From 052e14899910c188703d90997f3de232d97b4a87 Mon Sep 17 00:00:00 2001 From: hyginn Date: Wed, 14 Oct 2020 06:18:07 +1000 Subject: [PATCH] Removed lock-out message --- .utilities.R | 8 ++++---- RPR-SX-PDB.R | 38 ++++++++++++++++---------------------- 2 files changed, 20 insertions(+), 26 deletions(-) diff --git a/.utilities.R b/.utilities.R index 4fa4082..dbfe216 100644 --- a/.utilities.R +++ b/.utilities.R @@ -1,6 +1,6 @@ # tocID <- "./.utilities.R" # -# Miscellaneous R code to suppport the project +# Miscellaneous R code to support the project # # Version: 1.4 # Date: 2017-09 - 2020-09 @@ -20,7 +20,7 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> ----------------------------------------------------------- #TOC> 1 SCRIPTS TO SOURCE 52 @@ -45,7 +45,7 @@ #TOC> 5.04 sealKey() 593 #TOC> 5.05 selectChi2() 623 #TOC> 5.06 selectENSP() 636 -#TOC> +#TOC> #TOC> ========================================================================== @@ -574,7 +574,7 @@ selectPDBrep <- function(n, forCredit = FALSE) { seed <- as.integer(Sys.time()) cat("NOTE: This selection will not validate for a course submission.\n") cat(" If you intend to use it for an assignment task, invoke\n") - cat(" this function like \"selectPDBrep(n, forCredit = TRUE)\".\n\n") + cat(" it like \"selectPDBrep(n = 15, forCredit = TRUE)\".\n\n") } pdbRep <- readRDS("./data/pdbRep.rds") # loads pdbRep diff --git a/RPR-SX-PDB.R b/RPR-SX-PDB.R index 904d78e..14db8ca 100644 --- a/RPR-SX-PDB.R +++ b/RPR-SX-PDB.R @@ -1,11 +1,5 @@ # tocID <- "RPR-SX-PDB.R" # -# ---------------------------------------------------------------------------- # -# PATIENCE ... # -# Do not yet work wih this code. Updates in progress. Thank you. # -# boris.steipe@utoronto.ca # -# ---------------------------------------------------------------------------- # -# # Purpose: A Bioinformatics Course: # R code accompanying the RPR-SX-PDB unit. # @@ -38,22 +32,22 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> ---------------------------------------------------------- -#TOC> 1 Introduction to the bio3D package 62 -#TOC> 2 A Ramachandran plot 153 -#TOC> 3 Density plots 229 -#TOC> 3.1 Density-based colours 243 -#TOC> 3.2 Plotting with smoothScatter() 262 -#TOC> 3.3 Plotting hexbins 277 -#TOC> 3.4 Plotting density contours 305 -#TOC> 3.4.1 ... as overlay on a coloured grid 338 -#TOC> 3.4.2 ... as filled countour 355 -#TOC> 3.4.3 ... as a perspective plot 386 -#TOC> 4 cis-peptide bonds 404 -#TOC> 5 H-bond lengths 419 -#TOC> +#TOC> 1 Introduction to the bio3D package 63 +#TOC> 2 A Ramachandran plot 155 +#TOC> 3 Density plots 231 +#TOC> 3.1 Density-based colours 245 +#TOC> 3.2 Plotting with smoothScatter() 264 +#TOC> 3.3 Plotting hexbins 279 +#TOC> 3.4 Plotting density contours 307 +#TOC> 3.4.1 ... as overlay on a coloured grid 340 +#TOC> 3.4.2 ... as filled countour 357 +#TOC> 3.4.3 ... as a perspective plot 388 +#TOC> 4 cis-peptide bonds 406 +#TOC> 5 H-bond lengths 421 +#TOC> #TOC> ========================================================================== @@ -360,7 +354,7 @@ abline(h = 0, lwd = 0.5, col = "#00000044") abline(v = 0, lwd = 0.5, col = "#00000044") -# === 3.4.2 ... as filled countour +# === 3.4.2 ... as filled countour filled.contour(dPhiPsi, xlim = c(-180, 180), ylim = c(-180, 180), @@ -391,7 +385,7 @@ filled.contour(dPhiPsi, abline(v = 0, lwd = 0.5, col = "#00000044") }) -# === 3.4.3 ... as a perspective plot +# === 3.4.3 ... as a perspective plot persp(dPhiPsi, xlab = "phi",