--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualize_pc.R	Tue Feb 26 08:29:24 2019 -0500
@@ -0,0 +1,45 @@
+#!/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]
+id <- args[6] 
+pcid <- as.integer(id)
+
+pdbout <- args[7]
+
+
+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$xyz], use.svd=TRUE)
+}
+
+mktrj.pca(pc, pc=pcid, b=pc$au[,pcid], file=pdbout)
+