- list(
#' # TABLE = list(
#' # DNA = CANSAT_CODONS_DNA,
#' # RNA = CANSAT_CODONS_RNA
#' # ),
#' # FREQS = list(
#' # DNA = CANSAT_CODON_USAGE_DNA,
#' # RNA = CANSAT_CODON_USAGE_RNA
#' # )
#' # )
#' # usethis::use_data(CANSAT_CODONS, overwrite = T)
#'
#'
#' #' @title Dataset `AA_PROPERTIES`
#' # AA_PROPERTIES <- read.csv(
#' # 'inst/extdata/CBDAS\ Product\ Specificity/constants/aa-properties.csv'
#' # )
#' # usethis::use_data(AA_PROPERTIES)
#'
#' #' @title Dataset `AA_CATEGORIES`
#' # AA_CATEGORIES <-read.csv(
#' # 'inst/extdata/CBDAS\ Product\ Specificity/constants/aa-categories.csv'
#' # )
#' # usethis::use_data(AA_CATEGORIES)
#'
#' #' @name CANSAT_GENETIC_CODE
#' #' @title Dataset: \code{CANSAT_GENETIC_CODE}
#' #' @description Cannabis sativa genetic code formatted to match that of \code{Biostrings::GENETIC_CODE}
#' #' @source \code{fastalign::CANSAT_CODONS$TABLE$DNA}
#' # CANSAT_GENETIC_CODE <- list()
#' # CSGC <- CANSAT_CODONS$TABLE$DNA
#' # for(i in 1:length(CSGC)) {
#' # CANSAT_GENETIC_CODE[CSGC[[i]]] <- rep_len(names(CSGC)[[i]], length(CSGC[[i]]))
#' # }
#' # CANSAT_GENETIC_CODE[CANSAT_GENETIC_CODE %in% c('START', 'STOP')] <- '*'
#' # CSGC <- CANSAT_GENETIC_CODE
#' # CANSAT_GENETIC_CODE <- c()
#' # CANSAT_GENETIC_CODE_NAMES <- c()
#' # for(i in 1:length(GENETIC_CODE)) {
#' # triplet <- names(GENETIC_CODE)[i]
#' # CANSAT_GENETIC_CODE[[i]] <- CSGC[[triplet]]
#' # CANSAT_GENETIC_CODE_NAMES[[i]] <- triplet
#' # }
#' # names(CANSAT_GENETIC_CODE) <- CANSAT_GENETIC_CODE_NAMES
#' # usethis::use_data(CANSAT_GENETIC_CODE, overwrite = T)
#'
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#' #' @title Dataset `Z18_CBDAS`
#' #' @details Fig. 6B (Zirpel et al., 2018)
#' #' #' @format (Names: dact = "Percent change Kcat compared to WT", res1a = "WT residue", pos1 = "Homologous position in WT", res1b = "Mutant residue").
#' #' @source https://doi.org/10.1016/j.jbiotec.2018.07.031
#' Z18_CBDAS <- data.frame(
#' actv =
#' c(2.84,1.33,-0.99,-1.00,3.37,-0.75,-0.80,-0.84,-0.45,-0.35,4.14,3.63,2.17),
#'
#' res1a = c( 'S', 'S', 'S', 'S', 'A', 'A', 'L', 'A', 'I', 'I', 'A', 'S', 'S'),
#' pos1 = c( 116, 118, 116, 116, 414, 414, 414, 414, 445, 445, 414, 116, 116),
#' res1b = c( 'A', 'G', 'V', 'L', 'V', 'T', 'L', 'I', 'T', 'T', 'V', 'A', 'A'),
#'
#'
#' res2a = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , 'C', 'A', 'A', 'A'),
#' pos2 = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , 446, 46, 46, 414),
#' res2b = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , 'A', 'V', 'V', 'V'),
#'
#' res3a = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , 'T', 'T', NA ),
#' pos3 = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , 47, 47, NA ),
#' res3b = c( NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , 'A', 'A', NA )
#' )
#'
#' usethis::use_data(Z18_CBDAS, overwrite = TRUE)
#'
#' #' @title Dataset `Z18_THCAS`
#' #' @details Fig. 6C Zirpel et al., 2018
#' #' @format (Names: dact = "Percent change Kcat compared to WT", res1a = "WT residue", pos1 = "Homologous position in WT", res1b = "Mutant residue").
