Revision: 18464
http://sourceforge.net/p/jmol/code/18464
Author: hansonr
Date: 2013-07-18 18:06:27 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18 17:51:47 UTC
(rev 18463)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18 18:06:27 UTC
(rev 18464)
@@ -11,38 +11,23 @@
___JmolVersion="13.1.19_dev_2013.07.18"
-bug fix: set shift_XX not saved in state
-bug fix: JSmol menu not disappearing upon touch outside menu
-bug fix: PyMOL surface map reading error
+TODO: isosurface SLAB TRANSLUCENT 0.x color
+ -- inherits color of isosurface when color parameter is absent
+ -- TODO - properly save in JVXL file
+TODO: PyMOL uniqueAtomSettings for transparency
+ -- will require by-vertex translucent option
+TODO: allow PyMOL PSE files reading as part of a set of files, not just by
itself
+ (AtomSetCollection appendAtomSetCollection)
new feature: set exportScale x.x
-- adjusts export scale
-- only implemented for VRML and X3D exporters
-
-bug fix: magres measurement of dipole coupling constants do not reach just
min-distance set
-bug fix: "cs" for Cs symmetry broken in chemicalshift
-
-bug fix: cartoons with too small nonzero size will not render anything
-
-code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar
coupling constant display.
-
new feature: unitcell center {atomset}
new feature: unitcell center {fx fy fz}
new feature: {*}.ms, {*}.cs %[ms] %[cs] magnetic shielding and chemical shift
new feature: label <color red>xxx</color>
new feature: set shift_H xxx (ppm)
new feature: getProperty("nmrInfo")
-
-
-code: org.jmol.quantum.NMRCalculation implements
org.jmol.api.JmolNMRCalculation:
- public float getQuadrupolarConstant(Tensor efg);
- public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor t);
- public float getDipolarConstantHz(Atom a1, Atom a2);
- public float getDipolarCouplingHz(Atom a1, Atom a2, V3 vField);
- public JmolList<Tensor> getInteractionTensorList(String type, BS bs);
- public BS getUniqueTensorSet(BS bs);
- public Object getIsotopeInfo(String sym);
-
new feature: NMR analysis tools:
-- x = measure({a} {b} "isc_hz") -- J coupling
-- x = measure({a} {b} "dc_khz") -- dipolar constant
@@ -54,8 +39,11 @@
new feature: {xxx}.tensor(type,what)
-- type = "temp", "ms", "efg", etc.
- -- returns a list of data.
+ -- returns a list of data. isc-type returns a list of lists [index1, index2,
value]
-- what =
+ "j" (isc-type only)
+ "chi" (efg only)
+ "dc" (dipolar coupling constant; type ignored)
"eigenvalues" float[v1,v2,v3]
"eigenvectors" P3[V1,V2,V3]
"value" Float (v3)
@@ -83,15 +71,30 @@
new feature: SET ECHO POINT {atom or point}
-- allows 2D and 3D echos to have pointers to atoms or points
+
+bug fix: set shift_XX not saved in state
+bug fix: JSmol menu not disappearing upon touch outside menu
+bug fix: PyMOL surface map reading error
+bug fix: magres measurement of dipole coupling constants do not reach just
min-distance set
+bug fix: "cs" for Cs symmetry broken in chemicalshift
+bug fix: cartoons with too small nonzero size will not render anything
+
+code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar
coupling constant display.
