Revision: 20165
http://sourceforge.net/p/jmol/code/20165
Author: hansonr
Date: 2014-12-19 13:06:49 +0000 (Fri, 19 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.19"
bug fix: label, echo, and measurement text should not display when deeper
than zSlab with zShade is TRUE
bug fix: mmCIF reader load filter biomolecule 1
broken for viruses with symmetry ranges listed as "1-60" with a hyphen
bug fix: mmCIF reader coarse-grain load filter bysymop broken
bug fix: mmCIF reader coarse-grain load filter bychain broken
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/render/EchoRenderer.java
trunk/Jmol/src/org/jmol/render/LabelsRenderer.java
trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2014-12-18 00:45:21 UTC (rev 20164)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2014-12-19 13:06:49 UTC (rev 20165)
@@ -74,7 +74,7 @@
byChain = checkFilterKey("BYCHAIN");
bySymop = checkFilterKey("BYSYMOP");
isCourseGrained = byChain || bySymop;
- if (byChain) {
+ if (isCourseGrained) {
chainAtomMap = new Hashtable<String, P3>();
chainAtomCounts = new Hashtable<String, int[]>();
}
@@ -113,7 +113,8 @@
if (note != null)
appendLoadNote(note);
}
- applySymmetryAndSetTrajectory();
+ if (!isCourseGrained)
+ applySymmetryAndSetTrajectory();
}
if (htSites != null)
@@ -307,7 +308,7 @@
int iMolecule = parseIntStr(id);
String list = assem[ASSEM_LIST];
appendLoadNote("found biomolecule " + id + ": " + list);
- if (!checkFilterKey("ASSEMBLY " + id + ";"))
+ if (!checkFilterKey("ASSEMBLY " + id + ";") && !checkFilterKey("ASSEMBLY="
+ id + ";"))
return;
if (vBiomolecules == null) {
vBiomolecules = new Lst<Map<String, Object>>();
@@ -348,7 +349,7 @@
if (ops.indexOf("-") >= 0)
ops = BS.unescape(
"({" + ops.substring(1, ops.length() - 1).replace('-', ':') + "})")
- .toString();
+ .toJSON();
ops = PT.rep(ops, " ", "");
ops = ops.substring(1, ops.length() - 1);
}
@@ -841,6 +842,7 @@
a1.setT(sum);
a1.scale(1f / count);
a1.radius = 16;
+ asc.addAtom(a1);
}
} else {
nAtoms = bsAll.cardinality();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2014-12-18
00:45:21 UTC (rev 20164)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2014-12-19
13:06:49 UTC (rev 20165)
@@ -1045,6 +1045,7 @@
a.scale(1f / (atomMax - firstSymmetryAtom));
a.atomName = "Pt";
a.radius = 16;
+ asc.addAtom(a);
firstSymmetryAtom = atomMax++;
break;
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2014-12-18 00:45:21 UTC
(rev 20164)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2014-12-19 13:06:49 UTC
(rev 20165)
@@ -1053,16 +1053,13 @@
",[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL],[SOE]" +
",[XYL],[A2G],[LBT],[NGA],[SIA],[SLB]" +
",[AFL],[AGC],[GLB],[NAN],[RAA]"; //these 4 are deprecated in PDB
- // from Eric Martz; revision by Angel Herraez
+
+ // from Eric Martz; revision by Angel Herraez
public static short knownGroupID(String group3) {
- if (group3 != null) {
- if (group3.length() == 0)
- return 0;
- Short boxedGroupID = Group.htGroup.get(group3);
- if (boxedGroupID != null)
- return boxedGroupID.shortValue();
- }
- return -1;
+ if (group3 == null || group3.length() == 0)
+ return 0;
+ Short boxedGroupID = Group.htGroup.get(group3);
+ return (boxedGroupID == null ? -1 : boxedGroupID.shortValue());
}
/**
* @param group3 a potential group3 name
Modified: trunk/Jmol/src/org/jmol/render/EchoRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/EchoRenderer.java 2014-12-18 00:45:21 UTC
(rev 20164)
+++ trunk/Jmol/src/org/jmol/render/EchoRenderer.java 2014-12-19 13:06:49 UTC
(rev 20165)
@@ -42,6 +42,7 @@
.getScalePixelsPerAngstrom(true) * 10000 : 0);
imageFontScaling = vwr.getImageFontScaling();
boolean haveTranslucent = false;
+ setZcutoff();
for (Text t: echo.objects.values()) {
if (!t.visible || t.hidden) {
continue;
@@ -60,6 +61,8 @@
z = pt0i.z - vwr.tm.zValueFromPercent(0) + z;
t.setZs(z, z);
}
+ if (t.zSlab >= zCutoff)
