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return ChimeraX response invisibly and provide example of using the data for a plot

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hyginn 2020-09-29 14:12:11 +10:00
parent 12e3de439f
commit 9e77d948e9
2 changed files with 43 additions and 32 deletions
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33
.utilities.R
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@ -20,7 +20,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -----------------------------------------------------------
#TOC> 1 SCRIPTS TO SOURCE 51
@ -44,7 +44,7 @@
#TOC> 5.03 selectPDBrep() 560
#TOC> 5.04 selectChi2() 596
#TOC> 5.05 selectENSP() 609
#TOC>
#TOC>
#TOC> ==========================================================================
@ -481,36 +481,35 @@ H <- function(x, N) {
# == 4.11 CX() (ChimeraX remote command) ===================================
CX <- function(cmd, port = CXPORT, quietly = FALSE, capture = FALSE) {
CX <- function(cmd, port = CXPORT, quietly = FALSE) {
# send a command to ChimeraX listening on port CXPORT via its REST
# interface.
# Parameters:
# cmd char a ChireaX commandline command
# port int the portnumber on which ChimeraX is listening
# quietly logical if FALSE, cat() the contents of the response
# capture logical if TRUE, return the contents of the response
#
# Value: the reply by ChineraX, or invisible(NULL)
# Value: the reply by ChimeraX, invisibly.
CXREST <- sprintf("http://127.0.0.1:%s/run?", CXPORT)
cmd <- gsub("(^\\s+)|(\\s+$)", "", cmd) # trim whitespace
# percent encode reserved characters
cmd <- gsub("%", "%25", cmd) # %
cmd <- gsub("#", "%23", cmd) # #
cmd <- gsub("/", "%2F", cmd) # /
cmd <- gsub(":", "%3A", cmd) # :
cmd <- gsub("@", "%40", cmd) # @
cmd <- gsub(",", "%2C", cmd) # ,
cmd <- gsub("%", "%25", cmd) # %
cmd <- gsub("#", "%23", cmd) # #
cmd <- gsub("/", "%2F", cmd) # /
cmd <- gsub(":", "%3A", cmd) # :
cmd <- gsub("@", "%40", cmd) # @
cmd <- gsub(",", "%2C", cmd) # ,
cmd <- gsub("\\*", "%2A", cmd) # *
cmd <- gsub("\\?", "%3F", cmd) # ?
cmd <- gsub("!", "%21", cmd) # !
cmd <- gsub("=", "%3D", cmd) # =
cmd <- gsub("!", "%21", cmd) # !
cmd <- gsub("=", "%3D", cmd) # =
cmd <- gsub("\\(", "%28", cmd) # (
cmd <- gsub("\\)", "%29", cmd) # )
cmd <- gsub("\\[", "%5B", cmd) # [
cmd <- gsub("\\]", "%5D", cmd) # ]
cmd <- gsub("&", "%26", cmd) # &
cmd <- gsub("&", "%26", cmd) # &
cmd <- gsub("\\+", "%2B", cmd) # +
cmd <- gsub("\\s+", "+", cmd) # whitespace to "+"
@ -533,11 +532,7 @@ CX <- function(cmd, port = CXPORT, quietly = FALSE, capture = FALSE) {
cat(reply)
}
if (capture == TRUE) {
return(reply)
} else {
return(invisible(NULL))
}
return(invisible(reply))
}

42
RPR-ChimeraX_remote.R
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@ -32,7 +32,7 @@
#TOC> 1 ChimeraX REMOTE SCRIPTING 40
#TOC> 1.1 Defining a Port 58
#TOC> 1.2 Open ChimeraX 80
#TOC> 2 WORKED EXAMPLE: SUPERPOSITION 100
#TOC> 2 WORKED EXAMPLE: SUPERPOSITION 112
#TOC>
#TOC> ==========================================================================
@ -96,6 +96,18 @@ CX("camera sbs")
CX("lighting soft")
CX("color sequential #1 & protein target abc palette powderblue:orchid:white")
# The command echos Chimera's response if the parameter "quietly" is
# FALSE (default), and we can silence output with quietly = TRUE :
CX("info models #1 attribute num_residues")
CX("info models #1 attribute num_residues", quietly = TRUE)
# Either way, the command also returns Chimera's responses "invisibly";
# i.e. we can use the results by assigning the output to a variable:
hBonds <- CX("hbonds #1 & protein makePseudobonds false log true", quietly=TRUE)
x <- read.table(file = textConnection(hBonds), skip = 9,
blank.lines.skip = TRUE, fill = TRUE)
hist(x[,13], main="H-bonds", xlab="D···A (Å)", ylab="counts", col="#c9dcff")
# = 2 WORKED EXAMPLE: SUPERPOSITION =======================================
@ -103,31 +115,35 @@ CX("color sequential #1 & protein target abc palette powderblue:orchid:white")
# to explore possible DNA binding regions in 1BM8
# The model for 1BM8 is already open as model 1 (#1)
CX("hide #1 cartoons") # hide chain a cartoon representation
CX("open 1DUX")
CX("hide #1 cartoons") # hide model 1 cartoon representation
CX("open 1DUX") # assume this is opened as model #2
CX("hide #2") # hide everything ...
CX("show #2/a,b,c cartoons") # ... and show cartoons of chains a, b (DNA) and c
CX("view #2/c") # re-center the display
CX("select #2/a,b") # select the DNA chains
CX("color sel lightblue")
CX("surface sel enclose sel") # joint surface of both chains
CX("select #2/C") # chain c (protein)
CX("show sel cartoons") # ... and show cartoons of chain c (protein)
CX("color sequential sel target c palette steelblue:darkmagenta")
CX("view #2/C") # re-center the display
CX("cofr #2/C:62@CA") # set pivot to an interface residue
CX("select #2/A,B & nucleic-acid") # chains A, B are the cognate DNA
CX("style sel stick")
CX("show sel target ab") # show atoms/bonds
CX("color sequential #2/A & nucleic-acid target ab palette teal:lightcyan")
CX("color sequential #2/B & nucleic-acid target ab palette teal:lightcyan")
CX("surface sel enclose sel") # compute joint accessible surface of both chains
CX("transparency 50")
CX("select #2/c") # select the protein chain
CX("color sequential sel target c palette palegreen:lightblue")
CX("select clear")
# Now superimpose the 1BM8 chain onto 1DUX chain C
CX("show #1 cartoons")
CX("matchmaker #1/A to #2/C pairing ss") # the actual superposition
CX("select clear")
# study the general layout, and the position of the 1mb8 secondary structure
# elements relative to 1DUX
# Let's examine side chain orientations in more detail
CX("hide #2/c cartoons") # hide the 1DUX protein
CX("hide #2/C cartoons") # hide the 1DUX protein
# select all residues in 1BM8 that are within 3.5 A of the DNA chains (a, b)
CX("select zone #2/a,b 3.5 #1 & protein residues true")
CX("select zone #2/A,B 3.5 #1 & protein residues true")
CX("~select sel & H") # de-select H atoms
CX("show sel target ab")
CX("size stickRadius 0.4")