#### Documented in feproffeprof.minimafesminimafesminima.fesoneminimumoneminimum.fesplot.minimaplot.profilesprint.minimaprint.profilessummary.minimasummary.profiles

```#' Find free energy minima in the fes object (generic function for 'metadynminer'
#'
#' `fesminima` finds free energy minima on 1D or 2D free energy surface.
#' The surface is divided by a 1D or 2D grid and minima are found for each
#' bin. Next the program determines whether the minimum of a bin is a local
#' minimum of the whole free energy surface. Free energy minima are labeled
#' constitutively by capital letters.
#'
#' @param inputfes fes object.
#' @param nbins number of bins for each CV (default 8).
#' @return minima object.
#'
#' @export fesminima
fesminima<-function(inputfes, nbins) {
UseMethod("fesminima")
}

#' Find free energy minima in the fes object
#'
#' `fesminima.fes` finds free energy minima on 1D or 2D free energy surface.
#' The surface is divided by a 1D or 2D grid and minima are found for each
#' bin. Next the program determines whether the minimum of a bin is a local
#' minimum of the whole free energy surface. Free energy minima are labeled
#' constitutively by capital letters.
#'
#' @param inputfes fes object.
#' @param nbins number of bins for each CV (default 8).
#' @return minima object.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' minima
fesminima.fes<-function(inputfes, nbins=8) {
fes<-inputfes\$fes
rows<-inputfes\$rows
rb <- rows/nbins
if(rb<2) {
stop("Error: nbins too high, try to reduce it")
}
if(rows%%nbins>0) {
stop("Error: number of rows in FES must be integer multiple of nbins")
}
per<-inputfes\$per
if(inputfes\$dimension==2) {
minx<-c()
miny<-c()
for(i in 0:(nbins-1)) {
ni<-i*rb+0:(rb+1)
if(per[1]) {
ni[ni==0]<-rows
ni[ni==(rows+1)]<-1
} else {
ni<-ni[ni!=0]
ni<-ni[ni!=(rows+1)]
}
for(j in 0:(nbins-1)) {
nj<-j*rb+0:(rb+1)
if(per[2]) {
nj[nj==0]<-rows
nj[nj==(rows+1)]<-1
} else {
nj<-nj[nj!=0]
nj<-nj[nj!=(rows+1)]
}
binmin<-which(fes[ni,nj]==min(fes[ni,nj]), arr.ind = TRUE)
if(binmin[1]!=1 && binmin[2]!=1 && binmin[1]!=length(ni) && binmin[2]!=length(nj)) {
minx<-c(minx,i*rb+binmin[1]-1)
miny<-c(miny,j*rb+binmin[2]-1)
}
}
}
myLETTERS <- c(LETTERS, paste("A", LETTERS, sep=""), paste("B", LETTERS, sep=""))[1:length(minx)]
minima<-data.frame(myLETTERS, minx, miny, inputfes\$x[minx], inputfes\$y[miny], fes[cbind(minx,miny)])
names(minima) <- c("letter", "CV1bin", "CV2bin", "CV1", "CV2", "free_energy")
minima <- minima[order(minima[,6]),]
rownames(minima) <- seq(length=nrow(minima))
minima[,1]<-myLETTERS
minima<-list(minima=minima, hills=inputfes\$hills, fes=fes, rows=rows, dimension=inputfes\$dimension, per=per, x=inputfes\$x, y=inputfes\$y, pcv1=inputfes\$pcv1, pcv2=inputfes\$pcv2)
class(minima) <- "minima"
}
if(inputfes\$dimension==1) {
minx<-c()
for(i in 0:(nbins-1)) {
ni<-i*rb+0:(rb+1)
if(per[1]) {
ni[ni==0]<-rows
ni[ni==(rows+1)]<-1
} else {
ni<-ni[ni!=0]
ni<-ni[ni!=(rows+1)]
}
binmin<-which(fes[ni]==min(fes[ni]), arr.ind = TRUE)
if(binmin[1]!=1 && binmin[1]!=length(ni)) {
minx<-c(minx,i*rb+binmin[1]-1)
}
}
myLETTERS <- c(LETTERS, paste("A", LETTERS, sep=""), paste("B", LETTERS, sep=""))[1:length(minx)]
minima<-data.frame(myLETTERS, minx, inputfes\$x[minx], fes[minx])
names(minima) <- c("letter", "CV1bin", "CV1", "free_energy")
minima <- minima[order(minima[,4]),]
rownames(minima) <- seq(length=nrow(minima))
minima[,1]<-myLETTERS
minima<-list(minima=minima, hills=inputfes\$hills, fes=fes, rows=rows, dimension=inputfes\$dimension, per=per, x=inputfes\$x, pcv1=inputfes\$pcv1, pcv2=inputfes\$pcv2)
class(minima) <- "minima"
}
return(minima)
}

#' Creates one ad hoc free energy minimum for a fes object (generic function
#'
#' `oneminimum` creates an ad hoc free energy minimum on free energy surface.
