Revision: 20857
http://sourceforge.net/p/jmol/code/20857
Author: hansonr
Date: 2015-11-03 12:36:49 +0000 (Tue, 03 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.03"
bug fix: FOR without {} but with ";" after sole statement
followed immediately by second FOR improperly loops
for (var i from [1,5])
print i;
for (var i from [1,5])
print i
bug fix: OXT missing from BACKBONE selection
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-03 12:34:41 UTC
(rev 20856)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-03 12:36:49 UTC
(rev 20857)
@@ -3167,7 +3167,8 @@
plane = e.getHklPlane(pt);
break;
case T.varray:
- pt = (last == 2 ? SV.ptValue(args[1]) : last == 1 ? P3.new3(Float.NaN,
0, 0) : null);
+ pt = (last == 2 ? SV.ptValue(args[1]) : last == 1 ? P3.new3(Float.NaN, 0,
+ 0) : null);
if (pt == null)
return false;
break;
@@ -3194,12 +3195,12 @@
CubeIterator iter;
if (Float.isNaN(pt.x)) {
// internal comparison
- Point3fi p;
- Point3fi[] pt3 = new Point3fi[sv.size()];
+ Point3fi p;
+ Point3fi[] pt3 = new Point3fi[sv.size()];
for (int i = pt3.length; --i >= 0;) {
P3 p3 = SV.ptValue(sv.get(i));
if (p3 == null)
- return false;
+ return false;
p = new Point3fi();
p.setT(p3);
p.i = i;
@@ -3214,26 +3215,41 @@
int n = 0;
while (iter.hasMoreElements()) {
Point3fi pt2 = (Point3fi) iter.nextElement();
- if (bsp.get(pt2.i) && pt2.distanceSquared(p) <= d2
- && (++n > 1))
+ if (bsp.get(pt2.i) && pt2.distanceSquared(p) <= d2 && (++n > 1))
bsp.clear(pt2.i);
}
}
- for (int i = bsp.nextSetBit(0); i >= 0; i = bsp.nextSetBit(i + 1))
+ for (int i = bsp.nextSetBit(0); i >= 0; i = bsp.nextSetBit(i + 1))
pts.addLast(P3.newP(pt3[i]));
return mp.addXList(pts);
-
+
}
+ float d2;
+ if (distance == 0) {
+ // closest
+ P3 pt3 = null, pta;
+ d2 = Float.MAX_VALUE;
+ for (int i = sv.size(); --i >= 0;) {
+ pta = SV.ptValue(sv.get(i));
+ distance = pta.distanceSquared(pt);
+ if (distance < d2) {
+ pt3 = pta;
+ d2 = distance;
+ }
+ }
+ return (pt3 == null ? mp.addXStr("") : mp.addXPt(pt3));
+ }
for (int i = sv.size(); --i >= 0;)
bspt.addTuple(SV.ptValue(sv.get(i)));
iter = bspt.allocateCubeIterator();
iter.initialize(pt, distance, false);
- float d2 = distance * distance;
+ d2 = distance * distance;
while (iter.hasMoreElements()) {
T3 pt2 = iter.nextElement();
if (pt2.distanceSquared(pt) <= d2)
pts.addLast(pt2);
}
+ iter.release();
return mp.addXList(pts);
}
return mp.addXBs(vwr.getAtomsNearPt(distance, pt));
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-11-03 12:34:41 UTC (rev
20856)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-11-03 12:36:49 UTC (rev
20857)
@@ -622,7 +622,7 @@
// structure related
//
"@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever?
- "@_bb protein&_a>=1&_a<6 |
nucleic&(_a>=6&_a<14|_a>=73&&_a<=79||_a==99||_a=100)", // no H atoms
+ "@_bb protein&(_a>=1&_a<6|_a=64) |
nucleic&(_a>=6&_a<14|_a>=73&&_a<=79||_a==99||_a=100)", // no H atoms
"@backbone _bb | _H && connected(single, _bb)",
"@spine protein&_a>=1&_a<4|nucleic&(_a>=6&_a<11|_a=13)",
"@sidechain (protein,nucleic) & !backbone",
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-03 12:34:41 UTC
(rev 20856)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-03 12:36:49 UTC
(rev 20857)
@@ -62,13 +62,24 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.11.01"
+Jmol.___JmolVersion="14.5.0_2015.11.03"
+bug fix: FOR without {} but with ";" after sole statement
+ followed immediately by second FOR improperly loops
+ for (var i from [1,5])
+ print i;
+ for (var i from [1,5])
+ print i
+
+bug fix: OXT missing from BACKBONE selection
+bug fix: (JSmol) CIF parser fails to read CIF files containing only a single
(non-loop) _struct_ref_seq_dif.align_id
+
new feature: polyhedra ID xxx SCALE x.x
-- ID named polyhedra only
-- x.x is the scaling factor, initially 1
+ -- x.x > 0 does normal scaling
-- x.x < 0 does "explode" from {0 0 0} (for higher-order Brillouin zones,
for instance)
- -- x.x > 0 does normal scaling
+
bug fix: slabbing should reset area and volume of isosurface
bug fix: meshSlicer may fail to add edge to sliced pmesh
@@ -242,7 +253,7 @@
unitcell(uc) // copies unit cell
unitcell(uc, "reciprocal") // reciprocal lattice for specified unit cell
unitcell("reciprocal") // reciprocal lattice for current model's unit cell
- unitcell(ucconv, "primitive","BCC"|"FCC") // convert primitive to
conventional
+ unitcell(ucconv, "primitive","BCC"|"FCC") // convert conventional to
primitive
unitcell("primitive","BCC"|"FCC")
unitcell(ucprim, "conventional","BCC"|"FCC") // convert primitive to
conventional
unitcell("conventional","BCC"|"FCC")
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