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Removed lock-out message

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hyginn 2020-10-14 06:18:07 +10:00
parent 55a0d18a66
commit 052e148999
2 changed files with 20 additions and 26 deletions
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8
.utilities.R
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@ -1,6 +1,6 @@
# tocID <- "./.utilities.R" # tocID <- "./.utilities.R"
# #
# Miscellaneous R code to suppport the project # Miscellaneous R code to support the project
# #
# Version: 1.4 # Version: 1.4
# Date: 2017-09 - 2020-09 # Date: 2017-09 - 2020-09
@ -20,7 +20,7 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ----------------------------------------------------------- #TOC> -----------------------------------------------------------
#TOC> 1 SCRIPTS TO SOURCE 52 #TOC> 1 SCRIPTS TO SOURCE 52
@ -45,7 +45,7 @@
#TOC> 5.04 sealKey() 593 #TOC> 5.04 sealKey() 593
#TOC> 5.05 selectChi2() 623 #TOC> 5.05 selectChi2() 623
#TOC> 5.06 selectENSP() 636 #TOC> 5.06 selectENSP() 636
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -574,7 +574,7 @@ selectPDBrep <- function(n, forCredit = FALSE) {
seed <- as.integer(Sys.time()) seed <- as.integer(Sys.time())
cat("NOTE: This selection will not validate for a course submission.\n") 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(" 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 pdbRep <- readRDS("./data/pdbRep.rds") # loads pdbRep

38
RPR-SX-PDB.R
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@ -1,11 +1,5 @@
# tocID <- "RPR-SX-PDB.R" # 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: # Purpose: A Bioinformatics Course:
# R code accompanying the RPR-SX-PDB unit. # R code accompanying the RPR-SX-PDB unit.
# #
@ -38,22 +32,22 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ---------------------------------------------------------- #TOC> ----------------------------------------------------------
#TOC> 1 Introduction to the bio3D package 62 #TOC> 1 Introduction to the bio3D package 63
#TOC> 2 A Ramachandran plot 153 #TOC> 2 A Ramachandran plot 155
#TOC> 3 Density plots 229 #TOC> 3 Density plots 231
#TOC> 3.1 Density-based colours 243 #TOC> 3.1 Density-based colours 245
#TOC> 3.2 Plotting with smoothScatter() 262 #TOC> 3.2 Plotting with smoothScatter() 264
#TOC> 3.3 Plotting hexbins 277 #TOC> 3.3 Plotting hexbins 279
#TOC> 3.4 Plotting density contours 305 #TOC> 3.4 Plotting density contours 307
#TOC> 3.4.1 ... as overlay on a coloured grid 338 #TOC> 3.4.1 ... as overlay on a coloured grid 340
#TOC> 3.4.2 ... as filled countour 355 #TOC> 3.4.2 ... as filled countour 357
#TOC> 3.4.3 ... as a perspective plot 386 #TOC> 3.4.3 ... as a perspective plot 388
#TOC> 4 cis-peptide bonds 404 #TOC> 4 cis-peptide bonds 406
#TOC> 5 H-bond lengths 419 #TOC> 5 H-bond lengths 421
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -360,7 +354,7 @@ abline(h = 0, lwd = 0.5, col = "#00000044")
abline(v = 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, filled.contour(dPhiPsi,
xlim = c(-180, 180), ylim = c(-180, 180), xlim = c(-180, 180), ylim = c(-180, 180),
@ -391,7 +385,7 @@ filled.contour(dPhiPsi,
abline(v = 0, lwd = 0.5, col = "#00000044") abline(v = 0, lwd = 0.5, col = "#00000044")
}) })
# === 3.4.3 ... as a perspective plot # === 3.4.3 ... as a perspective plot
persp(dPhiPsi, persp(dPhiPsi,
xlab = "phi", xlab = "phi",