#' This can be used to calculate free energy surface evolution at arbitrary
#' point of free energy surface.
#'
#' @param inputfes fes object.
#' @param cv1 the value of collective variable 1.
#' @param cv2 the value of collective variable 2.
#' @param cv3 the value of collective variable 3.
#' @return minima object.
#'
#' @export oneminimum
oneminimum<-function(inputfes, cv1, cv2, cv3) {
UseMethod("oneminimum")
}

#' Creates one ad hoc free energy minimum for a fes object
#'
#' `oneminimum.fes` creates an ad hoc free energy minimum on free energy surface.
#' This can be used to calculate free energy surface evolution at arbitrary
#' point of free energy surface.
#'
#' @param inputfes fes object.
#' @param cv1 the value of collective variable 1.
#' @param cv2 the value of collective variable 2.
#' @param cv3 the value of collective variable 3.
#' @return minima object.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme1d)
#' minima<-fesminima(tfes)
#' minima<-minima+oneminimum(tfes, cv1=0, cv2=0)
#' minima
oneminimum.fes<-function(inputfes, cv1, cv2, cv3) {
fes<-inputfes\$fes
rows<-inputfes\$rows
per<-inputfes\$per
if(inputfes\$dimension==2) {
icv1<-as.integer(rows*(cv1-min(inputfes\$x))/(max(inputfes\$x)-min(inputfes\$x)))+1
if(icv1<0)    stop("Error: Out of range")
if(icv1>rows) stop("Error: Out of range")
icv2<-as.integer(rows*(cv2-min(inputfes\$y))/(max(inputfes\$x)-min(inputfes\$x)))+1
if(icv2<0)    stop("Error: Out of range")
if(icv2>rows) stop("Error: Out of range")
minima<-data.frame(c("A"), c(icv1), c(icv2), c(cv1), c(cv2), c(fes[icv1,icv2]))
names(minima) <- c("letter", "CV1bin", "CV2bin", "CV1", "CV2", "free_energy")
minima<-list(minima=minima, hills=inputfes\$hills, fes=fes, rows=rows, dimension=inputfes\$dimension, per=per, x=inputfes\$x, y=inputfes\$y, pcv1=inputfes\$pcv1, pcv2=inputfes\$pcv2)
class(minima) <- "minima"
}
if(inputfes\$dimension==1) {
icv1<-as.integer(rows*(cv1-min(inputfes\$x))/(max(inputfes\$x)-min(inputfes\$x)))+1
if(icv1<0)    stop("Error: Out of range")
if(icv1>rows) stop("Error: Out of range")
minima<-data.frame(c("A"), c(icv1), c(cv1), c(fes[icv1]))
names(minima) <- c("letter", "CV1bin", "CV1", "free_energy")
minima<-list(minima=minima, hills=inputfes\$hills, fes=fes, rows=rows, dimension=inputfes\$dimension, per=per, x=inputfes\$x, pcv1=inputfes\$pcv1, pcv2=inputfes\$pcv2)
class(minima) <- "minima"
}
return(minima)
}

#' @export
`+.minima`<-function(min1, min2) {
if(class(min1)!="minima") {
stop("Error: You can sum only two minima objects")
}
if(class(min2)!="minima") {
stop("Error: You can sum only two minima objects")
}
if(sum(min1\$fes)!=sum(min2\$fes)) {
stop("Error: You can sum only minima objects with same FESes")
}
myLETTERS <- c(LETTERS, paste("A", LETTERS, sep=""), paste("B", LETTERS, sep=""))[1:(nrow(min1\$minima)+nrow(min2\$minima))]
minima1<-min1\$minima
minima2<-min2\$minima
minima<-rbind(minima1, minima2)
if(min1\$dimension==2) {
names(minima) <- c("letter", "CV1bin", "CV2bin", "CV1", "CV2", "free_energy")
minima <- minima[order(minima[,6]),]
rownames(minima) <- seq(length=nrow(minima))
minima[,1]<-myLETTERS
minima<-list(minima=minima, hills=min1\$hills, fes=min1\$fes, rows=min1\$rows, dimension=min1\$dimension, per=min1\$per, x=min1\$x, y=min1\$y, pcv1=min1\$pcv1, pcv2=min1\$pcv2)
class(minima) <- "minima"
}
if(min1\$dimension==1) {
names(minima) <- c("letter", "CV1bin", "CV1", "free_energy")
minima <- minima[order(minima[,4]),]
rownames(minima) <- seq(length=nrow(minima))
minima[,1]<-myLETTERS
minima<-list(minima=minima, hills=min1\$hillsfile, fes=min1\$fes, rows=min1\$rows, dimension=min1\$dimension, per=min1\$per, x=min1\$x, pcv1=min1\$pcv1, pcv2=min1\$pcv2)
class(minima) <- "minima"
}
return(minima)
}

#' Print minima object
#'
#' `print.minima` prints free energy minima (identifier, values of bins and collective variables and free energy).
