Revision: 20368
http://sourceforge.net/p/jmol/code/20368
Author: hansonr
Date: 2015-03-09 01:36:16 +0000 (Mon, 09 Mar 2015)
Log Message:
-----------
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-07
17:51:32 UTC (rev 20367)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-09
01:36:16 UTC (rev 20368)
@@ -8,431 +8,91 @@
synchronized with 14.3.12_2015.03.07
bug fix: x[2] = y[2] fails
-
-adds IMAGE command, Windows BMP image file reading
-
-new feature: NBO command with no arguments starts NBO panel (Java application
only)
-
-JmolVersion="14.3.12_2015.03.05b"
-synchronized with 14.2.13_2015.03.05
-
bug fix: reading legacy mapped plane (2ptn-molecular_slice1.jvxl.txt) crashes
Jmol
+bug fix: late discovery of mmCIF format does not load secondary structure
-JmolVersion="14.3.12_2015.03.05"
-synchronized with 14.2.13_2015.03.05
-released
+Jmol.___JmolVersion="14.2.12_2015.02.28"
-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: {*}.find("~d~G:C") broken (find with bioSMARTS)
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
+JmolVersion="14.2.12_2015.02.26"
-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)
+bug fix: legacy non-XML JVXL reading does not color map
-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="14.2.12_2015.02.22b"
-
-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: WRITE PDB broken
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_2015.02.18b"
-JmolVersion="14.3.12_2015.02.19"
-
+bug fix: POV-Ray renderer does not show proper backbone
+bug fix: POV-Ray renderer with a translucent surface shows bonds that should
be hidden
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"
+JmolVersion="14.2.12_2015.02.16"
-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)
+ about an atom center (follow-up ROTATESELECTED was broken in
14.2.11_2014.12.17)
-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"
+JmolVersion="14.2.12_2015.02.11"
+released
-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"
+JmolVersion="14.2.12_2015.02.10"
+released
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="14.2.12_2015.02.07"
-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
-
-JmolVersion="14.3.12_2015.02.07"
-released
-
bug fix: set meshScale is not being applied to isosurface contours
bug fix: zoomTo{xxx} 0 does not center (broken in 13.1.16_dev_2013.05.23)
bug fix: appending a model to a model with data can fail
-bug fix: 02.04 select conformation=1 broken
-bug fix: 02.04 select within(chain,...) broken
-
bug fix: hydrogen addition should not follow component file
- ILE7 HG12 != ILE7 HG13
- ILE7 HG13 != ILE7 HG12
- ARG10 HB2 != ARG10 HB3
- ARG10 HB3 != ARG10 HB2
- ARG10 HG2 != ARG10 HG3
- ARG10 HG3 != ARG10 HG2
- ARG10 HD2 != ARG10 HD3
- ARG10 HD3 != ARG10 HD2
-
- LEU18 HB3 != LEU18 HB2
- LEU18 HB2 != LEU18 HB3
-
- PRO19 HD2 != PRO19 HD3
- PRO19 HD3 != PRO19 HD2
-
- ILE25 HG12 != ILE25 HG13
- ILE25 HG13 != ILE25 HG12
-
-
-
-JmolVersion="14.3.12_2015.02.04"
+JmolVersion="14.2.12_2015.02.04"
released
-new feature: print data({*},"xyz")
- -- (lower case) writes only atom data lines
-
-new feature: print data({*},"XYZ", true)
- -- third parameter TRUE writes all trajectories
-
bug fix: show mouse fails in JavaScript
-- we cannot test using PT.isAI() in org.jmol.viewer.binding.Binding
- -- because of a Java2Script compiler creates standard array [...]
- -- from new int[] {....} whereas it should create Clazz.newArray() and fill
it
-bug fix: writing of file formats was inconsistent between WRITE and data()
(not fixed in 14.2)
-bug fix: Jmol writing of PDB file data did not include TER records (not fixed
in 14.2)
+ because the Java2Script compiler creates standard array [...]
