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[Jmol-commits] SF.net SVN: jmol:[16189] trunk/Jmol/src
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From: <ha...@us...> - 2011-10-01 11:38:39
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Revision: 16189
http://jmol.svn.sourceforge.net/jmol/?rev=16189&view=rev
Author: hansonr
Date: 2011-10-01 11:38:32 +0000 (Sat, 01 Oct 2011)
Log Message:
-----------
version=12.2.RC8
# PLEASE RELEASE AS 12.2.0 with new branch
# new feature: JmolSmilesApplet method (smiles1)
# new feature: JmolSmilesApplet method getRelationship(smiles1, smiles2)
# bug fix: xxx = {*}; xxx.property_x = 3 improperly parsed as a script command
# 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":"JmolApp","event":"out"}
#
# 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" : "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.viewer.ActionManagerMT::processEvent
# 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
# bug fix: getproperty minimizationInfo returns JSON instead of readable string
# bug fix: JaguarReader not reading D6 MOs properly
# 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 nioTerminatorMessage
# to the desired values. For example:
# Jmol -k -P 31461 -j "nioContentPath='./%ID%/%ID%.json';nioTerminatorMessage='SCRIPT_DONE'"
#
# code: all references to java.awt and javax.swing isolated to
# org.jmol.awt, rg.jmol.export, and org.jmol.multitouch
# new feature: Jmol.js adds jmolSwitchToSignedApplet().
# This needed a new <span> tag that is now inserted around the applet.
# bug fix: MOLDEN reader not reading spherical basis functions
# bug fix: contact command not symmetric
# Set A should generally be the ligand. However, consider note:
# // check for O--H...N or O...H--N and not considering
# // hydrogens and still have a filter
# // a bit of asymmetry here: set A may or may not have H atoms added.
# // This is particularly important for amines
# The issue here is that we do not assume that hydrogens have been
# added to ligands. So we make some allowances there.
#
# bug fix: null pointer exceptions when model with unit cell is appended to model without unit cell
# bug fix: CIF reader not implemented with filter "CONF n"
# bug fix: unit cell not turned off in state for PDB files loaded with biomolecule
# new feature: filter "_Xx" for filtering element Xx
# code: refactored Jmol core Swing classes restricted to
# applet, console, export, modelkit, multitouch, popup
# bug fix: SMILES [#6]-[#6] should not match bonds in benzene, only biphenyl
# bug fix: in SMARTS matching of SMILES string, aromatic ring conditions were not matched
# TODO: Question about what c=c should do. For now, changing that to NOT match C=C of benzene
Modified Paths:
--------------
trunk/Jmol/src/JmolSmilesApplet.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/JmolSmilesApplet.java
===================================================================
--- trunk/Jmol/src/JmolSmilesApplet.java 2011-09-30 19:31:27 UTC (rev 16188)
+++ trunk/Jmol/src/JmolSmilesApplet.java 2011-10-01 11:38:32 UTC (rev 16189)
@@ -32,6 +32,18 @@
import org.jmol.smiles.InvalidSmilesException;
import org.jmol.smiles.SmilesMatcher;
+/*
+ * JmolSmilesApplet is a small applet that can do interesting things with
+ * SMILES strings. It is a subset of Jmol with no graphics capability
+ *
+ * find(String pattern, String smiles, boolean isSmarts, boolean isAll)
+ * getLastError()
+ * getRelationship(String smiles1, String smiles2)
+ * reverseChiralit(String smiles)
+ * setDebug(boolean TF)
+ *
+ *
+ */
public class JmolSmilesApplet extends Applet {
@Override
@@ -101,6 +113,17 @@
return (new SmilesMatcher()).getRelationship(smiles1, smiles2);
}
+
+ /**
+ * reverse the chirality throughout a SMILES string
+ *
+ * @param smiles
+ * @return reversed chirality SMILES string
+ */
+ public String reverseChiralit(String smiles) {
+ return (new SmilesMatcher()).reverseChirality(smiles);
+ }
+
@Override
public String getAppletInfo() {
return "JmolSmilesApplet";
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java 2011-09-30 19:31:27 UTC (rev 16188)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java 2011-10-01 11:38:32 UTC (rev 16189)
@@ -36,7 +36,9 @@
optOnly = checkFilter("OPTONLY");
loadGeometries = !vibOnly && desiredVibrationNumber < 0 && !checkFilter("NOOPT");
loadVibrations = !optOnly && desiredModelNumber < 0 && !checkFilter("NOVIB");
-
+
+ if (checkFilter("NORMALIZED"))
+ moData.put("isNormalized", Boolean.TRUE);
if (checkFilter("ALPHA"))
filter = "alpha";
else if (checkFilter("BETA"))
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-09-30 19:31:27 UTC (rev 16188)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-10-01 11:38:32 UTC (rev 16189)
@@ -1,8 +1,12 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=12.2.RC8_dev
+version=12.2.RC8
+
+# PLEASE RELEASE AS 12.2.0 with new branch
+
+# new feature: JmolSmilesApplet method (smiles1)
# new feature: JmolSmilesApplet method getRelationship(smiles1, smiles2)
# bug fix: xxx = {*}; xxx.property_x = 3 improperly parsed as a script command
# new feature: The Jmol application can now communicate via sockets
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