Revision: 20100
http://sourceforge.net/p/jmol/code/20100
Author: hansonr
Date: 2014-11-10 22:55:24 +0000 (Mon, 10 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.9_2014.11.11"
bug fix: JmolVersion 14.3.3_2014.07.27 broke ligand bond reading when fetching
ligands.
-- mmCIF reader was not being selected by the Resolver
-- Requires an increment of version number to 14.3.9
Modified Paths:
--------------
trunk/Jmol/src/javajs/img/GifEncoder.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/awtjs2d/Platform.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/OutputManager.java
Modified: trunk/Jmol/src/javajs/img/GifEncoder.java
===================================================================
--- trunk/Jmol/src/javajs/img/GifEncoder.java 2014-11-10 12:26:03 UTC (rev
20099)
+++ trunk/Jmol/src/javajs/img/GifEncoder.java 2014-11-10 22:55:24 UTC (rev
20100)
@@ -495,6 +495,9 @@
private void quantizePixels(Map<Integer, ColorCell> colorMap,
Lst<ColorCell> boxes) {
P3[] pixelErr = new P3[pixels.length];
+ // We should replace, not overwrite, pixels
+ // as this may be the raw canvas.buf32.
+ int[] newPixels = new int[pixels.length];
P3 err = new P3();
P3 lab;
int rgb;
@@ -507,7 +510,8 @@
rgb = pixels[p];
} else {
lab = toLAB(pixels[p]);
- err = pixelErr[p]; // it does not matter that we repurpose errors[p]
here.
+ err = pixelErr[p];
+ // it does not matter that we repurpose errors[p] here.
// important not to round the clamp here -- full floating precision
err.x = clamp(err.x, -75, 75);
err.y = clamp(err.y, -75, 75);
@@ -551,12 +555,14 @@
}
}
}
- pixels[p] = cell.index;
+ newPixels[p] = cell.index;
}
}
+ pixels = newPixels;
}
private void addError(P3 err, int f, P3[] pixelErr, int p) {
+ // GIMP will allow changing the background color.
if (pixels[p] == backgroundColor)
return;
P3 errp = pixelErr[p];
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2014-11-10 12:26:03 UTC (rev 20099)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2014-11-10 22:55:24 UTC (rev 20100)
@@ -62,6 +62,10 @@
private P3 chainSum;
private int[] chainAtomCount;
+
+ private boolean isLigandBondBug;
+ // Jmol-14.3.3_2014.07.27 broke mmCIF bond reading for ligands
+ // Jmol-1
@Override
protected void initSubclass() {
@@ -77,6 +81,10 @@
if (checkFilterKey("BIOMOLECULE")) // PDB format
filter = PT.rep(filter, "BIOMOLECULE", "ASSEMBLY");
isBiomolecule = checkFilterKey("ASSEMBLY");
+
+ isLigandBondBug = (stateScriptVersionInt >= 140204 &&
stateScriptVersionInt <= 140208
+ || stateScriptVersionInt >= 140304 && stateScriptVersionInt <= 140308);
+
}
@Override
@@ -880,6 +888,12 @@
};
private boolean processLigandBondLoopBlock() throws Exception {
parseLoopParametersFor(FAMILY_COMPBOND, chemCompBondFields);
+ // alas -- saved states must not read ligand bonding
+ // the problem was that these files were not recognized as mmCIF
+ // files by the resolver when this MMCifReader was created.
+
+ if (isLigandBondBug)
+ return false;
for (int i = propertyCount; --i >= 0;)
if (fieldOf[i] == NONE) {
Logger.warn("?que? missing property: " + chemCompBondFields[i]);
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-10
12:26:03 UTC (rev 20099)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-10
22:55:24 UTC (rev 20100)
@@ -703,7 +703,7 @@
////////////////////////////////////////////////////////////////
private final static String[] mmcifLineStartRecords =
- { "MMCif", "_entry.id", "_database_PDB_", "_pdbx_", "_audit_author.name" };
+ { "MMCif", "_entry.id", "_database_PDB_", "_pdbx_", "_chem_comp.pdbx_type",
"_audit_author.name" };
private final static String[] cifLineStartRecords =
{ "Cif", "data_", "_publ" };
Modified: trunk/Jmol/src/org/jmol/awtjs2d/Platform.java
===================================================================
--- trunk/Jmol/src/org/jmol/awtjs2d/Platform.java 2014-11-10 12:26:03 UTC
(rev 20099)
+++ trunk/Jmol/src/org/jmol/awtjs2d/Platform.java 2014-11-10 22:55:24 UTC
(rev 20100)
@@ -217,7 +217,7 @@
@Override
public int[] grabPixels(Object canvas, int width, int height,
int[] pixels, int startRow, int nRows) {
- // from PNG and JPG image creators, also g3d.ImageRenderer.plotImage
via drawImageToBuffer
+ // from PNG and GIF and JPG image creators, also
g3d.ImageRenderer.plotImage via drawImageToBuffer
/**
*
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-10 12:26:03 UTC
(rev 20099)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-10 22:55:24 UTC
(rev 20100)
@@ -15,6 +15,13 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
+
+Jmol.___JmolVersion="14.3.9_2014.11.11"
+
+bug fix: JmolVersion 14.3.3_2014.07.27 broke ligand bond reading when fetching
ligands.
+ -- mmCIF reader was not being selected by the Resolver
+ -- Requires an increment of version number to 14.3.9
+
Jmol.___JmolVersion="14.3.8_2014.11.10"
bug fix: slightly better GIF processing
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-10 12:26:03 UTC
(rev 20099)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-10 22:55:24 UTC
(rev 20100)
@@ -130,7 +130,7 @@
String fileName = (String) params.get("fileName");
String[] scripts = (String[]) params.get("scripts");
Object objImage = params.get("image");
- int[] rgbbuf = (int[]) params.get("rgbbuf");
+ int[] rgbbuf = (int[]) params.get("rgbbuf"); // only from OBJ exporter
creating PNG output
OC out = (OC) params.get("outputChannel");
boolean asBytes = (out == null && fileName == null);
boolean closeChannel = (out == null && fileName != null);
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