#' #' @source https://doi.org/10.1016/j.jbiotec.2018.07.031
#' Z18_THCAS <- data.frame(
#' actv =
#' c(-1.00,-0.12,0.17 ,-0.70,-0.90,-0.91,-0.96,-0.31,-0.46,-0.55,-1.00,-0.93,-0.69,-0.97,-1.00,-1.00,-0.15,-0.58,-1.00,-0.95,-0.90,-0.87),
#'
#' res1a = c( NA, 'K', 'Q', 'T', 'S', 'I', 'V', 'V', 'V', 'V', 'V', 'A', 'A', 'A', 'A', 'A', 'E', 'Y', 'Y', 'H', 'R', 'R'),
#' pos1 = c( 12, 377, 69 , 446, 382, 257, 415, 415, 415, 415, 415, 116, 116, 116, 116, 116, 442, 417, 484, 292, 110, 108),
#' res1b = c( NA, 'Q', 'H', 'I', 'K', 'M', 'A', 'I', 'L', 'T', 'N', 'S', 'G', 'V', 'T', 'Y', 'Q', 'F', 'F', 'A', 'A', 'A'),
#'
#' res2a = c( NA, 'K', NA , 'A', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' pos2 = c( NA, 378, NA , 447, NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' res2b = c( NA, 'N', NA , 'C', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#'
#' res3a = c( NA, 'T', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' pos3 = c( NA, 379, NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA ),
#' res3b = c( NA, 'G', NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA , NA )
#' )
#'
#' usethis::use_data(Z18_THCAS, overwrite = TRUE)
#'
#' Z18 <- list(
#' THCAS = Z18_THCAS,
#' CBDAS = Z18_CBDAS
#' )
#'
#' usethis::use_data(Z18, internal = T, overwrite = TRUE)
#'
#' #' @name ANNOTATIONS_Q8GTB6
#' #' @title Dataset: \code{ANNOTATIONS_Q8GTB6}
#' #' @description
#' #' @format A list
#' #' @source
#' #'\url{https://pfam.xfam.org/structure/3vte#tabview=tab0}
#' ANNOTATIONS_Q8GTB6 <- list(
#' 'Sites' = list(
#' 'FAD-binding' = list(
#' 'H292' = list(
#' type = 'Covalent',
#' label = 'C-N linkage',
#' description = 'FAD-binding site',
#' ranges = IRanges::IRangesList(
#' coordinates = IRanges(292)
#' )
#' ),
#' 'C417' = list(
#' type = 'Covalent',
#' label = 'C-S linkage',
#' description = 'FAD-binding site',
#' ranges = IRanges::IRangesList(
#' coordinates = IRanges(417)
#' )
#' )
#' ),
#' 'Active' = list(
#' 'Y484' = list(
#' type = 'Catalytic',
#' label = 'Active site',
#' description = 'Catalytic base Tyr484',
#' ranges = IRanges::IRangesList(
#' 'Y484' = IRanges::IRanges(484)
#' )
#' )
#' ),
#' 'Glycosylation' = list(
#' GlNAc = list(
#' type = 'Covalent',
#' label = 'GlcNAc',
#' description = 'N-Acetyl Glucosamine',
#' ranges = IRanges::IRangesList(
#' IRanges::IRanges(65)
#' IRanges::IRanges(89)
#' IRanges::IRanges(168)
#' IRanges::IRanges(297)
#' IRanges::IRanges(305)
#' IRanges::IRanges(329)
#' IRanges::IRanges(467)
#' IRanges::IRanges(499)
#' )
#' )
#' )
#' ),
#' 'Tertiary' = list(
#' 'Disulfide' = list(
#' S99 = list(
#' type = 'Covalent',
#' description = 'Disulfide bond S37-S99',
#' label = 'Disulfide bond',
#' ranges = IRanges::IRanges(37, 99, 2)
#' )
#' ),
#' 'Crosslink' = list(
#' H114 = list(
#' type = 'Covalent',
#' label = 'H114-[FAD]-C176',
#' description = 'Crosslink H114-[FAD]-C176',
