# Additional File 1: Program listing
# gt/plot.R 20080814 jmd
# plot protein metastability diagrams 
#
# to use, load CHNOSZ and source this file:
# library(CHNOSZ)
# source("plot.R.txt")
#
# then run one of the following commands:
# figure(3,do.ps=TRUE)  # 50s
# figure(4,do.ps=TRUE)  # 10s
# figure(5,do.ps=TRUE)  # 14s
# figure(6,do.ps=TRUE)  # 49s
# figure(7,do.ps=TRUE)  # 2m46s
# set do.ps=FALSE (the default) to show 
# the plots on screen
#
# to make Fig. 7a in less time at lower resolution, do
# res <- 40; plot.PT.buffer()  # 33s
#
# timings were obtained with res=300 on a P4 2.4GHz
# running Linux 2.6.24, R 2.7.1 and CHNOSZ 0.7

# plot resolution
res <- 300
# protein settings
organisms <- c("METSC","METJA","METFE","HALJP","METVO",
  "METBU","ACEKI","BACST","BACLI","AERSA")
proteins <- c(rep("CSG",6),rep("SLAP",4))
proteins <- paste(proteins,organisms,sep="_")
lwd <- c(rep(3,6),rep(1,4))
lty <- c(1:6,1:4)

plot.logfO2pH.1 <- function() {
  basis("CHNOS+")
  species(proteins)
  a <- affinity(pH=c(0,14,res),O2=c(-85,-60,res))
  diagram(a)
  # water line
  abline(h=-83.1,lty=2)
  label.plot("a")
}

plot.logfO2pH.2 <- function() {
  basis("CHNOS+")
  species(proteins)
  a <- affinity(pH=c(0,14,res),O2=c(-85,-60,res))
  ispecies <- c(1,3,6,7,8,9,10)
  names <- proteins[ispecies]
  diagram(a,ispecies=ispecies,names=names)
  # water line
  abline(h=-83.1,lty=2)
  label.plot("b")
}

plot.ZpH <- function() {
  basis("CHNOS+")
  species(metproteins <- proteins[1:6])  # archaeal proteins
  pl <- protein.length(metproteins)
  ionize()
  pHlim <- c(0,14)
  a <- affinity(pH=c(pHlim,res))
  z <- ionize(a$values,a$values)
  ylab=as.expression(quote(italic(Z[j])/residue))
  thermo.plot.new(xlab="pH",ylab=ylab,xlim=pHlim,ylim=c(-0.3,0.2),
    yline=2,mar=c(3,3.5,2,1),lwd=2,cex=2)
  pHs <- seq(pHlim[1],pHlim[2],length.out=res)
  for(i in 1:length(pl)) {
    Zs <- z[[i]]/pl[i]
    lines(pHs,Zs,lty=i)
  }
  text(7,-0.25,"HALJP")
  text(7,-0.05,"METBU")
  text(7,-0.13,"METJA")
  text(7,-0.19,"METVO")
  lines(c(8.5,9.8),c(-0.19,-0.17))
  text(7,0.03,"METFE")
  text(9.6,-0.025,"/METSC",srt=-40)
  label.plot("a")
}

plot.GpH <- function() {
  basis("CHNOS+")
  species(metproteins <- proteins[1:6])  # archaeal proteins
  pl <- protein.length(metproteins)
  ionize()
  pHlim <- c(0,14)
  a <- affinity(pH=c(pHlim,res))
  g <- affinity(pH=c(pHlim,res),property="G")
  G <- ionize(a$values,g$values)
  ylab=as.expression(quote(list(Delta*italic(G*degree[j])/residue,kcal/mol)))
  thermo.plot.new(xlab="pH",ylab=ylab,xlim=pHlim,ylim=c(-55,-35),
    yline=2,mar=c(3,3.5,2,1),lwd=2,cex=2)
  pHs <- seq(pHlim[1],pHlim[2],length.out=res)
  for(i in 1:length(pl)) {
    Gs <- G[[i]]/pl[i]/1000
    lines(pHs,Gs,lty=i)
  }
  text(7,-52.5,"HALJP")
  text(7,-47.5,"METJA")
  text(2,-42.3,"METBU")
  text(7,-44,"METVO")
  text(7,-40,"METSC")
  text(7,-38,"METFE")
  label.plot("b",xfrac=0.1)
}

plot.logfO2.1 <- function() {
  basis("CHNOS+")
  species(proteins)
  a <- affinity(O2=c(-90,-65,res))
  diagram(a,ylim=c(-5,-1),legend.x=NULL,lwd=lwd,
    ylab=as.expression(quote(log~italic(a[j]))),yline=1.7)
  text(-80,-1.7,"METJA")
  text(-74.5,-1.7,"METVO")
  text(-69,-1.8,"HALJP")
  # water line
  abline(v=-83.1,lty=2)
  label.plot("a")
}

