Revision: 20355
http://sourceforge.net/p/jmol/code/20355
Author: hansonr
Date: 2015-03-05 03:22:19 +0000 (Thu, 05 Mar 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.13_2015.03.05"
synchronized with 14.3.12_2015.03.05b
released
bug fix: reading legacy mapped plane (2ptn-molecular_slice1.jvxl.txt) crashes
Jmol
bug fix: (14.3 only) write VRML|MAYA|OBJ|POVRAY broken
JmolVersion="14.3.12_2015.03.01"
bug fix: late discovery of mmCIF format does not load secondary structure
bug fix: reading PNGJ file saved after load with /dssr or /rna3d annotations
ignores annotations
bug fix: {*}.find("~d~G:C") broken (find with bioSMARTS)
new feature: image # the current view as an image
new feature: image 300 400 # adjustable size
new feature: image "c:/temp/t.bmp" # image from a file
new feature: image "" close # close the current view image
new feature: image "c:/temp/t.bmp" close # close image from a file
new feature: image CLOSE # close all
new feature: image ID ...
-- id for IMAGE CLOSE;
-- displayed in title of frame
-- examples:
image ID "test"
image ID "test" 400 500
image ID "test" "bob.png"
image ID "test" close
new feature: write IMAGE
-- same as IMAGE
new feature: write IMAGE 500 500
-- same as IMAGE 500 500
new feature: (JavaScript/HTML5; see JSmol_Console.java)
// page designer may indicate one of three divs for images on the page:
// <appletID>_Image_app_holder for IMAGE command by itself (current app image)
// <appletID>_Image_<cleaned id or filename>_holder for IMAGE ID "xxx" ...
or IMAGE "xxx"
// where cleaning is with .replace(/\W/g,"_")
// <appletID>_Image_holder for all images not identified as above
// if a page div is not identified, then the image will be placed in a new
floating div
note: experimental SHOW IMAGE now replaced by new command IMAGE
JmolVersion="14.3.12_2015.02.26"
bug fix: imageFontScaling integer instead of float; does not scale
appropriately on resize
bug fix: writing image of MO fails to write info (Jmol 12 or before)
JmolVersion="14.3.12_2015.02.25c"
bug fix: legacy non-XML JVXL files with color mapping should default to RGB
color scheme
bug fix: Jmol 14.1.2_2013.12.13 disabled some mmCIF file reading for non-wwPDB
mmCIF files
JmolVersion="14.3.12_2015.02.25b"
new feature: random(low,high,seed)
-- provides a new seed for the random() function
-- seed may be any 48-bit integer.
-- x = random(0.0,1.0,121231223)
-- low and high are simply placeholders
-- does return the first number from this seed
-- note that Java and JavaScript will have DIFFERENT seedings
-- utilizes https://github.com/davidbau/seedrandom/blob/released/seedrandom.js
(appended to java.util.Random.js)
JmolVersion="14.3.12_2015.02.25"
new feature: show chemical drawing
new feature: show drawing
-- pops up window with drawing of model
-- service is from NCI
-- uses SMILES if structure was not loaded using $... (NCI) or :... (PubChem)
JmolVersion="14.3.12_2015.02.24"
// 02.28 removes "show " from these
new feature: show IMAGE
-- pops up a frame with the current image
-- allows "Save As..."
new feature: show IMAGE "filename"
-- pops up a frame with the image loaded from a file
-- allows "Save As..."
new feature: show image 300 400 # adjustable size
new feature: show image none # closes all image panels
new feature: show image CLOSE # "all" presumed
new feature: show image CLOSE "" # the model image
new feature: show image CLOSE "c:/temp/t.bmp" # the image for this file
new feature: write IMAGE
-- same as SHOW IMAGE
new feature: write IMAGE 500 500
-- same as SHOW IMAGE 500 500; allows customization of width and height
new feature: Windows BMP image reading
-- reads 24-bit (full color) as well as 16-, 8-, 4-, 2-, and 1-bit color
palette modes
-- 14-byte and 40-byte headers only
-- does not read compressed modes
bug fix: restriction against getting SMILES string for biomolecule lifted
bug fix: end-on bonds may appear to disappear
bug fix: JavaScript -2.format("%8.3") gives 2.000 not -2.000
bug fix: minimizer treats hydrogen bonds as covalent single bonds
code: javajs.img.BMPDecoder
code: org.openscience.jmol.app.jmolpanel.ImageDialog
JmolVersion="14.3.12_2015.02.19"
bug fix: CML reader does not show proper atom names for crystal structures
bug fix: POV-Ray renderer does not show proper backbone width (since forever)
bug fix: POV-Ray renderer with a translucent surface shows bonds that should be
hidden (since 13.1)
bug fix: unitcell info for PDB file biomolecule does not show "biomolecule 1"
JmolVersion="14.3.12_2015.02.18"
bug fix: load filter "biomolecule 1" broken in 14.3.12_2015.02.14
JmolVersion="14.3.12_2015.02.17b"
bug fix: writing to PNGJ data to .ZIP file should create a standard ZIP file.
