Revision: 20781
http://sourceforge.net/p/jmol/code/20781
Author: hansonr
Date: 2015-09-21 01:43:27 +0000 (Mon, 21 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.21"
bug fix: print within(0, "XXX", ...) ignores the "XXX" entirely. Should throw
an error (Ron Mignery)
bug fix: print within(0, "vdw", ...) ignores "vdw"; should accept that as
"vanderwaal"
bug fix: print within(-1.0, "vanderwaal", ...) ignores "vanderwaal" and does a
fractional-coordinate calculation
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-20 21:01:08 UTC (rev
20780)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-21 01:43:27 UTC (rev
20781)
@@ -86,8 +86,8 @@
"..helices.pairs.nt*" +
"..iloops.nts_long" +
"..isocanonpairs.nt*" +
+ "..junctions.nts_long" +
"..kissingloops.hairpins.nts_long" +
- "..junctions.nts_long" +
"..multiplets.nts_long" +
"..nonstacks.nts_long" +
"..nts.nt_id" +
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-09-20 21:01:08 UTC
(rev 20780)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-09-21 01:43:27 UTC
(rev 20781)
@@ -2805,7 +2805,6 @@
ModelSet ms = vwr.ms;
boolean isWithinModelSet = false;
boolean isWithinGroup = false;
- boolean isWithinUnitcell = false;
boolean isDistance = (isVdw || tok == T.decimal || tok == T.integer);
RadiusData rd = null;
switch (tok) {
@@ -2845,6 +2844,8 @@
tok == T.search ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES,
mp.asBitSet, false));
}
+
+
if (withinSpec instanceof String) {
if (tok == T.nada) {
tok = T.spec_seqcode;
@@ -2869,22 +2870,26 @@
String s = SV.sValue(args[1]);
if (s.startsWith("$"))
return mp.addXBs(getAtomsNearSurface(distance, s.substring(1)));
- isWithinGroup = (s.equalsIgnoreCase("group"));
- isVdw = (!isWithinGroup && s.equalsIgnoreCase("vanderwaals"));
- isWithinUnitcell = (!isWithinGroup && s.equalsIgnoreCase("unitcell"));
- if (isVdw) {
+ if (s.equalsIgnoreCase("group")) {
+ isWithinGroup = true;
+ tok = T.group;
+ } else
+ if (s.equalsIgnoreCase("vanderwaals") || s.equalsIgnoreCase("vdw")) {
withinSpec = null;
+ isVdw = true;
tok = T.vanderwaals;
- } else if (isWithinUnitcell) {
+ } else if (s.equalsIgnoreCase("unitcell")) {
tok = T.unitcell;
} else {
- tok = T.group;
+ return false;
}
break;
}
} else {
return false;
}
+
+
P3 pt = null;
P4 plane = null;
switch (i) {
@@ -2977,9 +2982,12 @@
return mp.addXBs(vwr.ms.getAtoms(tok, bs));
if (isWithinGroup)
return mp.addXBs(vwr.getGroupsWithin((int) distance, bs));
- if (isVdw)
+ if (isVdw) {
rd = new RadiusData(null, (distance > 10 ? distance / 100 : distance),
(distance > 10 ? EnumType.FACTOR : EnumType.OFFSET), VDW.AUTO);
+ if (distance < 0)
+ distance = 0; // not used, but this prevents a diversion
+ }
return mp.addXBs(vwr.ms.getAtomsWithinRadius(distance, bs,
isWithinModelSet, rd));
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-20 21:01:08 UTC
(rev 20780)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-21 01:43:27 UTC
(rev 20781)
@@ -61,8 +61,15 @@
TODO: Switch to dssr1 prior to full release
-Jmol.___JmolVersion="14.3.16_2015.09.20"
+Jmol.___JmolVersion="14.3.16_2015.09.21"
+bug fix: print within(0, "XXX", ...) ignores the "XXX" entirely. Should throw
an error (Ron Mignery)
+bug fix: print within(0, "vdw", ...) ignores "vdw"; should accept that as
"vanderwaal"
+bug fix: print within(-1.0, "vanderwaal", ...) ignores "vanderwaal" and does a
fractional-coordinate calculation
+
+
+JmolVersion="14.3.16_2015.09.20"
+
FEATURE CHANGE: 3DNA DSSR has switched over to JSON; some array names are
changed.
new feature: print @1.label("%[unitid]")
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