--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pca.R	Mon Oct 08 12:49:36 2018 -0400
@@ -0,0 +1,61 @@
+#!/usr/bin/env Rscript
+
+options(stringAsfactors = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+library(bio3d)
+
+dcdfile <- args[1]
+pdbfile <- args[2]
+
+dcd <- read.dcd(dcdfile)
+pdb <- read.pdb(pdbfile)
+
+method <- args[3]
+selection <- args[4]
+domain <- args[5]
+
+output <- args[6]
+pca_plot <- args[7]
+pca_cluster  <- args[8]
+pc1_rmsf <- args[9]
+
+
+if (selection == "string") {
+    inds <- atom.select(pdb, string = domain)
+} 
+if (selection == "elety") {
+    inds <- atom.select(pdb, elety = domain)
+}
+if (selection == "resid") {
+    inds <- atom.select(pdb, resid = domain)
+}
+if (selection == "segid") {
+    inds <- atom.select(pdb, segid = domain)
+}
+xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz)
+
+if (method == "FALSE") {
+    pc <- pca.xyz(xyz[,inds$xyz], use.svd=FALSE)
+}
+if (method == "TRUE") {
+    pc <- pca.xyz(xyz[,inds$xyz], use.svd=TRUE)
+}
+
+write.table(pc$au[,1:2:3], file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t")
+
+png(pca_plot)
+plot(pc, col=bwr.colors(nrow(xyz)) )
+dev.off()
+
+png(pca_cluster)
+hc <- hclust(dist(pc$z[,1:2]))
+grps <- cutree(hc, k=2)
+plot(pc, col=grps)
+dev.off()
+
+png(pc1_rmsf)
+plot.bio3d(pc$au[,1], ylab="PC1 (A)", xlab="Residue Position", typ="l")
+points(pc$au[,2], typ="l", col="blue")
+dev.off()
+