Remove 'basis' option and basis.text()

jedick · Mar 1, 2024 · dee1d8f · dee1d8f
1 parent 1588ccb
commit dee1d8f
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Showing 10 changed files with 950 additions and 595 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
-Date: 2024-02-29
+Date: 2024-03-01
 Package: canprot
-Version: 1.1.2-24
+Version: 1.1.2-25
 Title: Chemical Analysis of Proteins
 Authors@R: c(
     person("Jeffrey", "Dick", email = "j3ffdick@gmail.com", role = c("aut", "cre"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,8 +7,6 @@ export("protcomp", "CLES",
 "cplab",
 # 20200501, 20200505
 "MW",
-# 20200817
-"basis.text",
 # 20201016
 "nO2",
 # 20240225

diff --git a/R/metrics.R b/R/metrics.R
@@ -30,9 +30,9 @@ Zc <- function(AAcomp, ...) {
 
 # Calculate stoichiometric hydration state from amino acid compositions 20181228
 # Add `terminal_H2O` argument 20221018
-nH2O <- function(AAcomp, basis = getOption("basis"), terminal_H2O = 0) {
+nH2O <- function(AAcomp, basis = "QEC", terminal_H2O = 0) {
   if(basis == "QEC") {
-    # How to get the number of H2O in reactions to form amino acid residues from the "QEC" basis:
+    # To get the number of H2O in reactions to form amino acid residues from the "QEC" basis:
     ## library(CHNOSZ)
     ## basis("QEC")
     ## nH2O_AA <- species(aminoacids(""))$H2O
@@ -65,7 +65,7 @@ nH2O <- function(AAcomp, basis = getOption("basis"), terminal_H2O = 0) {
 }
 
 # Calculate stoichiometric oxidation state from amino acid compositions 20201016
-nO2 <- function(AAcomp, basis = getOption("basis"), ...) {
+nO2 <- function(AAcomp, basis = "QEC", ...) {
   if(basis == "QEC") {
     # How to get the number of O2 in reactions to form amino acid residues from the "QEC" basis:
     ## library(CHNOSZ)
@@ -175,12 +175,6 @@ plength <- function(AAcomp, ...) {
   rowSums(AAcomp[, isAA])
 }
 
-basis.text <- function(basis) {
-  if(basis=="QEC") bt <- "glutamine, glutamic acid, cysteine"
-  if(basis=="QCa") bt <- "glutamine, cysteine, acetic acid"
-  bt
-}
-
 #########################
 ### UNEXPORTED OBJECT ###
 ### ( used in pI() )  ###

diff --git a/R/zzz.R b/R/zzz.R
@@ -34,11 +34,3 @@ human <- new.env()
     uniprot_updates <- read.csv(system.file("/extdata/protein/uniprot_updates.csv", package = "canprot"), as.is = TRUE)
   })
 }
-
-# Set 'basis' option 20200817
-# Adapted from R/src/library/grDevices/zzz.R
-.onLoad <- function(libname, pkgname) {
-  op.canprot <- list(basis = "QEC")
-  toset <- !(names(op.canprot) %in% names(.Options))
-  if(any(toset)) options(op.canprot[toset])
-}