-- especially useful now that some zip readers will not open PNGJ files as
zip files
(with newer 7zip you can right-click file, then select 7zip...open
archive...zip)
var x = load("t.png", true)
write var x "t.zip"
bug fix: VASP POSCAR fix for atom symbols in header line
JmolVersion="14.3.12_2015.02.17"
new feature: set zshadePower 0
-- allows examination of depth buffer and writing to image for external
processing
set zShadePower 0
set zSlab 100
set zDepth 0
set zShade true
write z.jpg
set zShade false
write rgb.jpg
JmolVersion="14.3.12_2015.02.16"
new feature: x.dot(y) for planes and points -- was present but undocumented
and not working correctly
new feature: (undocumented) x.distance.all(y)
new feature: load MUTATE "==LYS"
-- loads using set appendNew false
-- bypasses regeneration of secondary structure
-- not to be documented
-- issued by MUTATE command only
bug fix: write isosurface "./xxx.jvxl" broken -- concatenates "isosurface"
with filename
bug fix: write ISOSURFACE by itself broken (similarly for write POINTGROUP and
others)
bug fix: MUTATE command adjustments for saving state
bug fix: MUTATE command should not force recreation of shapes
bug fix: MUTATE command should not change backbone atoms
bug fix: x = measure(a,b) where b is {none} crashes Jmol
bug fix: compare({atomA},{atomsB}) should return standard 4x4 matrix, not one
involving a rotation
about an atom center
-- (not adjusted when ROTATESELECTED was fixed in 14.3.11_2014.12.17; Angel
Herraez)
code: org.jmol.modelsetbio.BioExt
-- extracts struts, quaternion plots, polymerInfo, mutate into optional module
-- saves 15K in corebio.js
JmolVersion="14.3.12_2015.02.11"
bug fix: 14.3.12_2015.02.09 breaks MODEL "someTitle" syntax
bug fix: MUTATE not properly saved in state
bug fix: "USER MOD" not accepted at beginning of PDB file (MolProbity breaking
PDB format here)
bug fix: 02.10 may break loading ligand files
JmolVersion="14.3.12_2015.02.10"
bug fix: color $contact1 "roygb" range -0.5 1.0; broken (in state after using
CONTACT)
bug fix: mmCIF reader does not flag first model of a multimodel set as type PDB
JmolVersion="14.3.12_2015.02.09"
new feature: frame align {atoms} FIXED
-- shifts atom positions in each frame to match first atom in {atoms}
-- unlike just frame align {atoms}, frame * will still show alignment
-- objects such as DRAW and ISOSURFACE will NOT be shifted
-- needs testing
new feature: frame align [modelNo] [pt]
-- FIXED is assumed
-- used in state; shifts a model by a specific amount after removing any
current frame alignment
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2015-03-04 23:48:32 UTC (rev 20354)
+++ branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2015-03-05 03:22:19 UTC (rev 20355)
@@ -798,6 +798,7 @@
// still, if the scheme is translucent, we don't want to color the
vertices translucent
isTranslucent = false;
}
+ vcs = AU.ensureLengthShort(vcs, vc); // when reading contour plane may be
remapped
for (int i = vc; --i >= mergeVertexCount0;)
vcs[i] = ce.getColorIndex(vvs[i]);
setTranslucent(isTranslucent, translucentLevel);
@@ -813,7 +814,6 @@
color[0] = C.getArgb(colix[0]);
}
}
- //TODO -- still not right.
if (contourValues != null) {
contourColixes = new short[contourValues.length];
for (int i = 0; i < contourValues.length; i++)
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-04
23:48:32 UTC (rev 20354)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-05
03:22:19 UTC (rev 20355)
@@ -5,9 +5,11 @@
# BUG FIXES ONLY, PLEASE
Jmol.___JmolVersion="14.2.13_2015.03.05"
-synchronized with 14.3.12
+
+synchronized with 14.3.12_2015.03.05b
released
+bug fix: reading legacy mapped plane (2ptn-molecular_slice1.jvxl.txt) crashes
Jmol
bug fix: (14.3 only) write VRML|MAYA|OBJ|POVRAY broken
JmolVersion="14.3.12_2015.03.01"
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