Revision: 20651
http://sourceforge.net/p/jmol/code/20651
Author: hansonr
Date: 2015-07-10 03:51:03 +0000 (Fri, 10 Jul 2015)
Log Message:
-----------
released as 14.2.15
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 2015-07-10
03:27:09 UTC (rev 20650)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-10
03:51:03 UTC (rev 20651)
@@ -11,17 +11,103 @@
synchronized with 14.3.15_2015.07.09
+clarification:
-bug fix: load "xxx" 1 {10 10 10} does not recognize lattice information when
model number is given (broken in 07.07)
-
-JmolVersion="14.3.15_2015.07.08c"
-
+ load "" 1 # loads the first model in a file when not PDB or
mmCIF.
+ load "" 1 # loads the model with MODEL 1 record for a PDB file.
+ load "" 1 # loads the model with _atom_site.pdbx_PDB_model_num =
1 for an mmCIF file
+ load "" [1] # same as load "" 1; brackets allow for more than one
model, for instance [1 3 5]
+ load MODELS ({1}) "" # always loads the SECOND model in a file
+
bug fix: load files "xxx.png|xxxx" "xxx.png|zzzz" not read from state properly
-bug fix: polyhedra not saved in state property
bug fix: moving atoms with 4x4 matrix not saved in state
bug fix: moving of an atom having a polyhedron fails to move the polyhedron as
well
+bug fix: x.getProperty("[select name where composition[1] == 0.5]")
+ -- the [ there is tripping us up. True, ..1 could be used instead as well.
+bug fix: 2015.07.06 breaks text writing in JSmol
+bug fix: Crystal reader cannot handle TOTAL ENERGY CORRECTED... line
+bug fix: mmCIF reader does not recognize load MODEL ...
+bug fix: PDB reader should be reading load "" [1 3 4] as MODEL record numbers,
not sequential numbers
+bug fix: load MODELS "" [1 3 4] does not work (although load "" [1 3 4],
without with MODELS keyword, works)
+
+bug fix: SMARTS processing with "." may not find substructure
+
+bug fix: POVRay and VRML exporters mishandle label backgrounds
+bug fix: exports not handling rockets correctly
+
+bug fix: 1/{a b c} gives 0, not 1/length({a b c})
+
+bug fix: AFLOW binary file reader can fail with certain VASP formats
containing
+ both in-line atom labels and atom elements prior to #elements line.
(AlPd#5, for example)
+
+bug fix: ++x and x++ do not increment properly when in expressions
+ // no problem here because it is compiled as "x = x + 1"
+ x = 0
+ x++
+ print "x should be 1 " + x
+
+ // x does not increment, but the test passes
+ x = 0
+ if (++x) {
+ print "good"
+ }
+ print "x should be 1 " + x
+
+ // x does not increment, but the test passes ("bad" is not printed)
+ x = 0
+ if (x++) {
+ print "bad"
+ }
+ print "x should be 1 " + x
+ x = 0
+ // works
+ x++
+ // y is OK, but x does not increment
+ y = x++
+ print "x should be 2 " + x
+ x = 0
+ // z is OK, but x does not increment
+ z = ++x
+ print "x should be 1 " + x
+
+ // result:
+
+ x should be 1 1
+ good
+ x should be 1 0
+ x should be 1 0
+ x should be 2 1
+ x should be 1 0
+
+bug fix: msCIF reader can hang if occupancy is not fractional
+bug fix: JSmol applet not returning full set of parameters in animFrameCallback
+bug fix: load FILL command can fail if base unit cell is not part of the
needed set for the specified volume
+
+bug fix: wireframe ONLY (RESTRICT) executes polyhedral DELETE instead of OFF
+bug fix: Polygons not indicating visibility when they are the only thing
visible.
+bug fix: x[++y] did not increment y. x[y++] and other contexts were fine
+
+bug fix: msCIF reader failing for Legendre polynomials of order greater than 4
+ -- JavaScript fix for new double[m + 1][]
+ -- must use AU.newDouble2(m + 1);
+
+bug fix: var firstPARAM = "p1_b"; x = [FIRSTParam: "p1_a"]; results in
lowering of case as [firstparam:....]
