library(bio3d)
library(car)
source("confplot_funs.R")

pdb <- read.pdb("1XCK_apo_dimer_noH.pdb")


load("pca_dimers.RData")
load("projected.RData")
load("projected_1XCK-rhod.RData")

## initial tests
a <- c()
b <- c()
for ( i in c(1,3,5) ) {

  # every 10 ns
  inds <- c(500,1000,1500) + (1500* (i-1))
  
  # every 2 ns
  #inds <- seq(600, 1500, by=100)  + (1500* (i-1))
  a <- c(a, sim116$cis$proj[inds,1])
  a <- c(a, sim116$trans$proj[inds,1])
  b <- c(b, sim129$cis$proj[inds,1])
}
t.test(a,b)
wilcox.test(a,b, alternative="less")

a <- c()
b <- c()
for ( i in c(2,4,6) ) {
  
  ## every 10 ns
  inds <- c(500,1000,1500) + (1500* (i-1))

  ## ervery 2 ns
  #inds <- seq(600, 1500, by=100)  + (1500* (i-1))

  a <- c(a, sim116$cis$proj[inds,1])
  a <- c(a, sim116$trans$proj[inds,1])
  b <- c(b, sim129$cis$proj[inds,1])
}
t.test(a,b)
wilcox.test(a,b, alternative="less")



## test with both rhodanese simulation as well
a <- c()
b <- c()
for ( i in c(2,4,6) ) {
  inds <- seq(1, 1500, 500) + (1500* (i-1))
  a <- c(a, sim116$cis$proj[inds,1])
  a <- c(a, sim116$trans$proj[inds,1])
  b <- c(b, sim129$cis$proj[inds,1])
}

for ( i in c(2,4,6) ) {
  inds <- seq(1, 1500, 500) + (1500* (i-1))
  b <- c(b, sim171b$cis$proj[inds,1])
}
t.test(a,b, alternative="less")
wilcox.test(a,b, alternative="less")