#' ranges = IRanges::IRanges(114, 176, 2)
#' )
#' )
#' ),
#' 'Domains' = list(
#' 'FAD-binding' = list(
#' type = 'Covalent',
#' label = 'FAD-binding 80-219',
#' desciption = 'FAD-binding domain',
#' ranges = IRanges::IRanges(81, 219)
#' ),
#' 'BBE-domain' = list(
#' type = 'Covalent',
#' label = 'BBE-domain 480-438',
#' description = 'Berberine bidge-like domain',
#' ranges = IRanges::IRanges(480, 438)
#' ),
#' 'Signal-peptide' = list(
#' type = 'Covalent',
#' label = 'Signal peptide 1-28',
#' description = 'Signal peptide',
#' ranges = IRanges::IRanges(1, 28)
#' ),
#' ),
#' 'Families' = list(
#' 'FAD-binding' = list(
#' type = 'PCMH-type',
#' label = 'FAD-binding',
#' description = 'FAD-binding (PCMH family)',
#' ranges = IRanges::IRanges(77, 251)
#' )
#' ),
#' # 'Composition' = list(
#' # 'Bias' = list(
#' # type = 'Bias',
#' # label = 'Compositional bias 77-251',
#' # description = 'Compositional bias 77-251',
#' # ranges = IRanges::IRanges(77, 251)
#' # )
#' # ),
#' # 'Chains' = list(
#' # 'A' = list(
#' # type = 'Main',
#' # label = 'Chain-A',
#' # dscription = NULL,
#' # ranges = IRanges::IRanges(29, 545)
#' # )
#' # ),
#' 'Mutations' = list(
#' H92A = list(
#' effect = FALSE,
#' magnitude = '0',
#' desciption = 'No effect',
#' ranges = IRanges::IRanges(92)
#' ),
#' R108A = list(
#' effect = 'Kcat',
#' magnitude = '---',
#' desciption = 'Strongly reduced catalytic activity',
#' ranges = IRanges::IRanges(108)
#' ),
#' R110A = list(
#' effect = 'Kcat',
#' magnitude = '----',
#' desciption = 'Strongly reduced catalytic activity',
#' ranges = IRanges::IRanges(110)
#' ),
#' H114A = list(
#' effect = 'FAD',
#' magnitude = '-----',
#' desciption = 'Loss of FAD binding and loss of catalytic activity. 2 Publications',
#' ranges = IRanges::IRanges(114)
#' ),
#' H208A = list(
#' effect = FALSE,
#' magnitude = '0',
#' desciption = 'No effect',
#' ranges = IRanges::IRanges(208)
#' ),
#' H292A = list(
#' effect = 'Kcat',
#' magnitude = '----',
#' desciption = 'Strongly reduced catalytic activity',
#' ranges = IRanges::IRanges(292)
#' ),
#' Y417F = list(
#' effect = 'Kcat',
#' magnitude = '---',
#' desciption = 'Reduced catalytic activity',
#' ranges = IRanges::IRanges(417)
#' ),
#' E442Q = list(
#' effect = 'Kcat',
#' magnitude = '-',
#' desciption = 'Slightly reduced catalytic activity',
#' ranges = IRanges::IRanges(442)
#' ),
#' Y484F = list(
#' effect = 'Kcat',
#' magnitude = '-----',
#' desciption = 'Loss of catalytic activity',
#' ranges = IRanges::IRanges(484)
#' )
#' )
#' )
#' usethis::use_data(ANNOTATIONS_Q8GTB6, overwrite = TRUE)
#'
#' #' @name KINETICS
#' #' @title Dataset: \code{KINETICS_Q8GTB6}
#' #' @description
#' #' @format A list
#' #' @source
#' #'\url{https://pfam.xfam.org/structure/3vte#tabview=tab0}
#' KINETICS_Q8GTB6 <- list(
#' Kcat = list(
#' CBGA = list(
#' value = '0.30',
