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Move chem16S::calc_metrics() to calc.metrics()
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,52 @@ | ||
| # canprot/calc.metrics.R | ||
| # Calculate selected chemical metrics for proteins | ||
| # 20191027 initial version as canprot/metrics.R | ||
| # 20230704 adapted for chem16S/calc_metrics.R | ||
| # 20240302 moved to canprot | ||
| calc.metrics <- function(AAcomp, metrics = c("Zc", "nO2", "nH2O")) { | ||
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| ## Define objects used in various calculations | ||
| # The number of C in each amino acid residue; calculated in CHNOSZ: | ||
| # nC_AA <- sapply(makeup(info(info(aminoacids("")))$formula), "[", "C") | ||
| # nC_AA <- nC_AA | ||
| # names(nC_AA) <- aminoacids(3) | ||
| nC_AA <- c(Ala = 3, Cys = 3, Asp = 4, Glu = 5, Phe = 9, Gly = 2, His = 6, | ||
| Ile = 6, Lys = 6, Leu = 6, Met = 5, Asn = 4, Pro = 5, Gln = 5, | ||
| Arg = 6, Ser = 3, Thr = 4, Val = 5, Trp = 11, Tyr = 9) | ||
| # Identify columns with 3-letter abbreviations for the amino acids | ||
| isAA <- tolower(colnames(AAcomp)) %in% tolower(names(nC_AA)) | ||
| iAA <- match(tolower(colnames(AAcomp)[isAA]), tolower(names(nC_AA))) | ||
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| values <- lapply(metrics, function(metric) { | ||
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| if(metric == "Zc") { | ||
| Zc(AAcomp) | ||
| } else if(metric == "nH2O") { | ||
| nH2O(AAcomp) | ||
| } else if(metric == "nO2") { | ||
| nO2(AAcomp) | ||
| } else if(metric == "GRAVY") { | ||
| GRAVY(AAcomp) | ||
| } else if(metric == "pI") { | ||
| pI(AAcomp) | ||
| } else if(metric == "MW") { | ||
| MW(AAcomp) | ||
| } else if(tolower(metric) %in% c("length", "plength")) { | ||
| plength(AAcomp) | ||
| } else if(metric %in% c("H/C", "H_C", "HC")) { | ||
| HC(AAcomp) | ||
| } else if(metric %in% c("N/C", "N_C", "NC")) { | ||
| NC(AAcomp) | ||
| } else if(metric %in% c("O/C", "O_C", "OC")) { | ||
| OC(AAcomp) | ||
| } else if(metric %in% c("S/C", "S_C", "SC")) { | ||
| SC(AAcomp) | ||
| } else stop(paste0("'", metric, "' is not an available metric")) | ||
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| }) | ||
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| values <- do.call(cbind, values) | ||
| colnames(values) <- metrics | ||
| as.data.frame(values) | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| ## Tests for Zc, nO2, and nH2O adapted from canprot/tests/test-metrics.R on 20230704 | ||
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| info <- "Results are as expected for Zc, nO2, and nH2O" | ||
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| ## Calculate metrics for a few proteins the "long way" (using functions in CHNOSZ) | ||
| #library(CHNOSZ) | ||
| #basis(c("glutamine", "glutamic acid", "cysteine", "H2O", "O2")) | ||
| #Zc.ref <- ZC(protein.formula(1:6)) | ||
| #nO2.ref <- protein.basis(1:6)[, "O2"] / protein.length(1:6) | ||
| ## NOTE: subtract 1 so as exclude terminal groups from calculation of nH2O | ||
| #nH2O.ref <- (protein.basis(1:6)[, "H2O"] - 1) / protein.length(1:6) | ||
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| Zc.ref <- c(-0.11633875106929, -0.0272787757817698, -0.195689166193988, -0.0492957746478873, -0.170212765957447, 0.0163132137030995) | ||
| nO2.ref <- c(-0.699539170506912, -0.522294022617124, -0.81466049382716, -0.574137931034483, -0.716346153846154, -0.471317829457364) | ||
| nH2O.ref <- c(-1.17465437788018, -0.881098546042003, -0.941666666666667, -0.955172413793103, -0.730769230769231, -0.886821705426357) | ||
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| # Calculate metrics using calc.metrics() function in chem16S | ||
| AAcomp <- | ||