+code: org.jmol.quantum.NMRCalculation implements
org.jmol.api.JmolNMRCalculation:
+ public float getQuadrupolarConstant(Tensor efg);
+ public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor t);
+ public float getDipolarConstantHz(Atom a1, Atom a2);
+ public float getDipolarCouplingHz(Atom a1, Atom a2, V3 vField);
+ public JmolList<Tensor> getInteractionTensorList(String type, BS bs);
+ public BS getUniqueTensorSet(BS bs);
+ public JmolList<Object> getTensorInfo(String tensorType, String infoType, BS
bs);
+ public Map<String, Float> getMinDistances(MeasurementData md);
+ public boolean getState(SB sb);
+ public Object getInfo(String sym);
+
JmolVersion="13.1.18"
JmolVersion="13.1.17_dev_2013.06.27"
-TODO: isosurface SLAB TRANSLUCENT 0.x color
- -- inherits color of isosurface when color parameter is absent
- -- TODO - properly save in JVXL file
-TODO: PyMOL uniqueAtomSettings for transparency
- -- will require by-vertex translucent option
-
new feature: CASTEP reader filter option q=all
new feature: set picking DRAGLIGAND
-- won't move the protein
@@ -106,7 +109,7 @@
select :"0123" OK
select :"A*" or :"A'" or :'A"' or :"A\""
----TODO DOCUMENTED BACK TO THIS POINT---
+TODO: document these:
new feature: {atomset1}.distance.min({atomset2})
-- returns an array
@@ -168,6 +171,8 @@
-- distinct from color ATOMS because it doesn't get inherited
-- for PyMOL compatability with sphere_color
+TODO: document these:
+
new feature: restore SCENE "xxxx" nSec
new feature: Scene menu
@@ -496,9 +501,6 @@
JmolVersion="13.1.13"
-TODO: allow PyMOL PSE files reading as part of a set of files, not just by
itself
- (AtomSetCollection appendAtomSetCollection)
-
FEATURE CHANGE: multiple applets no longer share the same lighting space
new feature: animation DISPLAY {atomset}
@@ -554,19 +556,14 @@
bug fix: set picking IDENT when picking is already ident can cancel a pending
measurement
bug fix: applet does not refresh when mouse exits with pending measurement
-
bug fix: labels within fog should be hidden
bug fix: load CENTROID does not always work -- wrong implicit normalization
flag (was -1 instead of 1)
-
bug fix: property_xxx does not work (since 10/3/12, 13.1.7)
-
bug fix: The "show history" command is supposed to clear out the "show
history" command
itself, but only if it is a top-level command (from the console),
but it does more than that if it is part of script("show history").
Probably true with all recent versions of Jmol.
-
bug fix: isosurface binary file reading (MRC, CCP4, O, binary PMESH, etc.)
broken
-
bug fix: JavaScript: zoomTo [seconds > 0]... and restore rotation|orientation
[name] [seconds > 0] not waiting
code: Refactoring class names to reduce JSmol JavaScript footprint
@@ -582,7 +579,6 @@
JmolConstants --> JC
code: shader functions removed from Colix; Shader class made nonstatic
-
code: refactored to allow scriptless JavaScript. (reduces initial core code
load size by 25%, to 2.5Mb)
=============================================================================
@@ -607,19 +603,6 @@
new feature: axes labels "a" "b" "c" "xxx" where "xxx" is the label for the
origin
-JavaScript: fix for SMILES matcher and compare({*},{*},"isomer")
- -- j2s reminder: Can't use Java new int[n][]; must use
org.jmol.util.ArrayUtil.newInt2(n)
-
-JavaScript: going to Float64Array for all noninteger arrays -- all numbers
double
- Note that this could cause differences with Jmol, but I think we will have
to live with that.
- The problem was with (new Float32Array([13.48]))[0] != 13.48. So instead of
trying to force
- floats, it seems to make more sense to me to force doubles, using
Float64Array instead of Float32Array.
- Thanks given to Ira Hanson for clearing this up for me.
-
-JavaScript: JSmol writes PNG, PNGJ, JMOL, ZIP files from a web page
-
-JavaScript: JSmol writes text files from a web page
-
bug fix: PDB file reading of remediated 1A7Y and 1E9W error due to too many
CONECT bonds
-- now reads HEADER columns 63-66 for 4-digit PDB ID.
-- only if this ID is absent will the number of CONECT bonds be checked
in decision to autobond
@@ -633,6 +616,16 @@
-- Several html header tags updated or added (html5 doctype, charset, lang)
-- Hopefully all will display correctly after these changes!
+JavaScript: fix for SMILES matcher and compare({*},{*},"isomer")
+ -- j2s reminder: Can't use Java new int[n][]; must use
org.jmol.util.ArrayUtil.newInt2(n)
+JavaScript: going to Float64Array for all noninteger arrays -- all numbers
double
+ Note that this could cause differences with Jmol, but I think we will have
to live with that.
+ The problem was with (new Float32Array([13.48]))[0] != 13.48. So instead of
trying to force
+ floats, it seems to make more sense to me to force doubles, using
Float64Array instead of Float32Array.
+ Thanks given to Ira Hanson for clearing this up for me.