+bug fix: set drawPicking draw;set drawpicking does not show handles
+bug fix; point group not calculated when the selected atoms are a subset of a
model
+bug fix: x.find("SMILES") is incorrect for structures that have hypervalent
atoms and branches such as inorganic nitrates
+bug fix: msCIF reading with two models, and only one has displacement
modulation causes "render error" crash
+bug fix: msCIF reader failing for Legendre polynomials of order greater than 4
+bug fix: DRAW for quadrilateral broken when perspective depth is turned off.
+bug fix: SET ECHO IMAGE broken in JavaScript version
+
+bug fix: polyhedra broken for number of vertices > 6.
+ -- needed smaller default distanceFactor (set to 1.5; formerly 1.85)
+ -- this setting is for any
+
+
+
new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)
-- asMap = TRUE (default false) indicates you want an atom
correlation map indicating positions in smiles2 corresponding to smiles1
@@ -43,16 +129,6 @@
select {1.1}
rotateselected @mat
-JmolVersion="14.3.15_2015.07.07c"
-
-bug fix: x.getProperty("[select name where composition[1] == 0.5]")
- -- the [ there is tripping us up. True, ..1 could be used instead as well.
-
-JmolVersion="14.3.15_2015.07.07b"
-
-bug fix: 2015.07.06 breaks text writing in JSmol
-bug fix: Crystal reader cannot handle TOTAL ENERGY CORRECTED... line
-
new feature: JSmol Jmol._persistentMenu = true
-- allows menu to persist and not be removed
@@ -62,35 +138,6 @@
-- scales model based on a crystal lattice
-- allows volume matching for crystal comparison
-bug fix: SMARTS processing with "." may not find substructure
-
-JmolVersion="14.3.15_2015.07.03"
-
-bug fix: mmCIF reader does not recognize load MODEL ...
-bug fix: PDB reader should be reading load "" [1 3 4] as MODEL record numbers,
not sequential numbers
-bug fix: load MODELS "" [1 3 4] does not work (although load "" [1 3 4],
without with MODELS keyword, works)
-
-clarification:
-
- load "" 1 # loads the first model in a file when not PDB or
mmCIF.
- load "" 1 # loads the model with MODEL 1 record for a PDB file.
- load "" 1 # loads the model with _atom_site.pdbx_PDB_model_num =
1 for an mmCIF file
- load "" [1] # same as load "" 1; brackets allow for more than one
model, for instance [1 3 5]
- load MODELS ({1}) "" # always loads the SECOND model in a file
-
-
-
-JmolVersion="14.3.15_2015.06.30"
-
-bug fix: POVRay and VRML exporters mishandle label backgrounds
-bug fix: exports not handling rockets correctly
-
-JmolVersion="14.3.15_2015.06.19c"
-
-bug fix: 1/{a b c} gives 0, not 1/length({a b c})
-
-JmolVersion="14.3.15_2015.06.19b"
-
new feature: MACRO command
-- runs predefined script, generally defining new functions of general use
-- contributions welcome!
@@ -135,11 +182,6 @@
"modelNumber" : 260
}
-bug fix: AFLOW binary file reader can fail with certain VASP formats
containing
- both in-line atom labels and atom elements prior to #elements line.
(AlPd#5, for example)
-
-JmolVersion="14.3.15_2015.06.19"
-
new feature: pt.distance(plane,ptRef)
-- returns a negative distance if pt and ptRef are on different sides of the
plane
-- useful for constructing 3D convex hulls and polyhedra, where all points
@@ -156,23 +198,11 @@
print [0 3 4 "" 5 {} [] 6].find("")
[ "" {} [] ]
-bug fix: msCIF reader can hang if occupancy is not fractional
-bug fix: JSmol applet not returning full set of parameters in animFrameCallback
-bug fix: load FILL command can fail if base unit cell is not part of the
needed set for the specified volume
-
-JmolVersion="14.3.15_2015.06.18"
-
new feature: polyhedra ONLY
new feature: calculate symmetry POLYHEDRA
-- sets values for ShapeInfo.Polyhedra.smiles, .smarts, and .pointGroup
-bug fix: wireframe ONLY (RESTRICT) executes polyhedral DELETE instead of OFF
-bug fix: Polygons not indicating visibility when they are the only thing
visible.
