New script to demonstarte remote scripting of ChimeraX

RPR-ChimeraX_remote.R

@@ -0,0 +1,148 @@
+# tocID <- "RPR-ChimeraX_remote.R"
+#
+# Purpose:  A Bioinformatics Course:
+#              R code demonstrating remote scripting of ChimeraX.
+#
+# Version:  1.0
+#
+# Date:     2020-09
+# Author:   Boris Steipe (boris.steipe@utoronto.ca)
+#
+# Versions:
+#           1.0    First ABC units version
+#
+#
+# TODO:
+#    %-encode and escape quotes, or just pass-through?
+#
+#
+# == DO NOT SIMPLY  source()  THIS FILE! =======================================
+#
+# If there are portions you don't understand, use R's help system, Google for an
+# answer, or ask your instructor. Don't continue if you don't understand what's
+# going on. That's not how it works ...
+#
+# ==============================================================================
+
+
+#TOC> ==========================================================================
+#TOC> 
+#TOC>   Section  Title                                  Line
+#TOC> ------------------------------------------------------
+#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> 
+#TOC> ==========================================================================
+
+
+# =    1  ChimeraX REMOTE SCRIPTING  ===========================================
+
+
+# One of the cool features of ChimeraX is that it can be driven by Python code,
+# both within a running session and through Python scripts. What I find even
+# cooler though is that ChimeraX can be driven from any programming language via
+# its remote control function that can listen to commands sent from any other
+# application. The interface that is used here is the standard REST (method) -
+# the GET and POST verbs that ubiquitously underly the communication of clients
+# and servers on the Web.
+
+# In order to establish the communication between this script and ChimeraX, all
+# we need to do is:
+#  - open ChimeraX;
+#  - tell it to listen on a specific "port";
+#  - send commands to that port via httr::
+
+
+# ==   1.1  Defining a Port  ===================================================
+
+# The httr:: package needs to be available
+
+if (! requireNamespace("httr", quietly = TRUE)) {
+  install.packages("httr")
+}
+# Package information:
+#  library(help = httr)       # basic information
+#  browseVignettes("httr")    # available vignettes
+#  data(package = "httr")     # available datasets
+
+# We need to think od a port. Any available port number between 49152-65535 is
+# fine. We'll choose 61803 because that's the fractional part of the golden
+# ratio. But one could choose another.
+
+CXPORT <- 61803
+
+# Check that our current version of R supports sockets (default since V 3.3)
+capabilities("sockets")   # MUST be TRUE. If not, don't continue.
+
+
+# ==   1.2  Open ChimeraX  =====================================================
+
+#  - Open a fresh, new session of ChimeraX
+#  - type:
+#
+#       remotecontrol rest start port 61803
+#
+#    ... or whatever the value of CXPORT is.
+
+# Now watch what happens in ChimeraX when you execute the following line:
+( x <- httr::GET("http://127.0.0.1:61803/run?command=open+1BM8") )
+
+# The .utilities.R script includes the function CX(), based on this principle,
+# through which you can send commands to ChimeraX
+
+CX("camera sbs")
+CX("lighting soft")
+CX("color sequential #1 & protein target abc palette powderblue:orchid:white")
+
+
+# =    2  WORKED EXAMPLE: SUPERPOSITION  =======================================
+
+# We superimpose the 1BM8 structure with the 1DUX crystal structure to be able
+# 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 #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("transparency 50")
+CX("select #2/c")             # select the protein chain
+CX("color sequential sel target c palette palegreen:lightblue")
+
+# 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
+
+# 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 sel & H")  # de-select H atoms
+CX("show sel target ab")
+CX("size stickRadius 0.4")
+CX("select clear")
+
+# The overall architecture of the Mbp1 APSES domain is a good match for the Elk
+# transcription factor binding mode; the detailed conformations of side chains
+# would need to change only to a minor degree. There is a very significant
+# degree of structural similarity; remarkable, given that the DNA is not the
+# target sequence of the Mbp1 transcription factor, AND the 1MB8 structure was
+# determined without a DNA ligand.
+
+CX("remotecontrol rest stop")  # release the socket
+# Done.
+
+
+
+# [END]