+ from new int[] {....} whereas it should use Clazz.newIntArray(-1,....)
bug fix: label %r should print "1" for non-PDB file atoms
-bug fix: 01.30 mutate {xxx} ~... skips first-listed replacement group
identifier
-bug fix: 01.29 breaks loading non-trajectory file after a trajectory is loaded
-
-JmolVersion="14.3.12_2015.01.30b"
-
-bug fix: select %w %x %y %z not implemented
bug fix; lcaoCartoon broken in 14.3.10_2014.11.27/14.2.12_2015.01.22
bug fix: isosurface id surf1 solvent; select within(2.0, $surf1) broken
-
-JmolVersion="14.3.12_2015.01.30"
-
-new feature: MUTATE command
- -- operates only on last model present if multiple models are loaded
- -- replaces one or more amino acids group with others
- -- can read from RCSB or from user-specified file
- -- examples:
- mutate 33 lys // replace resno=33 with lysine
- mutate @3 arg // replaces group of atom 3 with arginine
- mutate @r gly // replaces groups in variable r with glycine
- mutate 22 "myfile.cif" // user-defined replacement
- mutate {1-3} ala // replace first three residues with alanine
- mutate {1-5} GLVAG // (sequence codes) replace residues 1-5 with
gly-leu-val-ala-gly
- mutate {1-3} ~LYS // (force 1-character sequence codes) replace 1-3
with leu-tyr-ser
- mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2
- mutate {within(sequence, "GAT")} GYT // replace locations of GAT with
GYT (needs testing)
- mutate 35 @fname // replaces resno=33 with file data (use "==ALA"
or "~A" for RCSB)
- mutate {r} his // same as above; r must be an atom selection
-
-
-bug fix: code fixes relating to calculate structure in 01.29
-
-JmolVersion="14.3.12_2015.01.29"
-
-bug fix: 01.28 version does not write correct PDB CONECT records
bug fix: 01.22 version may not correctly clear rasmol hydrogen bonds in
trajectories
-code: simplification of BioModel; extraction of legacy Chime messaging into
ChimeMessenger class
-code: extraction of org.jmol.modelset.Trajectory
-
-JmolVersion="14.3.12_2015.01.28"
-
-bug fix: write "t.pdb" now correctly sequences groups and atoms, even after
mutation
-
-new feature: resno is user settable
-
-JmolVersion="14.3.12_2015.01.27"
-
+bug fix: write "t.pdb" now correctly sequences groups and atoms
bug fix: select thisModel does not select all atoms in visible frame set
+bug fix: select %w %x %y %z not implemented
-new feature: @@3 for "atomno=3 and thisModel"
- -- provides a function distinct from @3 when there are multiple models
- -- includes all atoms in current frame set
- -- example:
-
- load "cyclohexane_movie.xyz"
- select @10
- 35 atoms selected
- select @@10
- 1 atom selected
- frame [1 2 4 6]
- select @@10
- 4 atoms selected
- @@10.label = "atom 10"
-
-
-new feature: frame [1 3 5 6]
- -- sets limited number of frames for animation and frame *
- -- same as animation frame [1 3 5 6]; frame *
-
-new feature: CGO SCREEN option
- -- CGO [SCREEN z ...]
- -- reads CGO 2D VERTEX records as screen coordinates, installing them at a
depth of z
- - where z > 0 indicates a percent (0.01 far back; 100 front)
- - z < 0 indicates an absolute screen z value as -z.
- - uses 2D VERTEX and other CGO point elements, not 3D
- -- example: a static border 20% from the back of the model
-
-cgo test2 [ SCREEN 20
- BEGIN LINE_LOOP
- VERTEX 10 10
- VERTEX 90 10
- VERTEX 90 90
- VERTEX 10 90
- END
-]
-
-new feature: CGO UVMAP option
- -- CGO [UVMAP @origin @x @y x0 y0 x1 y1 scaleX scaleY ...]