#'
#' @param x minima object.
#' @param ... further arguments passed to or from other methods.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' minima
print.minima<-function(x,...) {
print(x\$minima)
}

#' Print minima object summary
#'
#' `summary.minima` prints summary for free energy minima (identifier, values of bins and collective variables,
#' free energy and equilibrium populations).
#'
#' @param object minima object
#' @param temp temperature in Kelvins
#' @param eunit energy units (kJ/mol or kcal/mol, kJ/mol is default)
#' @param ... further arguments passed to or from other methods.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' summary(minima)
summary.minima<-function(object, temp=300, eunit="kJ/mol",...) {
minims<-object
toprint <- minims\$minima
tind = 6
if(minims\$dimension==1) {
tind = 4
}
if(eunit=="kJ/mol") {
toprint<-cbind(toprint, exp(-1000*toprint[,tind]/8.314/temp))
}
if(eunit=="kcal/mol") {
toprint<-cbind(toprint, exp(-1000*toprint[,tind]*4.184/8.314/temp))
}
sumpop<-sum(toprint[,tind+1])
toprint<-cbind(toprint, 100*toprint[,tind+1]/sumpop)
names(toprint)[tind+1]<-"relative_pop"
names(toprint)[tind+2]<-"pop"
print(toprint)
}

#' Plot minima object
#'
#' `plot.minima` plots free energy surface with minima. The free energy surface is plotted the same
#' way as by plot.fes with additional minima labels.
#'
#' @param x minima object.
#' @param plottype specifies whether 2D free energy surface will be plotted
#'        as image, contours or both (default "both").
#' @param colscale specifies whether color scale will be plotted (default False).
#' @param colscalelab color scale label (default "free energy").
#' @param main an overall title for the plot: see 'title'.
#' @param sub a sub title for the plot: see 'title'.
#' @param xlab a title for the x axis: see 'title'.
#' @param ylab a title for the y axis: see 'title'.
#' @param pch plotting 'character', i.e., symbol to use. See 'points'
#' @param bg background (fill) color for the open plot symbols given by
#'        'pch = 21:25'.
#' @param cex character (or symbol) expansion: a numerical vector. This
#'        works as a multiple of 'par("cex")'.
#' @param asp the y/x aspect ratio, see 'plot.window'.
#' @param col color of the free energy surface. For 1D surface it is the color
#'        of the line. For 2D it is a list of colors such as that generated by
#'        'rainbow', 'heat.colors', 'topo.colors', 'terrain.colors' or similar
#'        functions (default=rainbow(135)[100:1]).
#' @param xlim numeric vector of length 2, giving the x coordinates range.
#' @param ylim numeric vector of length 2, giving the y coordinates range.
#' @param zlim numeric vector of length 2, giving the z coordinates range.
#' @param nlevels number of contour levels desired if 'levels' is not
#'        supplied.
#' @param levels numeric vector of levels at which to draw contour lines.
#' @param labels a vector giving the labels for the contour lines.  If 'NULL'
#'        then the levels are used as labels, otherwise this is coerced
#'        by 'as.character'.
#' @param labcex 'cex' for contour labeling. This is an absolute size, not a
#'        multiple of 'par("cex")'.
#' @param drawlabels logical. Contours are labeled if 'TRUE'.
#' @param method character string specifying where the labels will be located.
