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

add CX() command for ChimeraX rempote control from R-scripts.

Browse Source
This commit is contained in:
hyginn 2020-09-27 23:40:01 +10:00
parent 0fb02b1f2f
commit df3dbb0fb6
1 changed files with 85 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

107
.utilities.R
View File

@ -20,30 +20,31 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -----------------------------------------------------------
#TOC> 1 SCRIPTS TO SOURCE 50
#TOC> 2 PACKAGES 56
#TOC> 3 DATA & CONSTANTS 67
#TOC> 4 SUPPORT FUNCTIONS 114
#TOC> 4.01 objectInfo() 117
#TOC> 4.02 biCode() 145
#TOC> 4.03 sameSpecies() 179
#TOC> 4.04 validateFA() 199
#TOC> 4.05 readFASTA() 248
#TOC> 4.06 writeFASTA() 283
#TOC> 4.07 pBar() 316
#TOC> 4.08 waitTimer() 338
#TOC> 4.09 fetchMSAmotif() 366
#TOC> 4.10 H() (Shannon entropy) 410
#TOC> 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 423
#TOC> 5.01 seal() 425
#TOC> 5.02 getMYSPE() 429
#TOC> 5.03 selectPDBrep() 438
#TOC> 5.04 selectChi2() 474
#TOC> 5.05 selectENSP() 487
#TOC>
#TOC> 1 SCRIPTS TO SOURCE 51
#TOC> 2 PACKAGES 57
#TOC> 3 DATA & CONSTANTS 68
#TOC> 4 SUPPORT FUNCTIONS 115
#TOC> 4.01 objectInfo() 118
#TOC> 4.02 biCode() 146
#TOC> 4.03 sameSpecies() 180
#TOC> 4.04 validateFA() 200
#TOC> 4.05 readFASTA() 308
#TOC> 4.06 writeFASTA() 343
#TOC> 4.07 pBar() 376
#TOC> 4.08 waitTimer() 398
#TOC> 4.09 fetchMSAmotif() 426
#TOC> 4.10 H() (Shannon entropy) 470
#TOC> 4.11 CX() (ChimeraX remote command) 483
#TOC> 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 545
#TOC> 5.01 seal() 547
#TOC> 5.02 getMYSPE() 551
#TOC> 5.03 selectPDBrep() 560
#TOC> 5.04 selectChi2() 596
#TOC> 5.05 selectENSP() 609
#TOC>
#TOC> ==========================================================================
@ -479,6 +480,68 @@ H <- function(x, N) {
}
# == 4.11 CX() (ChimeraX remote command) ===================================
CX <- function(cmd, port = CXPORT, quietly = FALSE, capture = 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)
CXREST <- sprintf("http://127.0.0.1:%s/run?", CXPORT)
cmd <- gsub("(^\\s+)|(\\s+$)", "", cmd) # trim whitespace
# percent encode reserved characters
cmd <- gsub("%", "%25", cmd) # %
cmd <- gsub("#", "%23", cmd) # #
cmd <- gsub("/", "%2F", cmd) # /
cmd <- gsub(":", "%3A", cmd) # :
cmd <- gsub("@", "%40", cmd) # @
cmd <- gsub(",", "%2C", cmd) # ,
cmd <- gsub("\\*", "%2A", cmd) # *
cmd <- gsub("\\?", "%3F", cmd) # ?
cmd <- gsub("!", "%21", cmd) # !
cmd <- gsub("=", "%3D", cmd) # =
cmd <- gsub("\\(", "%28", cmd) # (
cmd <- gsub("\\)", "%29", cmd) # )
cmd <- gsub("\\[", "%5B", cmd) # [
cmd <- gsub("\\]", "%5D", cmd) # ]
cmd <- gsub("&", "%26", cmd) # &
cmd <- gsub("\\+", "%2B", cmd) # +
cmd <- gsub("\\s+", "+", cmd) # whitespace to "+"
cmd <- URLencode(cmd) # encode special characters
cmd <- paste0(CXREST, "command=", cmd, collapse = "")
r <- httr::GET(cmd)
if (! r$status_code == 200) {
stop("ChimeraX returned status code %d", r$status_code)
}
if (length(r$content) == 0) {
reply <- ""
} else {
reply <- rawToChar(r$content)
}
if (quietly == FALSE) {
cat(reply)
}
if (capture == TRUE) {
return(reply)
} else {
return(invisible(NULL))
}
}
# = 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS ==================================
# == 5.01 seal() ===========================================================