- -- 2D VERTEX records are scaled and mapped to a plane defined by @origin @x @y
- -- example: a parallelogram based on atoms 1, 6, and 11
-
-cgo test1a [ UVMAP @1 @6 @11 0 0 80 80 1 1
- BEGIN LINE_LOOP
- VERTEX 0 0
- VERTEX 80 0
- VERTEX 80 80
- VERTEX 0 80
- END
-]
-
-new feature: CGO PostScript option
- -- CGO [ PS @origin @x @y ] data "PS" [primitive encapsulated postscript
data] end "PS"
- -- maps 2D EPS data onto a plane defined by an origin point, an x-axis point,
and a y-axis point.
- -- somewhat similar to UV mapping of textures in other programs
- -- allows 2D data to be superimposed on a model.
- -- a crude implementation still in development; doesn't properly implement
stroke;
- -- just for drawing lines; does not implement PS fill, gsave, grestore
- -- just moveto, lineto, newpath, closepath, setlinewidth, scale
- -- uses %%BoundingBox x0 y0 x1 y1 prolog record
- to map [x0 y0] to @origin, [x1 0] to @x, and [0 y1] to @y
- -- used for NBO contour mapping
-
-CGO[ PS @{point(-5,-5,0)} @{point(5,-5,0)} @{point(-5,5,0)] data "PS"
-%!PS-Adobe-2.0 EPSF-1.2
-%%Creator: Bob Hanson (from NBO)
-%%Title: nbo orbital slice
-%%CreationDate: 1/26/2015 5:36 AM
-%%DocumentFonts: Helvetica
-%%BoundingBox: 211 300 428 518
-%% note: above numbers are from 0.24*881 0.24*1781 0.24*1256 0.24*2156
-%%EndComments
-%%EndProlog
- 0.2400 0.2400 scale
- newpath
- 3 setlinewidth
- newpath
- 881 1256 moveto
- 1781 1256 lineto
- 1781 2156 lineto
- 881 2156 lineto
- closepath
- stroke
- 1241 1717 moveto
- 1250 1713 lineto
-...
- stroke
-%%Trailer
-showpage
-end "PS"
+JmolVersion="14.2.12_2015.01.27"
bug fix: CGO LINE_LOOP not closing
bug fix: configuration 1 broken
bug fix: display configuration=1 broken (in Jmol 12.0, 2011)
-JmolVersion="14.3.12_2015.01.25"
+JmolVersion="14.2.12_2015.01.25"
bug fix: image echos broken
-
-JmolVersion="14.3.12_2015.01.24"
-
-new feature: load NBO CH3CH2CH3
- -- retrieves the stucture of propane (in this case) from a local NBO server.
- -- including inorganics. For example:
-
- load nbo "Cr 3::acac"
- load nbo "Cr 2:::Bz"
-
-code: new interface for "services" that can provide valuable information to
Jmol
- over ports or by running executable processes.
- -- currently just NBO
-
-
bug fix: MOPAC reader loses two atoms in IRC calculation for MOPAC 2012
bug fix: _slabPlane and _depthPlane not set immediately when slab and depth
are set
-JmolVersion="14.3.12_2015.01.22"
-released simultaneously with 14.2.12
+JmolVersion="14.2.12_2015.01.22"
+released simultaneously with 14.3.12
+
bug fix: color rockets amino fails
bug fix: "color TRANSLUCENT -1" (screened translucency) restored;
-- had been removed in 14.3.12_2015.01.20 because broken in
jmol-11.7.27_02-27-09
@@ -523,8 +183,8 @@
cgo test1b [
BEGIN LINE_LOOP
- VERTEX 4 0 0
- VERTEX 6 2 2
+ VERTEX 4 0 0
+ VERTEX 6 2 2
VERTEX 5 2 0
END
]
@@ -550,7 +210,7 @@
BEGIN LINE_LOOP
DIAMETER 0.3
VERTEX 4 0 0
- VERTEX 6 2 2
+ VERTEX 6 2 2
VERTEX 5 2 0
END
]
@@ -6738,3 +6398,7 @@
October 4, 2011
+
+
+October 4, 2011
+
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