#'        Possible values are '"simple"', '"edge"' and '"flattest"'
#'        (the default). See the 'Details' section.
#' @param lwd contour line width.
#' @param contcol contour color.
#' @param lty line type for the lines drawn.
#' @param axes a logical value indicating whether both axes should be drawn
#'        on the plot.
#' @param textcol color of minima labels.
#' @param ... further arguments passed to or from other methods.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' plot(minima)
plot.minima <- function(x, plottype="both",
xlim=NULL, ylim=NULL, zlim=NULL,
colscale=F, colscalelab="free energy",
main=NULL, sub=NULL,
xlab=NULL, ylab=NULL,
nlevels=10, levels=NULL,
col=rainbow(135)[100:1],
labels=NULL, labcex=0.6, drawlabels=TRUE,
method="flattest", textcol="black",
pch=1, bg="red", cex=1,
contcol=par("fg"), lty=par("lty"), lwd=par("lwd"),
asp=NULL, axes=TRUE,...) {
minims <- x
fes<-minims\$fes
rows<-minims\$rows
minlabs<-minims\$minima[,1]
if(minims\$dimension==1) {
x<-minims\$x
if(is.null(xlab)) xlab="CV"
if(is.null(ylab)) ylab="free energy"
if(is.null(xlim)) xlim<-c(min(x),max(x))
if(is.null(ylim)) {
ylim<-range(pretty(range(fes)))
}
minpoints<-minims\$minima[,3:4]
minpoints[,2]<-minpoints[,2]+0.05*(ylim[2]-ylim[1])
plot(x, fes, type="l", lwd=lwd,
col=col, xlim=xlim, ylim=ylim,
xlab=xlab, ylab=ylab, axes=axes,
main=main, sub=sub, asp=asp)
text(minpoints, labels=minlabs, col=textcol, xlim=xlim, ylim=ylim, cex=cex)
} else {
minpoints<-minims\$minima[,4:5]
x<-minims\$x
y<-minims\$y
if(is.null(xlab)) xlab="CV1"
if(is.null(ylab)) ylab="CV2"
if(is.null(zlim)) {
zlim<-range(pretty(range(fes)))
}
if(is.null(levels)) {
levels<-pretty(zlim, nlevels)
}
if(is.null(xlim)) xlim<-c(min(x),max(x))
if(is.null(ylim)) ylim<-c(min(y),max(y))
if(colscale) {
layout(matrix(c(1,2), 1, 2, byrow = TRUE), widths=c(4,1))
}
if(plottype=="points") {
text(minpoints, labels=minlabs, col=textcol, xlim=xlim, ylim=ylim,
xlab=xlab, ylab=ylab, axes=axes,
pch=pch, bg=bg, cex=cex,
main=main, sub=sub, asp=asp)
}
if(plottype=="image" || plottype=="both") {
image(x,y,fes, zlim=zlim,
col=col, xlim=xlim, ylim=ylim,
xlab=xlab, ylab=ylab, axes=axes,
main=main, sub=sub, asp=asp)
text(minpoints, labels=minlabs, col=textcol, xlim=xlim, ylim=ylim, cex=cex)
}
if(plottype=="contour") {
contour(x,y,fes, zlim=zlim,
nlevels=nlevels, levels=levels,
labels=labels, labcex=labcex, drawlabels=drawlabels,
method=method, col=contcol, lty=lty, lwd=lwd,
main=main, sub=sub, asp=asp)
text(minpoints, labels=minlabs, col=textcol, xlim=xlim, ylim=ylim, cex=cex)
}
if(plottype=="both") {
contour(x,y,fes, zlim=zlim,
nlevels=nlevels, levels=levels,
labels=labels, labcex=labcex, drawlabels=drawlabels,
}
if(colscale) {
smat<-matrix(seq(from=zlim[1], to=zlim[2], length.out=100))
image(c(0), seq(from=zlim[1], to=zlim[2], length.out=100),
t(smat), zlim=zlim, col=col, xlab="", ylab=colscalelab, axes=F)
axis(2, lty=lty, lwd=lwd)
box(lwd=lwd)
par(mfrow=c(1,1))
}
}
}

#' Calculate free energy profile for minima object (generic function for 'metadynminer'
#'
#' `feprof` calculates free energy profiles for free energy minima. It finds the global minimum
#' at the `imax` and calculates the evolution of free energies of a local vs. the global free energy
#' minimum. The free energy of the global minimum is constant (zero).
#'
#' @param minims minima object.
