Revision: 20249
http://sourceforge.net/p/jmol/code/20249
Author: hansonr
Date: 2015-01-27 23:56:55 +0000 (Tue, 27 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.27"
bug fix: select thisModel does not select all atoms in visible frame set
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"
bug fix: CGO LINE_LOOP not closing
bug fix: configuration 1 broken
bug fix: display configuration=1 broken (in Jmol 12.0, 2011)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27 22:09:31 UTC
(rev 20248)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27 23:56:55 UTC
(rev 20249)
@@ -1226,7 +1226,6 @@
public P3 getAtomSetCenter(BS bs) {
P3 ptCenter = new P3();
int nPoints = 0;
- if (bs.cardinality() == 1)
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (!isJmolDataFrameForAtom(at[i])) {
nPoints++;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27 22:09:31 UTC
(rev 20248)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27 23:56:55 UTC
(rev 20249)
@@ -17,7 +17,7 @@
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.01.26"
+Jmol.___JmolVersion="14.3.12_2015.01.27"
bug fix: select thisModel does not select all atoms in visible frame set
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-01-27
22:09:31 UTC (rev 20248)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-01-27
23:56:55 UTC (rev 20249)
@@ -2440,6 +2440,7 @@
// model radius in pixels
modelRadiusPixels = modelRadius * scalePixelsPerAngstrom; // (s)
+
// model center offset for zoom 100
float offset100 = (2 * modelRadius) / visualRangeAngstroms *
referencePlaneOffset; // (s)
@@ -2462,9 +2463,11 @@
if (!scale3D || perspectiveDepth)
scalePixelsPerAngstrom *= (modelCenterOffset / offset100) * zmPct / 100;
// (s/m)
+
// so that's sppa = (spc / vR) * rPO * (vR / 2) / mR * rPO = spc/2/mR
modelRadiusPixels = modelRadius * scalePixelsPerAngstrom; // (s)
+
// System.out.println("transformman zoom scalppa modelrad " +
zoomPercent + " " +
// scalePixelsPerAngstrom + " " + modelRadiusPixels + " " +
visualRange
// + " -- "+ vwr.dimScreen.width+ " "+ vwr.dimScreen.height);
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
