demo/protein_Cp.R

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

# CHNOSZ/demo/protein_Cp.R
# Compare calculated and experimental Cp of proteins
# 20250510 demo extracted from anintro.Rmd

library(CHNOSZ)

# Experimental values from Privalov and Makhatadze (1990)
PM90 <- read.csv(system.file("extdata/misc/PM90.csv", package = "CHNOSZ"))
plength <- protein.length(colnames(PM90)[2:5])
Cp_expt <- t(t(PM90[, 2:5]) / plength)
matplot(PM90[, 1], Cp_expt, type = "p", pch = 19,
        xlab = axis.label("T"), ylab = axis.label("Cp0"), ylim = c(110, 280))
for(i in 1:4) {
  pname <- colnames(Cp_expt)[i]
  aq <- subcrt(pname, "aq", T = seq(0, 150))$out[[1]]
  cr <- subcrt(pname, "cr", T = seq(0, 150))$out[[1]]
  lines(aq$T, aq$Cp / plength[i], col = i)
  lines(cr$T, cr$Cp / plength[i], col = i, lty = 2)
}
legend("right", legend = colnames(Cp_expt),
       col = 1:4, pch = 19, lty = 1, bty = "n", cex = 0.9)
legend("bottomright", legend = c("experimental", "calculated (aq)",
       "calculated (cr)"), lty = c(NA, 1, 2), pch = c(19, NA, NA), bty = "n")
title("Calculated and experimental Cp of proteins", font.main = 1)