#' @param imax index of a hill from which summation stops (default the rest of hills).
#'
#' @export
feprof <- function(minims, imax) {
UseMethod("feprof")
}

#' Calculate free energy profile for minima object
#'
#' `feprof.minima` calculates free energy profiles for free energy minima. It finds the global minimum
#' at the `imax` and calculates the evolution of free energies of a local vs. the global free energy
#' minimum. The free energy of the global minimum is constant (zero).
#'
#' @param minims minima object.
#' @param imax index of a hill from which summation stops (default the rest of hills).
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' prof<-feprof(minima)
#' prof
feprof.minima <- function(minims, imax=NULL) {
fes<-minims\$fes
rows<-minims\$rows
mins<-minims\$minima
hills<-minims\$hills
if(is.null(imax)) {
imax<-nrow(hills)
}
if(imax>nrow(hills)) {
imax<-nrow(hills)
cat("Warning: You requested more hills by imax than available, using all hills\n")
}
tt <- 1:imax
mms <- data.frame(tt)
if(minims\$dimension==1) {
for(i in 1:nrow(mins)) {
if(minims\$per[1]==T) {
mm<-fe1dp(hills[,2], hills[,3], hills[,4], mins[i,3], minims\$pcv1[2]-minims\$pcv1[1], 0, imax-1)
} else {
mm<-fe1d(hills[,2], hills[,3], hills[,4], mins[i,3], 0, imax-1)
}
mms<-cbind(mms,mm)
}
}
if(minims\$dimension==2) {
for(i in 1:nrow(mins)) {
if(minims\$per[1]==T && minims\$per[2]==T) {
mm<-fe2dp12(hills[,2], hills[,3], hills[,4], hills[,5], hills[,6], mins[i,4], mins[i,5], minims\$pcv1[2]-minims\$pcv1[1], minims\$pcv2[2]-minims\$pcv2[1], 0, imax-1)
}
if(minims\$per[1]==T && minims\$per[2]==F) {
mm<-fe2dp1(hills[,2], hills[,3], hills[,4], hills[,5], hills[,6], mins[i,4], mins[i,5], minims\$pcv1[2]-minims\$pcv1[1], 0, imax-1)
}
if(minims\$per[1]==F && minims\$per[2]==T) {
mm<-fe2dp2(hills[,2], hills[,3], hills[,4], hills[,5], hills[,6], mins[i,4], mins[i,5], minims\$pcv2[2]-minims\$pcv2[1], 0, imax-1)
}
if(minims\$per[1]==F && minims\$per[2]==F) {
mm<-fe2d(hills[,2], hills[,3], hills[,4], hills[,5], hills[,6], mins[i,4], mins[i,5], 0, imax-1)
}
mms<-cbind(mms,mm)
}
}
profs<-list(mms=mms, mins=mins, fes=fes, rows=rows, dimension=minims\$dimension, per=minims\$per, pcv1=minims\$pcv1, pcv2=minims\$pcv2)
class(profs) <- "profiles"
return(profs)
}

#' Print profiles object
#'
#' `print.profiles` prints free energy profile.
#'
#' @param x minima object.
#' @param ... further arguments passed to or from other methods.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' prof<-feprof(minima)
#' prof
print.profiles <- function(x,...) {
outprofile <- x\$mins
print(outprofile)
}

#'
#' `summary.profiles` prints the list of free energy minima with maximal
#' and minimal free energy differences.
#'
#' @param object profiles object.
#' @param imind index of a hill from which calculation of difference
#'        starts (default 1).
#' @param imaxd index of a hill from which calculation of difference
#'        stops (default the rest of hills).