+ continue;
if (t.pointerPt == null) {
t.pointer = JC.POINTER_NONE;
} else {
Modified: trunk/Jmol/src/org/jmol/render/LabelsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/LabelsRenderer.java 2014-12-18 00:45:21 UTC
(rev 20164)
+++ trunk/Jmol/src/org/jmol/render/LabelsRenderer.java 2014-12-19 13:06:49 UTC
(rev 20165)
@@ -49,7 +49,6 @@
byte fidPrevious;
- private int zCutoff;
private P3 pTemp = new P3();
protected short bgcolix;
@@ -70,6 +69,8 @@
protected int zSlab = Integer.MIN_VALUE;
+ protected int zCutoff;
+
private int zBox;
private float[] boxXY;
@@ -79,8 +80,6 @@
@Override
protected boolean render() {
fidPrevious = 0;
- zCutoff =(tm.zShadeEnabled ? tm.zDepthValue : 0);
-
Labels labels = (Labels) shape;
String[] labelStrings = labels.strings;
@@ -88,6 +87,7 @@
int[] offsets = labels.offsets;
if (labelStrings == null)
return false;
+ setZcutoff();
Atom[] atoms = ms.at;
short backgroundColixContrast = vwr.cm.colixBackgroundContrast;
int backgroundColor = vwr.getBackgroundArgb();
@@ -121,7 +121,7 @@
textAlign = Labels.getAlignment(offsetFull);
pointer = offsetFull & JC.LABEL_POINTER_FLAGS;
zSlab = atom.sZ - atom.sD / 2 - 3;
- if (zCutoff > 0 && zSlab > zCutoff)
+ if (zSlab > zCutoff)
continue;
if (zSlab < 1)
zSlab = 1;
@@ -157,6 +157,10 @@
return false;
}
+ protected void setZcutoff() {
+ zCutoff =(tm.zShadeEnabled ? tm.zSlabValue : Integer.MAX_VALUE);
+ }
+
protected Text renderLabelOrMeasure(Text text, String label) {
boolean newText = false;
if (text != null) {
Modified: trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java 2014-12-18
00:45:21 UTC (rev 20164)
+++ trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java 2014-12-19
13:06:49 UTC (rev 20165)
@@ -91,6 +91,7 @@
return false;
boolean showMeasurementLabels = vwr.getBoolean(T.measurementlabels);
measures.setVisibilityInfo();
+ setZcutoff();
for (int i = measures.measurementCount; --i >= 0;) {
m = measures.measurements.get(i);
if (!m.isVisible || !m.isValid || (count = m.count) == 1 && m.traceX ==
Integer.MIN_VALUE)
@@ -199,7 +200,7 @@
int zB = b.sZ - b.sD - 10;
int radius = drawLine(a.sX, a.sY, zA, b.sX,
b.sY, zB, mad);
- if (s == null)
+ if (s == null || zB >= zCutoff)
return;
if (mad > 0)
radius <<= 1;
@@ -230,7 +231,7 @@
b.sY, zB, mad);
radius += drawLine(b.sX, b.sY, zB, c.sX,
c.sY, zC, mad);
- if (s == null)
+ if (s == null || zB >= zCutoff)
return;
radius = (radius + 1) / 2;
if (m.value > 175) {
@@ -305,14 +306,14 @@
c.sY, zC, mad);
radius += drawLine(c.sX, c.sY, zC, d.sX,
d.sY, zD, mad);
- if (s == null)
+ int zLabel = (zA + zB + zC + zD) / 4;
+ if (s == null || zLabel >= zCutoff)
return;
radius /= 3;
if (m.text == null) {
g3d.setC(labelColix);
drawString((a.sX + b.sX + c.sX + d.sX) / 4,
- (a.sY + b.sY + c.sY + d.sY) / 4,
- (zA + zB + zC + zD) / 4, radius, false, false, false,
+ (a.sY + b.sY + c.sY + d.sY) / 4, zLabel, radius, false, false, false,
(doJustify ? 0 : Integer.MAX_VALUE), s);
} else {
atomPt.add2(a, b);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-18 00:45:21 UTC
(rev 20164)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-19 13:06:49 UTC
(rev 20165)
@@ -16,8 +16,17 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.11_2014.12.17"
+Jmol.___JmolVersion="14.3.11_2014.12.19"
+bug fix: label, echo, and measurement text should not display when deeper
+ than zSlab with zShade is TRUE
+bug fix: mmCIF reader load filter biomolecule 1
+ broken for viruses with symmetry ranges listed as "1-60" with a
hyphen
+bug fix: mmCIF reader coarse-grain load filter bysymop broken
+bug fix: mmCIF reader coarse-grain load filter bychain broken
+
+JmolVersion="14.3.11_2014.12.17"
+
bug fix: rotate selected <4x4 matrix> should not rotate about center of atoms
bug fix: use of a subset command will change value of a variable bitset if
"select x" is used
-- example:
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