#' units = '1/sec',
#' label = 'Kcat[CBGA] = 0.30 sec(-1)',
#' description = 'Kcat value for CBGA substrate 0.30 sec(-1)',
#' references = c(NULL)
#' )
#' ),
#' Km = list(
#' CBGA = list(
#' value = c('134', '254'),
#' units = 'µM',
#' label = 'Km[CBGA] = (134 µM, 254 µM)',
#' description = 'Km values for CBGA (134 µM, 254 µM)',
#' references = c(
#' 'https://doi.org/10.1074/jbc.M403693200',
#' 'https://doi.org/10.1021/ja00143a024'
#' )
#' )
#' ),
#' Vmax = list(
#' CBGA = list(
#' value = c('0.36', '2.68'),
#' units = 'nmol/sec/mg',
#' label = 'Vmax[CBGA] = 2.68 nmol/sec/mg',
#' desciption = 'Vmax values for CBGA substrate (0.36 nmol/sec/mg, 2.68 nmol/sec/mg)',
#' references = c(
#' 'https://doi.org/10.1074/jbc.M403693200',
#' 'https://doi.org/10.1021/ja00143a024'
#' )
#' ),
#' ),
#' pH = list(
#' CBGA = list(
#' value = c('5.5', '6.0'),
#' units = 'pH',
#' label = 'Optimum pH 5.5-6.0',
#' desciption = 'Optimum catalytic pH for CBGA substrate between 5.5-6.0',
#' references = c(
#' 'https://doi.org/10.1074/jbc.M403693200',
#' 'https://doi.org/10.1021/ja00143a024'
#' )
#' )
#' ),
#' )
#' usethis::use_data(KINETICS_Q8GTB6, overwrite = TRUE)
#'
#' #' @title Dataset AA86BTB6
#' #' @desciption Amino acid sequence of active THCAS
#' #' @source https://www.uniprot.org/uniprot/Q8GTB6
#' # usethis::use_data(AA_Q8GTB6)
#' # usethis::use_data(AA_Q8GTB6, internal = T, overwrite = T)
#'
#' #' @title Dataset AA_Q33DQ2
#' #' @desciption Amino acid sequence of inactive THCAS
#' #' @source https://www.uniprot.org/uniprot/Q33DQ2
#' # usethis::use_data(AA_Q33DQ2)
#' # usethis::use_data(AA_Q33DQ2, internal = T, overwrite = T)
#'
#'
#' #' @name CANSAT_CODONS_DNA
#' #' @title Dataset: \code{CANSAT_CODONS}
#' #' @description Cannabis sativa codons and codon usage table
#' #' @format A list
#' #' \describe{
#' #' \item{TABLE}{DNA/RNA triplets and their translations}
#' #' \item{FREQS}{DNA/RNA codon usage as pecent frequency}
#' #' }
#' #' @source
#' #' \url{https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3483}
#' # CANSAT_CODONS_DNA <- list(
#' # 'A' = c('GCT', 'GCC', 'GCA', 'GCG'),
#' # 'R' = c('CGT', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'),
#' # 'N' = c('AAT', 'AAC'),
#' # 'D' = c('GAT', 'GAC'),
#' # 'C' = c('TGT', 'TGC'),
#' # 'Q' = c('CAA', 'CAG'),
#' # 'E' = c('GAA', 'GAG'),
#' # 'G' = c('GGT', 'GGC', 'GGA', 'GGG'),
#' # 'H' = c('CAT', 'CAC'),
#' # 'I' = c('ATT', 'ATC', 'ATA'),
#' # 'L' = c('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'),
#' # 'K' = c('AAA', 'AAG'),
#' # 'M' = c('ATG'),
#' # 'F' = c('TTT', 'TTC'),
#' # 'P' = c('CCT', 'CCC', 'CCA', 'CCG'),
#' # 'S' = c('TCT', 'TCC', 'TCA', 'TCG', 'AGT', 'AGC'),
#' # 'T' = c('ACT', 'ACC', 'ACA', 'ACG'),
#' # 'W' = c('TGG'),
#' # 'Y' = c('TAT', 'TAC'),
#' # 'V' = c('GTT', 'GTC', 'GTA', 'GTG'),
#' # 'START' = c('ATG'),