| structure(list(protein = c("O08452", "AMY", "AMYA", "BPT1", "CYC", | ||
| "LYSC"), organism = c("PYRFU", "BACSU", "PYRFU", "BOVIN", "BOVIN", | ||
| "CHICK"), ref = c("UniProt", "UniProt", "UniProt", "UniProt", | ||
| "UniProt", "UniProt"), abbrv = c("O08452", "P00691", "P49067", | ||
| "P00974", "P62894", "P00698"), chains = c(1L, 1L, 1L, 1L, 1L, | ||
| 1L), Ala = c(28, 49, 26, 6, 6, 12), Cys = c(5, 1, 2, 6, 2, 8), | ||
| Asp = c(33, 44, 35, 2, 3, 7), Glu = c(23, 23, 66, 2, 9, 2 | ||
| ), Phe = c(20, 20, 37, 4, 4, 3), Gly = c(45, 51, 44, 6, 14, | ||
| 12), His = c(12, 16, 14, 0, 3, 1), Ile = c(25, 35, 41, 2, | ||
| 6, 6), Lys = c(19, 30, 48, 4, 18, 6), Leu = c(27, 36, 59, | ||
| 2, 6, 8), Met = c(4, 10, 12, 1, 2, 2), Asn = c(21, 54, 24, | ||
| 3, 5, 14), Pro = c(20, 23, 28, 4, 4, 2), Gln = c(7, 29, 15, | ||
| 1, 3, 3), Arg = c(14, 24, 35, 6, 2, 11), Ser = c(21, 55, | ||
| 33, 1, 1, 10), Thr = c(16, 45, 12, 3, 8, 7), Val = c(31, | ||
| 32, 59, 1, 3, 6), Trp = c(26, 14, 17, 0, 1, 6), Tyr = c(37, | ||
| 28, 41, 4, 4, 3)), row.names = c(NA, 6L), class = "data.frame") | ||
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| metrics <- calc.metrics(AAcomp) | ||
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| # Perform the tests | ||
| expect_equivalent(metrics$Zc, Zc.ref, info = info) | ||
| expect_equivalent(metrics$nO2, nO2.ref, info = info) | ||
| expect_equivalent(metrics$nH2O, nH2O.ref, info = info) | ||
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| ## Tests for H/C, N/C, O/C, and S/C added on 20230707 | ||
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| AAcomp <- | ||
| structure(list(protein = c("LYSC", "RNAS1", "AMYA", "CSG"), organism = c("CHICK", | ||
| "BOVIN", "PYRFU", "HALJP"), ref = c("UniProt", "UniProt", "UniProt", | ||
| "UniProt"), abbrv = c("P00698", "P61823", "P49067", "Q9C4B4"), | ||
| chains = c(1L, 1L, 1L, 1L), Ala = c(12, 12, 26, 61), Cys = c(8, | ||
| 8, 2, 0), Asp = c(7, 5, 35, 122), Glu = c(2, 5, 66, 86), | ||
| Phe = c(3, 3, 37, 20), Gly = c(12, 3, 44, 78), His = c(1, | ||
| 4, 14, 4), Ile = c(6, 3, 41, 47), Lys = c(6, 10, 48, 4), | ||
| Leu = c(8, 2, 59, 47), Met = c(2, 4, 12, 0), Asn = c(14, | ||
| 10, 24, 51), Pro = c(2, 4, 28, 29), Gln = c(3, 7, 15, 21), | ||
| Arg = c(11, 4, 35, 19), Ser = c(10, 15, 33, 74), Thr = c(7, | ||
| 10, 12, 79), Val = c(6, 9, 59, 66), Trp = c(6, 0, 17, 2), | ||
| Tyr = c(3, 6, 41, 18)), row.names = c(6L, 9L, 3L, 14L), class = "data.frame") | ||
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| # library(CHNOSZ) | ||
| # pf <- as.data.frame(protein.formula(AAcomp)) | ||
| # pf$H <- pf$H - 2 # Remove terminal H-OH | ||
| # pf$O <- pf$O - 1 # Remove terminal H-OH | ||
| # HCref <- pf$H / pf$C | ||
| # OCref <- pf$O / pf$C | ||
| # NCref <- pf$N / pf$C | ||
| # SCref <- pf$S / pf$C | ||
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| HC.ref <- c(1.56117455138662, 1.57739130434783, 1.50964265456608, 1.53856636685745) | ||
| OC.ref <- c(0.300163132137031, 0.333913043478261, 0.276517300056721, 0.405287544289997) | ||
| NC.ref <- c(0.314845024469821, 0.297391304347826, 0.250992626205332, 0.264649768329245) | ||
| SC.ref <- c(0.0163132137030995, 0.0208695652173913, 0.00397050482132728, 0) | ||
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| metrics <- calc.metrics(AAcomp, c("HC", "OC", "NC", "SC")) | ||
| expect_equivalent(metrics$HC, HC.ref) | ||
| expect_equivalent(metrics$NC, NC.ref) | ||
| expect_equivalent(metrics$OC, OC.ref) | ||
| expect_equivalent(metrics$SC, SC.ref) | ||
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| # Test for length added 20240302 | ||
| length.ref <- c(129, 124, 648, 828) | ||
| length.calc <- calc.metrics(AAcomp, "Length")[, 1] | ||
| expect_equal(length.calc, length.ref) |
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