#' @param ... further arguments passed to or from other methods.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' prof<-feprof(minima)
#' summary(prof)
summary.profiles <- function(object, imind=1, imaxd=NULL,...) {
profs<-object
if(!is.null(imaxd)) {
if(nrow(profs\$mms)<imaxd) {
cat("Warning: You requested more hills by imaxd than available, using all hills\n")
imaxd<-nrow(profs\$mms)
}
}
if(is.null(imaxd)) {
imaxd<-nrow(profs\$mms)
}
if(imind>imaxd) {
stop("Error: imaxd cannot be lower than imind")
}
if(profs\$dimension==1) {
outprofile <- profs\$mins
mms<-profs\$mms[,2:ncol(profs\$mms)]-profs\$mms[,2]
outprofile <- cbind(outprofile,apply(mms[imind:imaxd,],2,min))
outprofile <- cbind(outprofile,apply(mms[imind:imaxd,],2,max))
outprofile <- cbind(outprofile,t(mms[imaxd,]))
names(outprofile)[5:7]<-c("min diff", "max diff", "tail")
print(outprofile)
} else if(profs\$dimension==2) {
outprofile <- profs\$mins
mms<-profs\$mms[,2:ncol(profs\$mms)]-profs\$mms[,2]
outprofile <- cbind(outprofile,apply(mms[imind:imaxd,],2,min))
outprofile <- cbind(outprofile,apply(mms[imind:imaxd,],2,max))
outprofile <- cbind(outprofile,t(mms[imaxd,]))
names(outprofile)[7:9]<-c("min diff", "max diff", "tail")
print(outprofile)
} else if(profs\$dimension==3) {
outprofile <- profs\$mins
mms<-profs\$mms[,2:ncol(profs\$mms)]-profs\$mms[,2]
outprofile <- cbind(outprofile,apply(mms[imind:imaxd,],2,min))
outprofile <- cbind(outprofile,apply(mms[imind:imaxd,],2,max))
outprofile <- cbind(outprofile,t(mms[imaxd,]))
names(outprofile)[9:11]<-c("min diff", "max diff", "tail")
print(outprofile)
}
}

#' Plot free energy profile
#'
#' `plot.profiles` plots evolution of free energy differences between minima.
#' They are colored by rainbow colors from the global one (blue) to the highest (red).
#'
#' @param x profiles object.
#' @param which vector of indexes of profiles to be plotted (default all).
#' @param ignoretime time in the first column of the HILLS file will be ignored.
#' @param main an overall title for the plot: see 'title'.
#' @param sub a sub title for the plot: see 'title'.
#' @param xlab a title for the x axis: see 'title'.
#' @param ylab a title for the y axis: see 'title'.
#' @param asp the y/x aspect ratio, see 'plot.window'.
#' @param col color code or name, see 'par'.
#' @param xlim numeric vector of length 2, giving the x coordinates range.
#' @param ylim numeric vector of length 2, giving the y coordinates range.
#' @param lwd line width.
#' @param axes a logical value indicating whether both axes should be drawn
#'        on the plot.
#' @param ... further arguments passed to or from other methods.
#'
#' @export
#' @examples
#' tfes<-fes(acealanme, imax=5000)
#' minima<-fesminima(tfes)
#' prof<-feprof(minima)
#' plot(prof)
plot.profiles <- function(x, which=NULL,
ignoretime=FALSE,
xlim=NULL, ylim=NULL,
main=NULL, sub=NULL,
xlab=NULL, ylab=NULL,
col=NULL, asp=NULL, lwd=1, axes=T,...) {
profs<-x
if(is.null(which)) which<-1:(ncol(profs\$mms)-1)
if(is.null(xlab)) xlab<-"Index"
if(is.null(ylab)) ylab<-"Free Energy Difference (kJ/mol)"
if(is.null(col)) col<-rainbow(ceiling(1.35*length(which)))[length(which):1]
col<-rep(col, (ncol(profs\$mms)-1))
mms<-profs\$mms[,2:ncol(profs\$mms)]-profs\$mms[,2]
if(is.null(xlim)) xlim<-c(min(profs\$mms[,1]),max(profs\$mms[,1]))
if(is.null(ylim)) {
yliml <- min(mms[,1:ncol(mms)])
ylimu <- max(mms[,1:ncol(mms)])
ylim<-c(yliml-0.05*(ylimu-yliml), ylimu+0.05*(ylimu-yliml))
}
if(ignoretime) {
plot(seq(from=profs\$mms[1,1], by=profs\$mms[1,1], length.out=nrow(profs\$mms)),
mms[,1], type="l",
xlab=xlab, ylab=ylab,
main=main, sub=sub,
xlim=xlim, ylim=ylim,
lwd=lwd, asp=asp, axes=axes)
for(i in 1:length(which)) {
lines(profs\$mms[,1], mms[,which[i]],
lwd=lwd, col=col[i])
}
} else {
plot(profs\$mms[,1], mms[,1], type="l",
xlab=xlab, ylab=ylab,
main=main, sub=sub,
xlim=xlim, ylim=ylim,
lwd=lwd, asp=asp, axes=axes)
for(i in 1:length(which)) {
lines(profs\$mms[,1], mms[,which[i]],
lwd=lwd, col=col[i])
}
}
}
```