+JavaScript: JSmol writes PNG, PNGJ, JMOL, ZIP files from a web page
+JavaScript: JSmol writes text files from a web page
+
=============================================================================
version="13.1.11"
@@ -660,24 +653,25 @@
version="13.1.10"
+FEATURE CHANGE: set perspectiveMode removed
+ -- nonlinear version 10 perspective mode no longer supported
+
+bug fix: !quit was not stopping animation and vibration
bug fix: slowed zoomTo in Java version of 13.1.9
-code: JmolApplet0_Navigate.jar and JmolApplet0_Parallel.jar added
bug fix: PDB occupancies for first atoms may be 0.0 instead of 1.0 (broken in
11.7)
bug fix: select *W does not work
+bug fix: setEllipsoid... options not implemented for nonthermal ellipsoids in
13.0 or 13.1
+bug fix: nonthermal ellipsoids broken in 13.1.
+
JavaScript: !quit and navigation enabled
JavaScript: script queue enabled
-bug fix: !quit was not stopping animation and vibration
+JavaScript: move thread implemented; needs navigation threads
-FEATURE CHANGE: set perspectiveMode removed
- -- nonlinear version 10 perspective mode no longer supported
-
+code: JmolApplet0_Navigate.jar and JmolApplet0_Parallel.jar added
code: Navigator separated from TransformManager11
code: TransformManager10 removed
code: TransformManager11 combined with TransformManager
-bug fix: setEllipsoid... options not implemented for nonthermal ellipsoids in
13.0 or 13.1
-bug fix: nonthermal ellipsoids broken in 13.1.
-JavaScript: move thread implemented; needs navigation threads
=============================================================================
@@ -695,7 +689,6 @@
load co2.smol; mo homo squared // displays cylindrical electron density
mo next squared // lumo, provided homo was just displayed
-code: adding quotes to above properties allows them to be used in JavaScript;
j2sNative in JmolConstants.java
bug fix: Molden reader tweaks
bug fix: Jmol application toolbar picking tool should not select none
bug fix: ellipsoid rendering fails
@@ -725,16 +718,15 @@
JavaScript: Note -- org.jmol.adapter.smarter.Atom is not fully cloned
(anisoBorU and ellipsoid are not copied
and their values must be considered "final")
+
+code: adding quotes to above properties allows them to be used in JavaScript;
j2sNative in JmolConstants.java
code: refactoring org.jmol.util into org.jmol.io and org.jmol.io2
+
=============================================================================
version=13.1.8
-code: clearing font cache upon zap.
-code: HTML5-only JavaScript full text working
-code: HTML5-only JavaScript version working
-
new feature: much better text rendering using 3-bit translucency
bug fix: boundbox $pmeshID, center $pmeshID, and zoomto $pmeshID not
implemented
@@ -748,14 +740,20 @@
bug fix: MRC surface file reader with symmetry error
bug fix: (13.1 only) minimization broken
+code: clearing font cache upon zap.
+code: HTML5-only JavaScript full text working
+code: HTML5-only JavaScript version working
+
=============================================================================
version=13.1.7
FEATURE CHANGE: getProperty isosurfaceInfo no longer returns vertex data
+
new feature: getProperty isosurfaceData returns vertex data
new feature: set cartoonFancy -- creates elliptical ribbon for cartoons
-- if ribbonAspectRatio is its default value of 16, it is reset to 4
while cartoonFancy = true.
+
bug fix: (13.1 only) reading of states with select BONDS fails to select bonds
broken in 13.1.6
bug fix: (13.1 only) centered/right-aligned text only aligned after first line
bug fix: export WRL missing various objects requiring transformMatrixInv
@@ -774,39 +772,8 @@
version=13.1.6
-bug fix: PDB 4B2Q, with faulty (incomplete) REMARK 350 not read
-
-code: successfully refactored for JavaScript
- (see http://chemapps.stolaf.edu/jmol/jsmol-10-1/jsmol2.htm)
- -- note that all code development is done in Jmol, then
- Java src code is transferred to JSmol project
-
- -- adding:
- javax.util.BitSet
- javax.util.StringXBuilder
- -- streamlining:
- javax.vecmath...
- -- removed all references to StringBuffer
- -- StringXBuilder allows optimization of performance in JavaScript
- -- workaround for Java2Script compiler bug setting "char x;" to 0
- -- Java2Script compiler is not distinguishing int[] from float[] when
creating the array
- -- StringXBuilder takes care of adding ".0" to floats and doubles, but
- we need to be on the lookout for not places where we are constructing
- a string where the difference between an int and a float is
significant.
- -- optimize class hierarchy return by cataloging classes
- as org_jmol_xxxx in addition to org.jmol.xxxx
- -- tie in graphics on JavaScript side
- -- add fonts
- -- add "billboard" objects such as labels, 3D echos, etc.
