Updating package for publication. Commit 1

FigurePaper/exampleA/dependencies.R

@@ -21,9 +21,9 @@ function(ntIDs) {
     return(rmsd(pdb1$xyz[,sel1$xyz],fit[,sel2$xyz]))
 }
 
-## "filter_pyle" reproduces the iterative process of RMSD comparison to chose
+## "filter_helical" reproduces the iterative process of RMSD comparison to chose
 ## an helical nucleotide of reference
-filter_pyle <- 
+filter_helical <- 
 function(ntinfo, helicalntID, RMSD, bandwidths=c(40,40), cutoff=0.85) {
 
     twideMatrix <- t(acast(RMSD, nt1~nt2, value.var="rmsd"))

FigurePaper/exampleA/etatheta.R

@@ -21,7 +21,7 @@ cat("Getting data\n")
 ## ----------------------------------------------------------------------------
 
 ## Get latest Leontist non-redundant list of RNA structures
-infochains <- getLeontisList(threshold="2.5A", as.df=TRUE)
+infochains <- getRNAList(threshold="2.5A", as.df=TRUE)
 
 ## Get structural data
 ntinfo <- pipeNucData(pdbID=infochains$pdb, model=infochains$model,
@@ -56,7 +56,7 @@ 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)
+ref <- filter_helical(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)

README.md

@@ -7,7 +7,7 @@ VeriNA3d is an R package for the analysis of Nucleic Acid structural data. The s
 ## Installation
 ---------------
 
-Instructions for Unix systems
+Instructions
 
 1- Make sure you have all the dependencies already installed in R. If not the case, open R and run:
  
@@ -16,17 +16,9 @@ Instructions for Unix systems
 
 2- Install veriNA3d according with your R version:
 
-For R >= 3.5
  
 
-    install.packages("https://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d/raw/master/veriNA3d_R-3.5.tar.gz", repos = NULL)
-
-If you have R-3.4:
- 
-
-    install.packages("https://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d/raw/master/veriNA3d_R-3.4.tar.gz", repos = NULL)
-
-The whole package has been developed and tested in R-3.5, which makes it the recommended option. Furthermore, using R-3.5 speeds up the cifParser function, which has a dramatic effect when working with large mmCIF files. The package has been also made available for R-3.4 since some unix users are experiencing problems when installing R-3.5.
+    install.packages("https://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d/raw/master/veriNA3d.tar.gz", repos = NULL)
 
 3- To start using it, just load the package!