Revision: 20735
http://sourceforge.net/p/jmol/code/20735
Author: hansonr
Date: 2015-08-25 14:07:19 +0000 (Tue, 25 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.08.25"
bug fix: JmolThread should use setTimeout in resumeEval
new feature: JmolSMILES $(.x:1,2,3,4,5,6,7,8)
-- x is oen of d,a,t
-- up to four ranges per measurement
new feature: print {2.1}.find("SMILES",{1.1})
bug fix: compare() function returning matrix with translation about center, not
origin
bug fix: print compare({1.1},{2.1}, "SMILES", "stddev") broken
bug fix: select search("[$(select atomno < 5)]") broken
bug fix: select search("[$(select atomno < 5) or @5]") broken
new feature: _hoverLabel
-- reports general hover label set by hover command
new feature: _hoverEnabled
-- reports if hover is enabled or not
bug fix: calculate partialCharge does not store result if all values are 0
(Otis Rothenberger)
bug fix: still problems with aTest = "testing"; x = [aTest:aTest] or a =
[property_MYINFO:aTest] (Rolf Huehne)
bug fix: cross(a,b) broken
bug fix: write PDB broken; works without "PDB" keyword broken in
14.3.15_2015.06.18
new feature: /invertStereo/ flag for SMARTS search
-- allows quick check for enantiomers
-- example: select search("/invertStereo/C[C@H](Br)CC") will match
(R)-2-bromobutane
even though it is for (S)-2-bromobutane
FEATURE CHANGE: Definitions of dna, rna, purine, and pyrimidine were ambiguous
and
not particularly viable for group fragments. This is much
clearer
now: Fragments and P-only and N-only monomers are identified by
name only:
// These masks are only used for P-only and N-only polymers
// or cases where there are so few atoms that a monomer's type
// cannot be determined by checking actual atoms and connections.
// They are used for NucleicMonomer or AminoMonomer classes only as
// a last resort.
//
// I A G
// purine: 100101 = 0x25
// UT C
// pyrimidine: 011010 = 0x1A
//
// +IUTACGDIUTACG IUTACG
// rna: 110000 000000 110111 = 0x30037
// +IUTACGDIUTACG IUTACG
// dna: 001111 111111 001000 = 0x0FFC8
bug fix: SMILES recognizes atom name [*.CA] but not residue name [ALA.*]
bug fix: Jmol BioSMILES broken
bug fix: set cartoonLadders with phosphorus-only polymers crashes Jmol
bug fix: protein and nucleic are not set properly for non-monomer groups (Eric
Martz)
-- broken in Jmol 14.3.11 (12/13/2014)
-- general definition of protein is from having CA, C, and N. But there
are situations where we know it is protein from its group name (ALA,LEU..)
despite the fact that it is just one atom. Same for nucleic.
-- note that non-canonical (HETERO) amino acids or nucleic bases that do not
have
the requisite atoms to identify them as such will still not test positive
for
"protein" or "nucleic".
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/thread/JmolThread.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/thread/JmolThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/JmolThread.java 2015-08-25 05:56:29 UTC
(rev 20734)
+++ trunk/Jmol/src/org/jmol/thread/JmolThread.java 2015-08-25 14:07:19 UTC
(rev 20735)
@@ -73,9 +73,19 @@
if (eval == null || !isJS && !vwr.testAsync || !useTimeout)
return;
sc.mustResumeEval = !stopped;
- eval.resumeEval(sc);
- eval = null;
- sc = null;
+ JmolScriptEvaluator eval = this.eval;
+ ScriptContext sc = this.sc;
+ this.eval = null;
+ this.sc = null;
+ /**
+ * @j2sNative
+ *
+ * setTimeout(function() { eval.resumeEval(sc); }, 1);
+ *
+ */
+ {
+ eval.resumeEval(sc);
+ }
}
@Override
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-25 05:56:29 UTC
(rev 20734)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-25 14:07:19 UTC
(rev 20735)
@@ -56,8 +56,13 @@
appear at a different location. An interesting challenge to figure out the
algorithm
that still places it in the "proper" place even when perspective is on.
(Daniele Tomerini)
-Jmol.___JmolVersion="14.3.16_2015.08.24"
+TODO: image off stops JSmol
+TODO: Rolf's errors in Safari due to move + zoomto
+Jmol.___JmolVersion="14.3.16_2015.08.25"
+
+bug fix: JmolThread should use setTimeout in resumeEval
+
new feature: JmolSMILES $(.x:1,2,3,4,5,6,7,8)
-- x is oen of d,a,t
-- up to four ranges per measurement
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