ydeng/bch441-work-abc-units
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Removed lock-out message

Browse Source
This commit is contained in:
hyginn 2020-10-14 06:18:07 +10:00
parent 55a0d18a66
commit 052e148999
2 changed files with 20 additions and 26 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
.utilities.R
View File

@ -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

38
RPR-SX-PDB.R
View File

@ -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",