library(gclus)
library(maptools)
library(bio3d)
source("confplot_funs.R")
#load("xrayPCA.RData")
load("xrayPCA_Tstates.RData")


pdb.closed <- read.pdb("1XCK_chainA_noWAT_noH.pdb")
ca.inds <- atom.select(pdb.closed, "calpha")


      

trj.inds <- seq(1, 1500, by=1)

sim117 <- NULL
prefix117 <- "/net/gulrotkake/slars/groel_md/1XCK/117_1XCK_hepta/results/traj_monomer/"

prefix <- "20-50ns_noWAT_1500frames_noH_chain_"

for ( i in 1:7 ) {
  tmptrj <- read.ncdf(paste(prefix117, prefix, i , ".nc", sep=""))
  sim117$xyzfit[[i]] <- fit.xyz(fixed = pdbs$xyz[1,gaps.pos$f.inds],
                                mobile = tmptrj[trj.inds, ca.inds$xyz],
                                fixed.inds = core$c1A.xyz,
                                mobile.inds = core$c1A.xyz,
                                full.pdbs = FALSE)
}

sim128 <- NULL
prefix128 <- "/net/gulrotkake/slars/groel_md/1XCK/128_1XCK_hepta_MGATP/results/traj_monomer/"

prefix <- "20-50ns_noWAT_1500frames_noH_chain_"

for ( i in 1:7 ) {
  tmptrj <- read.ncdf(paste(prefix128, prefix, i , ".nc", sep=""))
  sim128$xyzfit[[i]] <- fit.xyz(fixed = pdbs$xyz[1,gaps.pos$f.inds],
                                mobile = tmptrj[trj.inds, ca.inds$xyz],
                                fixed.inds = core$c1A.xyz,
                                mobile.inds = core$c1A.xyz,
                                full.pdbs = FALSE)
}

## 1XCK heptamers
tmptrj <- NULL
for ( i in 1:7 ) {
  tmptrj=rbind(tmptrj, sim117$xyzfit[[i]])
}
sim117$cis$proj <- pca.project(tmptrj, pc.xray)

tmptrj <- NULL
for ( i in 1:7 ) {
  tmptrj=rbind(tmptrj, sim128$xyzfit[[i]])
}
sim128$cis$proj <- pca.project(tmptrj, pc.xray)


sim117$xyzfit <- NULL
sim128$xyzfit <- NULL
save(sim117, sim128, file="projected_1XCK-heptamers.RData")