Deleted old folders

FigurePaper/example1/dependencies.R

-## "cache" saves trinucleotide backbones in RAM for latter RMSD calculations
-cache <-
-function(ntID, name, ntinfo) {
-    ## Trim trinucleotide backbone
-    pdb <- trimByID(ntID=ntID, ntinfo=ntinfo, prev=1, post=1,
-                    alt=c("uniq"), cutoff=0, justbackbone=TRUE,
-                    verbose=FALSE)
-    ## Save as an independent pdb file in RAM
-    assign(name, pdb, envir=.GlobalEnv)
-}
-
-## "pwrmsd" calculates pair wise RMSD between nucleotides presaved in RAM
-pwrmsd <-
-function(ntIDs) {
-    pdb1 <- get(paste("nt", ntIDs[1], sep=""))
-    pdb2 <- get(paste("nt", ntIDs[2], sep=""))
-    sel1 <- atom.select(pdb1)
-    sel2 <- atom.select(pdb2)
-    fit=fit.xyz(pdb1$xyz, pdb2$xyz,
-                fixed.inds=sel1$xyz, mobile.inds=sel2$xyz)
-    return(rmsd(pdb1$xyz[,sel1$xyz],fit[,sel2$xyz]))
-}
-
-## "filter_pyle" reproduces the iterative process of RMSD comparison to chose
-## an helical nucleotide of reference
-filter_pyle <- 
-function(ntinfo, helicalntID, RMSD, bandwidths=c(40,40), cutoff=0.85) {
-
-    twideMatrix <- t(acast(RMSD, nt1~nt2, value.var="rmsd"))
-    twideMatrix<-rbind(rep(NA,length(helicalntID)-1),twideMatrix)
-    twideMatrix<-cbind(twideMatrix,rep(NA,length(helicalntID)))
-    rownames(twideMatrix)[1]<-helicalntID[1]
-    colnames(twideMatrix)[length(helicalntID)]<-helicalntID[length(helicalntID)]
-
-    Matrix <- twideMatrix
-    while (length(helicalntID) > 1) {
-        Matrix <- Matrix[which(rownames(Matrix) %in% helicalntID),
-                            which(colnames(Matrix) %in% helicalntID)]
-
-        column_sums <- colSums(Matrix, na.rm=TRUE)
-        row_sums <- rowSums(Matrix, na.rm=TRUE)
-        RMSDaverages <- (column_sums + row_sums)/(length(row_sums) - 1)
-        index <- which.min(RMSDaverages)
-        lowestaverage <- RMSDaverages[index]
-        reference_nt <- helicalntID[index]
-        A <- Matrix[which(rownames(Matrix) == reference_nt), ]
-        names(A) <- colnames(Matrix)
-        A <- A[complete.cases(A)]
-        B <- Matrix[, which(colnames(Matrix) == reference_nt)]
-        names(B) <- colnames(Matrix)
-        B <- B[complete.cases(B)]
-        reference_nt_RMSD <- append(A,B); rm(list=c("A","B"))
-        helicalntID <- sort(append(reference_nt, as.numeric(
-                            names(reference_nt_RMSD)[which(
-                            reference_nt_RMSD < lowestaverage)])))
-    }
-
-    return(helicalntID)
-}

FigurePaper/example1/etatheta.R

-#!/usr/bin/Rscript
-## EXAMPLE 1
-## Description: From Leontis non-redundant RNA list, get eta-theta plot
-##              following Pyle's method.
-## Author: Diego Gallego
-
-## ----------------------------------------------------------------------------
-## Preprocess
-## ----------------------------------------------------------------------------
-## Load necessary packages for the example
-library(veriNA3d)
-library(bio3d)
-library(reshape2) ## Specific dependency for this example!
-
-## Load specific functions for the example
-source("dependencies.R")
-
-## ----------------------------------------------------------------------------
-## Get Raw data
-cat("Getting data\n")
-## ----------------------------------------------------------------------------
-
-## Get latest Leontist non-redundant list of RNA structures
-infochains <- getLeontisList(threshold="2.5A", as.df=TRUE)
-
-## Get structural data
-ntinfo <- pipeNucData(pdbID=infochains$pdb, model=infochains$model,
-                        chain=infochains$chain, cores=1)
-
-## ----------------------------------------------------------------------------
-## Clean data. Raw -> Tidy
-cat("Cleaning data\n")
-## ----------------------------------------------------------------------------
-
-## Subset north nucleotides
-north <- ntinfo[cleanByPucker(ntinfo, surenorth=TRUE), ]
-
-## Find non-broken canonical nucleotides
-id <- which(north$puc_valid==TRUE & north$Break==FALSE & north$big_b == FALSE & 
-            north$eta_valid == TRUE & north$theta_valid == TRUE &
-            grepl("^[GAUC]-[GAUC]-[GAUC]$", north$localenv, perl=TRUE))
-usefulnt <- north$ntID[id]
-
-## Filter helical nucleotides before ploting =================================
-
-## Create all the necessary trinucleotides for pair-wise RMSD calculations
-invisible(mapply(FUN=cache, ntID=usefulnt, name=paste("nt", usefulnt, sep=""),
-                    MoreArgs=list(ntinfo=ntinfo)))
-
-## Find helical nucleotides
-HDR <- findHDR(ntID=usefulnt, ntinfo=ntinfo, x="eta", y="theta", SD_DENS=15)
-
-## Compute pair-wise RMSD between helical nucleotides
-pairwise <- t(combn(HDR[[1]], 2))
-RMSD_calc <- apply(FUN=pwrmsd, MARGIN=1, X=pairwise)
-RMSD <- data.frame(nt1=pairwise[, 1], nt2=pairwise[, 2], rmsd=RMSD_calc)
-
-## Apply Pyle method
-ref <- filter_pyle(ntinfo=ntinfo, helicalntID=HDR[[1]], RMSD=RMSD)
-
-pairs <- data.frame(usefulnt=usefulnt, reference=rep(ref, length(usefulnt)))
-RMSD2 <- apply(FUN=pwrmsd, MARGIN=1, X=pairs)
-
-## ===========================================================================
-## ----------------------------------------------------------------------------
-## Exploratory analysis. Plot
-cat("Plotting data\n")
-## ----------------------------------------------------------------------------
-tiff("example1.tiff", height=10.5, width=16.5, units="cm", res=300)
-plot2D(ntinfo=ntinfo, x="eta", y="theta", etatheta=TRUE,
-        ntID=pairs[which(RMSD2 > 0.85), 1])
-dev.off()

FigurePaper/example1/timing.txt

-real    125m49.951s
-user    113m31.407s
-sys     0m21.852s