--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmsd.R	Mon Oct 08 12:49:59 2018 -0400
@@ -0,0 +1,67 @@
+#!/usr/bin/env Rscript
+
+options(stringAsfactors = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+library(bio3d)
+
+dcdfile <- args[1]
+pdbfile <- args[2]
+selection <- args[3]
+
+dcd <- read.dcd(dcdfile)
+pdb <- read.pdb(pdbfile)
+
+
+if (selection == "string") {
+    domain <- args[4]
+    output <- args[5]
+    rmsd_plot <- args[6]
+    rmsd_hist <- args[7]
+    inds <- atom.select(pdb, string = domain)
+} 
+if (selection == "resno") {
+    res1 <- args[4]
+    res2 <- args[5]
+    output <- args[6]
+    rmsd_plot <- args[7]
+    rmsd_hist <- args[8]
+    inds <- atom.select(pdb, resno=res1:res2)
+} 
+if (selection == "elety") {
+    domain <- args[4]
+    output <- args[5]
+    rmsd_plot <- args[6]
+    rmsd_hist <- args[7]
+    inds <- atom.select(pdb, elety = domain)
+}
+if (selection == "resid") {
+    domain <- args[4]
+    output <- args[5]
+    rmsd_plot <- args[6]
+    rmsd_hist <- args[7]
+    inds <- atom.select(pdb, resid = domain)
+}
+if (selection == "segid") {
+    domain <- args[4]
+    output <- args[5]
+    rmsd_plot <- args[6]
+    rmsd_hist <- args[7]
+    inds <- atom.select(pdb, segid = domain)
+}
+
+xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz)
+
+rd <- rmsd(xyz[1,inds$xyz], xyz[,inds$xyz])
+
+write.table(rd, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t")
+
+png(rmsd_plot)
+plot(rd, typ="l", ylab="RMSD (Å)", xlab="Frame No.")
+points(lowess(rd), typ="l", col="red", lty=2, lwd=2)
+dev.off()
+
+png(rmsd_hist)
+hist(rd, breaks=40, freq=FALSE, main="RMSD Histogram", xlab="RMSD")
+lines(density(rd), typ="l", col="red", lty=2, lwd=2)
+dev.off()