- -- add 2D echos
- -- ultimately write an asynchronous version of JSmol
-
new feature: showTiming
-code: org.jmol.jvxl.readers classes accessed reflexively (for JavaScript
optimization)
-code: JSmol classes incorporated into Jmol code -- org.jmol.awtjs,
org.jmol.appletjs, org.jmol.exportjs
-code: refactored for JavaScript (mostly removing ambiguity in method names)
-
new feature: CIF reader reads assembly information
-- load =1vif.cif filter "ASSEMBLY 1"
-- load =1vif.cif filter "ASSEMBLY 1;$A" # just label_asym_id A
@@ -858,21 +825,51 @@
-- option reserved to allow different data names for different purposes
-- not general yet -- specific to CIF reader.
+
+bug fix: PDB 4B2Q, with faulty (incomplete) REMARK 350 not read
+
+code: successfully refactored for JavaScript
+ (see http://chemapps.stolaf.edu/jmol/jsmol-10-1/jsmol2.htm)
+ -- note that all code development is done in Jmol, then
+ Java src code is transferred to JSmol project
+
+ -- adding:
+ javax.util.BitSet
+ javax.util.StringXBuilder
+ -- streamlining:
+ javax.vecmath...
+ -- removed all references to StringBuffer
+ -- StringXBuilder allows optimization of performance in JavaScript
+ -- workaround for Java2Script compiler bug setting "char x;" to 0
+ -- Java2Script compiler is not distinguishing int[] from float[] when
creating the array
+ -- StringXBuilder takes care of adding ".0" to floats and doubles, but
+ we need to be on the lookout for not places where we are constructing
+ a string where the difference between an int and a float is
significant.
+ -- optimize class hierarchy return by cataloging classes
+ as org_jmol_xxxx in addition to org.jmol.xxxx
+ -- tie in graphics on JavaScript side
+ -- add fonts
+ -- add "billboard" objects such as labels, 3D echos, etc.
+ -- add 2D echos
+ -- ultimately write an asynchronous version of JSmol
+
+code: org.jmol.jvxl.readers classes accessed reflexively (for JavaScript
optimization)
+code: JSmol classes incorporated into Jmol code -- org.jmol.awtjs,
org.jmol.appletjs, org.jmol.exportjs
+code: refactored for JavaScript (mostly removing ambiguity in method names)
+
=============================================================================
version=13.1.5
bug fix: CASTEP PHONON files not loading
+
code: refactored for JavaScript
=============================================================================
version=13.1.4
-bug fix: translate selected x ... bug
-code: refactored for JavaScript
-
new feature: ISOSURFACE PLANE ... MAP ... LATTICE {i j k} [volume data]
-- allows periodic volume data to be mapped to a plane
based on a specified translational lattice
@@ -881,11 +878,15 @@
new feature: POLYHEDRA {atom1} to {atoms_including_atom1}
-- polyhedra with or without central atom, but with a reference atom
+bug fix: translate selected x ... bug
+
bug fix: ISOSURFACE saving in state broken 7/30/12 in 13.0.RC3
bug fix: simple isosurface PLANE not saved in state
bug fix: isosurface command with MAP from state when saved to state may fail
bug fix: 13.1.2 offsets label positions incorrectly
+code: refactored for JavaScript
+
=============================================================================
version=13.1.3
@@ -910,9 +911,6 @@
for example: write INLINE "testing" "myfile.txt"
for example: write INLINE @{load("$caffeine")} "caffeine.mol"
new feature: set defaultDropScript for drag-drop and File|Open
-code: (JmolViewer) public void cacheFile(String fileName, byte[] bytes)
- -- allows a mechanism for applets or embedding apps to deliver file content
as bytes
- -- for applets, first getPropertyAsJavaObject("Viewer")
bug fix: translate x 0 does not recenter the model in the window
bug fix: PDB polymers of length 1 allow size to be set and appear {visible}
but are not
@@ -921,6 +919,9 @@
bug fix: pngj storage of Spartan directory zip files or Spartan directories
cannot be read
because the PNGJ files created do not contain the necessary files
from the directory
+code: (JmolViewer) public void cacheFile(String fileName, byte[] bytes)
+ -- allows a mechanism for applets or embedding apps to deliver file content
as bytes
+ -- for applets, first getPropertyAsJavaObject("Viewer")
code: refactored for Java2Script due to inner class bug there.
=============================================================================
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