plot.logfO2.2 <- function() {
  basis("CHNOS+")
  species(proteins)
  a <- affinity(O2=c(-90,-65,res))
  diagram(a,ylim=c(-5,-1),residue=TRUE,legend.x=NULL,lwd=lwd,
    ylab=as.expression(quote(log~italic(a[j]))),yline=1.7)
  text(-80,-1.9,"METJA")
  text(-74.5,-1.9,"METVO")
  text(-69,-1.9,"HALJP")
  text(-78,-2.85,"METBU",cex=0.8,srt=-22)
  text(-79,-3.15,"ACEKI",cex=0.8,srt=-25)
  text(-81,-3.3,"METSC",cex=0.8,srt=-25)
  text(-87,-3.1,"METFE",cex=0.8,srt=-17)
  text(-79,-4.3,"BACST",cex=0.8)
  text(-85.5,-4.7,"AERSA",cex=0.8,srt=38)
  text(-87,-4.25,"BACLI",cex=0.8,srt=30)
  # water line
  abline(v=-83.1,lty=2)
  label.plot("b")
}

plot.logfO2T <- function() {
  basis("CHNOS+")
  species(proteins)
  a <- affinity(T=c(0,150,res),O2=c(-85,-55,res))
  diagram(a,names=NULL)
  text(43,-58,"CSG_HALJP")
  text(60,-67,"CSG_METVO",srt=32)
  text(75,-74,"CSG_METJA",srt=35)
  text(100,-77,"SLAP_ACEKI",srt=30)
  text(120,-82,"CSG_METFE")
  label.plot("a",xfrac=0.1)
  # water line
  T <- seq(0,150,length.out=res)
  TK <- convert(T,'K')
  water.lines(xaxis='T',yaxis='O2',T=TK,xpoints=T)
}

plot.logfO2P <- function() {
  basis("CHNOS+")
  species(proteins)
  a <- affinity(P=c(1,3000,res),O2=c(-85,-65,res))
  proteins[2] <- ""
  diagram(a,names=proteins)
  text(1500,-80,"CSG_METJA")
  label.plot("b",xfrac=0.1)
  P <- seq(1,3000,length.out=res)
  water.lines(xaxis='P',yaxis='O2',T=298.15,P=P)
}

plot.PT.buffer <- function() {
  basis("CHNOS+")
  myprot <- proteins[c(2,1,5,6,3)] # METXX proteins
  basis("O2",-58)
  # buffer specification
  mod.buffer("s-layer",myprot)
  basisnames <- c("CO2","NH3","H2S","H2O")
  basis(basisnames,"s-layer")
  # buffer calculation
  species(myprot)
  b <- affinity(return.buffer=TRUE,T=100,P=1000)
  basis(basisnames,as.numeric(b)[match(basisnames,names(b))])
  # plot calculation
  a <- affinity(T=c(95,105,res),P=c(10,3000,res))
  myprot[c(1,2)] <- ""
  diagram(a,names=myprot)
  text(100.8,2200,"CSG_METJA")
  lines(c(99,98),c(2200,2000))
  label.plot("a")
}

plot.logfO2pH.buffer <- function() {
  basis("CHNOS+")
  myprot <- proteins[c(2,1,5,6,3)]  # METXX proteins
  basis("O2",-58)
  # buffer specification
  mod.buffer("s-layer",myprot)
  basisnames <- c("CO2","NH3","H2S","H2O")
  basis(basisnames,"s-layer")
  # buffer calculation
  species(myprot)
  b <- affinity(return.buffer=TRUE,T=100,P=1000)
  basis(basisnames,as.numeric(b)[match(basisnames,names(b))])
  # plot calculation
  a <- affinity(pH=c(0,14,res),O2=c(-64,-54,res),T=100,P=1000)
  myprot[c(1,4)] <- ""
  diagram(a,names=myprot)
  text(11.2,-58.5,"CSG_METJA")
  text(4.2,-59,"CSG_METBU")
  lines(c(6.7,7.7),c(-59,-58.5))
  # water stability line
  s <- subcrt(c("H2O","O2","H2"),c(-1,0.5,1),T=100,P=1000)
  abline(h=2*s$out$logK,lty=2)
  label.plot("b")
}

figure <- function(n,do.ps=FALSE) {
  if(do.ps) thermo.postscript(paste(n,"ps",sep="."),width=8,height=12)
  layout(matrix(1:2,nrow=2))
  par(mar=c(3,3.5,2,1))
  if(do.ps) par(cex=2,lwd=2)
  if(n==1) {
    # fig 1 is a flowchart for the package
    # (not done here)
  } else if(n==2) {
    # fig 2 is program interaction text
    # (not done here)
  } else if(n==3) {
    plot.logfO2pH.1()
    plot.logfO2pH.2()
  } else if(n==4) {
    plot.ZpH()
    plot.GpH()
  } else if(n==5) {
    plot.logfO2.1()
    plot.logfO2.2()
  } else if(n==6) {
    plot.logfO2T()
    plot.logfO2P()
  } else if(n==7) {
    plot.PT.buffer()
    plot.logfO2pH.buffer()
  }
  if(do.ps) dev.off()
}