Jmol 12.2 has been released with other 200 new features
Written for Jmol by Nicolas Vervelle on 2011-10-03
# 224 new features
# summary of feature changes between Jmol 12.0 and 12.2:
# FEATURE CHANGE: "ligand" definition changed to
# !(protein,
# instead of "hetero and not solvent"
# FEATURE CHANGE: default zShadePower set to 3
# FEATURE CHANGE: undocumented a[13] = 3 (where a is a matrix, for a[1][3]) removed
# FEATURE CHANGE: DSSP default for "calculate structure"
# -- old way is now "calculate structure RAMACHANDRAN"
# FEATURE CHANGE: DSSP default for LOAD of PDB file with no header.
# in previous versions, Jmol used a ramachandran-
# for secondary structure determination when a PDB file had no HELIX or SHEET records.
# It just seems reasonable to use the industry-standard DSSP method instead.
# new feature: JmolSmilesApplet method (smiles1)
# new feature: JmolSmilesApplet method getRelationship
# new feature: The Jmol application can now communicate via sockets
# with other Jmol applications or specialized servers.
# The SYNC command has been expanded to make this very easy:
#
# sync -nnnn starts a server on local port nnnn accepting only local connections
# sync nnnn "background white" (from another app, generally) would execute that
# command on the app acting as a server
#
# You can also do this from one app frame to another, because they are independent
# instances of Jmol.
#
# Jmol can provide server service to other apps using:
#
# sync -3000
# [start other app, connecting on 3000]
# sync 3000 .....
#
# Because once the server is started and another app has connected,
# Jmol will send messages to that other app, not itself.
#
# To test the service within one application, just create the server and send
# commands to itself using a negative port number:
#
# sync -3000;sync -3000 'Mouse: rotateZBy 30'
#
# Note that in this context the "server" is the one getting commands from the "client"
# But the server can also send commands to the client provided the client has given the
# appropriate handshake: {"magic"
#
# Sent from Jmol (via outSocket):
#
# {"magic" : "JmolApp", "role" : "out"} (socket initialization for messages TO jmol)
# {"magic" : "JmolApp", "role" : "in"} (socket initialization for messages FROM jmol)
# {"type" : "script", "event" : "done"} (script completed)
#
# Sent to Jmol (via inSocket):
#
# {"type" : "banner", "visibility" : "ON" or "OFF" } (set banner for kiosk)
# {"type" : "banner", "text" : bannerText } (set banner for kiosk)
# {"type" : "command", "command" : command } (script command request)
# {"type" : "content", "id" : id } (load content request)
# {"type" : "move", "style" : (see below) } (mouse command request)
# {"type" : "quit" } (shut down request)
# {"type" : "sync", "sync" : (see below) } (sync command request)
# {"type" : "touch", (a raw touch event)
# "eventType" : eventType,
# "touchID" : touchID,
# "iData" : idata,
# "time" : time,
# "x" : x, "y" : y, "z" : z }
#
# For details on the "touch" type, see org.jmol.
# Content is assumed to be in a location determined by the Jmol variable
# nioContentPath, with %ID% being replaced by some sort of ID number of tag provided by
# the other half of the system. That file contains more JSON code:
#
# {"startup_script" : scriptFileName, "banner_text" : text }
#
# An additional option "banner" : "off" turns off the title banner.
# The startup script must be in the same directory as the .json file, typically as a .spt file
#
# Move/sync commands include:
#
# {"type" : "move", "style" : "rotate", "x" : deltaX, "y", deltaY }
# {"type" : "move", "style" : "translate", "x" : deltaX, "y", deltaY }
# {"type" : "move", "style" : "zoom", "scale" : scale } (1.0 = 100%)
# {"type" : "sync", "sync" : syncText }
#
# Note that all these moves utilize the Jmol sync functionality originally intended for
# applets. So any valid sync command may be used with the "sync" style. These include
# essentially all the actions that a user can make with a mouse, including the
# following, where the notation <....> represents a number of a given type. These
# events interrupt any currently running script, just as with typical mouse actions.
#
# "centerAt <int:x> <int:y> <float:ptx> <float:pty> <float:ptz>"
# -- set {ptx,pty,ptz} at screen (x,y)
# "rotateMolecule <float:deltaX> <float:deltaY>"
# "rotateXYBy <float:deltaX> <float:deltaY>"
# "rotateZBy <int:degrees>"
# "rotateZBy <int:degrees> <int:x> <int:y>" (with center reset)
# "rotateArcBall <int:x> <int:y> <float:factor>"
# "spinXYBy <int:x> <int:y> <float:speed>"
# -- a "flick" gesture
# "translateXYBy <float:deltaX, float:deltaY>"
# "zoomBy <int:pixels>"
# "zoomByFactor <float:factor>"
# "zoomByFactor <float:factor> <int:x> <int:y>" (with center reset)
#
# new feature: preliminary QuantumEspresso XML reader
# new feature: Jmol Application flags -k and -P
# -- -k kiosk mode: like applet, but with a banner across the top
# -- -P <port> JSON NIO client mode over port <port>
# -- for JSON NIO, use -J or -j to set nioContentPath and nioTerminatorMe
# to the desired values. For example:
# Jmol -k -P 31461 -j "nioContentPath
#
# new feature: Jmol.js adds jmolSwitchToSig
# This needed a new <span> tag that is now inserted around the applet.
# new feature: filter "_Xx" for filtering element Xx