-bug fix: x[++y] did not increment y. x[y++] and other contexts were fine
-
-JmolVersion="14.3.15_2015.06.17"
-
new feature: extracting array of sequential arrays from array of associative
arrays
-- pull out just the values desired into a sequential array
-- example, where b is an array of associative arrays [....., energy:...,
pointGroup....]
@@ -199,7 +229,6 @@
print b.format(["energy", "pointGroup"]).sort(1).reverse.format("%5.3f
%5s")
-
new feature: polyhedra highlight with select ON or set selectionHalos ON
new feature: getProperty("ShapeInfo.polyhedra") includes keys
@@ -244,70 +273,12 @@
// make the current frame set just those models
frame @z
- -- not fully worked out
-
new feature: array.getProperty("xxxx")
-- same as getproperty(array, "xxxx")
-- drills down into an array of associative arrays to get sublist
-- can be used with [SELECT ... WHERE]
-bug fix: ++x and x++ do not increment properly when in expressions
- // no problem here because it is compiled as "x = x + 1"
- x = 0
- x++
- print "x should be 1 " + x
-
- // x does not increment, but the test passes
- x = 0
- if (++x) {
- print "good"
- }
- print "x should be 1 " + x
-
- // x does not increment, but the test passes ("bad" is not printed)
- x = 0
- if (x++) {
- print "bad"
- }
- print "x should be 1 " + x
- x = 0
- // works
- x++
- // y is OK, but x does not increment
- y = x++
- print "x should be 2 " + x
- x = 0
- // z is OK, but x does not increment
- z = ++x
- print "x should be 1 " + x
-
- // result:
-
- x should be 1 1
- good
- x should be 1 0
- x should be 1 0
- x should be 2 1
- x should be 1 0
-
-JmolVersion="14.3.15_2015.06.16"
-bug fix: msCIF reader failing for Legendre polynomials of order greater than 4
- -- JavaScript fix for new double[m + 1][]
- -- must use AU.newDouble2(m + 1);
-
-JmolVersion="14.3.15_2015.06.14c"
-
-bug fix: var firstPARAM = "p1_b"; x = [FIRSTParam: "p1_a"]; results in
lowering of case as [firstparam:....]
-bug fix: set drawPicking draw;set drawpicking does not show handles
-bug fix; point group not calculated when the selected atoms are a subset of a
model
-bug fix: x.find("SMILES") is incorrect for structures that have hypervalent
atoms and branches such as inorganic nitrates
-bug fix: msCIF reading with two models, and only one has displacement
modulation causes "render error" crash
-bug fix: msCIF reader failing for Legendre polynomials of order greater than 4
-bug fix: DRAW for quadrilateral broken when perspective depth is turned off.
-bug fix: SET ECHO IMAGE broken in JavaScript version
-
-
feature note: This version introduces several very powerful and very different
capabilities
to Jmol in the area of crystallography. Many of these features
are nonexistent
in other programs. They involve:
@@ -501,14 +472,8 @@
code: SMILES code cleaned up.
code: most image loading is now asynchronous. (Not BMP, not from PNGJ files
with "|" in filename)
-code: introducing interfaces to allow less use of @j2sNative and more
traceability of method calls in Eclipse
+code: introducing interfaces to allow less use of @j2sNative and more
traceability of method calls in Eclipse
-
-
-bug fix: polyhedra broken for number of vertices > 6.
- -- needed smaller default distanceFactor (set to 1.5; formerly 1.85)
- -- this setting is for any
-
code: to be released 6/11/15
JmolVersion="14.3.14_2015.06.10c"
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