#' # 'STOP' = c('TAG', 'TGA', 'TAA')
#' # )
#' #
#' # CANSAT_CODON_USAGE_RNA <- list(
#' # UUU = 33.5, UCU = 15.0, UAU = 30.7, UGU = 5.9,
#' # UUC = 22.7, UCC = 9.3, UAC = 13.9, UGC = 8.3,
#' # UUA = 20.6, UCA = 18.8, UAA = 1.5, UGA = 0.3,
#' # UUG = 23.7, UCG = 6.2, UAG = 0.3, UGG = 17.8,
#' #
#' # CUU = 20.9, CCU = 17.8, CAU = 19.6, CGU = 6.5,
#' # CUC = 9.3, CCC = 4.6, CAC = 8.0, CGC = 2.3,
#' # CUA = 7.2, CCA = 16.0, CAA = 27.1, CGA = 7.2,
#' # CUG = 3.1, CCG = 1.3, CAG = 4.1, CGG = 1.5,
#' #
#' # AUU = 37.7, ACU = 22.7, AAU = 46.7, AGU = 15.5,
#' # AUC = 14.7, ACC = 9.8, AAC = 17.5, AGC = 5.7,
#' # AUA = 24.3, ACA = 18.1, AAA = 43.1, AGA = 16.5,
#' # AUG = 26.3, ACG = 2.6, AAG = 28.1, AGG = 6.7,
#' #
#' # GUU = 28.6, GCU = 24.5, GAU = 37.7, GGU = 21.2,
#' # GUC = 10.8, GCC = 5.2, GAC = 9.5, GGC = 9.0,
#' # GUA = 11.6, GCA = 14.2, GAA = 37.9, GGA = 24.0,
#' # GUG = 8.0, GCG = 6.5, GAG = 22.7, GGG = 7.2
#' # )
#' #
#' # CANSAT_CODON_USAGE_DNA <- setNames(CANSAT_CODON_USAGE_RNA, lapply(names(CANSAT_CODON_USAGE_RNA), function(rna) {
#' # stringr::str_replace_all(rna, 'U', 'T')
#' # }))
#' #
#' # CANSAT_CODONS_RNA <- lapply(CANSAT_CODONS_DNA, function(dna){
#' # stringr::str_replace_all(dna, 'T', 'U')
#' # })
#' #
#' # CANSAT_CODONS <- list(
#' # TABLE = list(
#' # DNA = CANSAT_CODONS_DNA,
#' # RNA = CANSAT_CODONS_RNA
#' # ),
#' # FREQS = list(
#' # DNA = CANSAT_CODON_USAGE_DNA,
#' # RNA = CANSAT_CODON_USAGE_RNA
#' # )
#' # )
#' # usethis::use_data(CANSAT_CODONS, overwrite = T)
#'
#'
#' #' @title Dataset `AA_PROPERTIES`
#' # AA_PROPERTIES <- read.csv(
#' # 'inst/extdata/CBDAS\ Product\ Specificity/constants/aa-properties.csv'
#' # )
#' # usethis::use_data(AA_PROPERTIES)
#'
#' #' @title Dataset `AA_CATEGORIES`
#' # AA_CATEGORIES <-read.csv(
#' # 'inst/extdata/CBDAS\ Product\ Specificity/constants/aa-categories.csv'
#' # )
#' # usethis::use_data(AA_CATEGORIES)
#'
#' #' @name CANSAT_GENETIC_CODE
#' #' @title Dataset: \code{CANSAT_GENETIC_CODE}
#' #' @description Cannabis sativa genetic code formatted to match that of \code{Biostrings::GENETIC_CODE}
#' #' @source \code{fastalign::CANSAT_CODONS$TABLE$DNA}
#' # CANSAT_GENETIC_CODE <- list()
#' # CSGC <- CANSAT_CODONS$TABLE$DNA
#' # for(i in 1:length(CSGC)) {
#' # CANSAT_GENETIC_CODE[CSGC[[i]]] <- rep_len(names(CSGC)[[i]], length(CSGC[[i]]))
#' # }
#' # CANSAT_GENETIC_CODE[CANSAT_GENETIC_CODE %in% c('START', 'STOP')] <- '*'
#' # CSGC <- CANSAT_GENETIC_CODE
#' # CANSAT_GENETIC_CODE <- c()
#' # CANSAT_GENETIC_CODE_NAMES <- c()
#' # for(i in 1:length(GENETIC_CODE)) {
#' # triplet <- names(GENETIC_CODE)[i]
#' # CANSAT_GENETIC_CODE[[i]] <- CSGC[[triplet]]
#' # CANSAT_GENETIC_CODE_NAMES[[i]] <- triplet
#' # }
#' # names(CANSAT_GENETIC_CODE) <- CANSAT_GENETIC_CODE_NAMES
#' # usethis::use_data(CANSAT_GENETIC_CODE, overwrite = T)
#'
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