- All Implemented Interfaces:
JsonNioServer
public class JsonNioService
extends naga.NIOService
implements JsonNioServer
A class for interacting with Jmol over local sockets.
See also org.molecularplayground.MPJmolApp.java for how this works.
Note that this service does not require MPJmolApp -- it is a package
in the standard Jmol app.
Listens over a port on the local host for instructions on what to display.
Instructions come in over the port as JSON strings.
This class uses the Naga asynchronous socket network I/O package (NIO), the
JSON.org JSON package and Jmol.
http://code.google.com/p/naga/
Initial versions of this code, including the JSON-base protocol were created
by Adam Williams, U-Mass Amherst see http://MolecularPlayground.org and
org.openscience.jmol.molecularplayground.MPJmolApp.java
Sequence of events:
1) Jmol initiates server listening on a port using the JmolScript
command with an arbitrary negative port number.
(-30000 used here just for an example):
sync -30000
This can be done also through the command line using
jmol -P -30000
or
jmol --port -30000
Jmol will respond to System.out:
JsonNioServerThread-JmolNioServer JsonNioServerSocket on 30000
2) Client sends handshake to port 30000. As with all communications to this service,
there must be no new-line characters (\n) ANYWHERE in the JSON being sent EXCEPT
for a single message terminator:
{"magic": "JmolApp", "role": "out"}\n
where "out" here indicates that this socket is for Jmol (reply) output.
Jmol will reply with the 30-byte response:
{"type":"reply","reply":"OK"}\n
(The client may see only 29 bytes, as it may or may not strip the final \n.)
Optionally, the client may also indicate a specified port for Jmol input.
But typically this is just the currently active port.
{"magic": "JmolApp", "role": "in"}\n
Jmol will reply with
{"type": "reply", "reply": "OK"}\n;
3) Client sequentially sends Jmol script commands over the "in" socket:
{"type": "command", "command": command}\n
where required command is some JSON-escaped string such as "rotate x 30" or "load $caffeine".
For example:
{"type": "command", "command": "var atoms = {_C or _H};select atoms"}\n
For the rest of this discussion, we will use the Jmol command that communicates with another Jmol instance
rather than this JSON context:
SYNC 30000 "var atoms = {_C or _H};select atoms"
in this case.
4) Jmol throughout this process is sending replies that come
from the Jmol Statuslistener class. For example:
{"type":"reply","reply":"SCRIPT:script 8 started"}
{"type":"reply","reply":"SCRIPT:Script completed"}
{"type":"reply","reply":"SCRIPT:Jmol script terminated"}
Note that your client will be subscribed to many of the Jmol status callbacks
(see org.openscience.jmol.app.jmolpanel.StatusListener), including:
LOADSTRUCT
ANIMFRAME
SCRIPT
ECHO
PICK
CLICK
RESIZE
ERROR
MINIMIZATION
STRUCTUREMODIFIED
All scripts and callback messages run in order but asynchronously in Jmol. You do not need
to wait for one script to be finished before issuing another; there is a queue that handles that.
If you want to be sure that a particular script has been run, simply add a MESSAGE command
as its last part:
sync 30000 "background blue;message The background is blue now"
and it will appear as a SCRIPT callback:
{"type":"reply","reply":"SCRIPT:The background is blue now"}
after which you can handle that event appropriately.
The SCRIPT callback can be particularly useful to monitor:
sync 30000 "backgrund blue"
{"type":"reply","reply":"SCRIPT:script compiler ERROR: command expected\n----\n >>>> background blue <<<<"}
Note that the ERROR callback does not fire for compile errors,
only for errors found while running a parsed script:
{"type":"reply","reply":"ERROR:ScriptException"}
Note that all of these messages are "thumbnails" in the sense that they are just a message string.
You can subscribe to a full report for any of these callbacks using 'SYNC:ON' for the
callback function:
set XxxxxCallback SYNC:ON
For example, issuing
sync 30000 "load $caffeine"
gives the simple reply:
{"type":"reply","reply":"LOADSTRUCT:https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true"}
but after
sync 30000 "set LoadStructCallback 'SYNC:ON'
we get additional details, and array of data with nine elements:
{"type":"reply","reply":["LOADSTRUCT",
"https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true",
"file?format=sdf&get3d=true",
"C8H10N4O2", null, 3, "1.1", "1.1", null]}
Exact specifications for these callbacks are not well documented.
See org.jmol.viewer.StatusManager code for details.
Remove the callback listener using
set XxxxxCallback SYNC:OFF
Note that unlike Java, you get only one SYNC callback; this is not an array of listeners.
5) Shutdown can be requested by sending
{"type": "quit"}\n
or by issuing the command
sync 30000 "exitjmol"
Note that the Molecular Playgournd implemented an extensive set of gesture-handling methods
that are also available via this interface. Many of these methods utilize the JmolViewer.syncScript()
method, which directly manipulates the display as though someone were using a mouse.
{"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 }
{"type" : "touch",
"eventType" : eventType,
"touchID" : touchID,
"iData" : idata,
"time" : time, "x" : x, "y" : y, "z" : z }
For details on the "touch" type, see org.jmol.viewer.ActionManagerMT::processEvent
Note that all of the move and sync commands 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)
In addition, a Jmol client send "raw" JSON strings over the socket via the SYNC command:
sync 30000 '{"type": "command", "command": "var atoms = {_C or _H};select atoms"}'
and since JmolScript's associative array is equivalent to JSON, this message does not have
to be a string; it can be an associative array:
sync 30000 {"type":"command","command":"background orange"}
Even simpler, Jmol's native associative array uses [...] instead of {...}
and does not require quoting keys (unless they contain spaces):
sync 30000 [type:"command", command:"background orange"]
And, finally, the message can be in the form of a JmolScript variable:
x = [type:"command", command:"background orange"]
sync 30000 x