Revision: 21482
http://sourceforge.net/p/jmol/code/21482
Author: hansonr
Date: 2017-04-04 23:09:31 +0000 (Tue, 04 Apr 2017)
Log Message:
-----------
fixes for color property dssr xxxxx so that "n/a" is gray
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolAnnotationParser.java
trunk/Jmol/src/org/jmol/dssx/AnnotationParser.java
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/ColorManager.java
Modified: trunk/Jmol/src/org/jmol/api/JmolAnnotationParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAnnotationParser.java 2017-04-04
16:44:00 UTC (rev 21481)
+++ trunk/Jmol/src/org/jmol/api/JmolAnnotationParser.java 2017-04-04
23:09:31 UTC (rev 21482)
@@ -22,7 +22,7 @@
String getHBonds(ModelSet ms, int modelIndex, Lst<Bond> vHBonds, boolean
doReport);
- void getAtomicDSSRData(ModelSet ms, int modelIndex, int[] dssrData,
+ void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData,
String dataType);
String calculateDSSRStructure(Viewer vwr, BS bsAtoms);
Modified: trunk/Jmol/src/org/jmol/dssx/AnnotationParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/AnnotationParser.java 2017-04-04 16:44:00 UTC
(rev 21481)
+++ trunk/Jmol/src/org/jmol/dssx/AnnotationParser.java 2017-04-04 23:09:31 UTC
(rev 21482)
@@ -900,7 +900,7 @@
}
@Override
- public void getAtomicDSSRData(ModelSet ms, int modelIndex, int[] dssrData,
String dataType) {
+ public void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData,
String dataType) {
}
@Override
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2017-04-04 16:44:00 UTC (rev
21481)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2017-04-04 23:09:31 UTC (rev
21482)
@@ -457,7 +457,7 @@
@SuppressWarnings("unchecked")
@Override
- public void getAtomicDSSRData(ModelSet ms, int modelIndex, int[] dssrData,
String dataType) {
+ public void getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData,
String dataType) {
Map<String, Object> info = (Map<String, Object>) ms.getInfo(modelIndex,
"dssr");
Lst<Object> list;
if (info == null || (list = (Lst<Object>) info.get(dataType)) == null)
@@ -470,7 +470,7 @@
bs.clearAll();
ms.getSequenceBits(map.toString(), bsAtoms, bs);
for (int j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1))
- dssrData[j] = i + 1;
+ dssrData[j] = i;
}
} catch (Throwable e) {
}
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-04 16:44:00 UTC (rev
21481)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-04 23:09:31 UTC (rev
21482)
@@ -1102,8 +1102,6 @@
return group.chain.chainNo;
case T.color:
return group.chain.model.ms.vwr.gdata.getColorArgbOrGray(colixAtom);
- case T.dssr:
- return group.chain.model.ms.getAtomicDSSRData(i);
case T.element:
case T.elemno:
return getElementNumber();
@@ -1188,6 +1186,8 @@
case T.atomz:
case T.z:
return z;
+ case T.dssr:
+ return group.chain.model.ms.getAtomicDSSRData(i);
case T.backbone:
case T.cartoon:
case T.dots:
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2017-04-04
16:44:00 UTC (rev 21481)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2017-04-04
23:09:31 UTC (rev 21482)
@@ -190,7 +190,7 @@
int[] atomSerials;
int[] atomResnos;
int[] atomSeqIDs;
- int[] dssrData;
+ float[] dssrData;
public Vibration[] vibrations;
public float[] occupancies;
short[] bfactor100s;
@@ -2590,7 +2590,7 @@
nAtoms);
atomSeqIDs = (int[]) AU.deleteElements(atomSeqIDs, firstAtomIndex,
nAtoms);
- dssrData = (int[]) AU.deleteElements(dssrData, firstAtomIndex,
+ dssrData = (float[]) AU.deleteElements(dssrData, firstAtomIndex,
nAtoms);
bfactor100s = (short[]) AU.deleteElements(bfactor100s,
firstAtomIndex, nAtoms);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-04-04 16:44:00 UTC
(rev 21481)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-04-04 23:09:31 UTC
(rev 21482)
@@ -4056,17 +4056,16 @@
if (dataType == null)
return;
if (dssrData == null || dssrData.length < ac)
- dssrData = new int[ac];
- else
- for (int i = 0; i < ac; i++)
- dssrData[i] = 0;
+ dssrData = new float[ac];
+ for (int i = 0; i < ac; i++)
+ dssrData[i] = Float.NaN;
for (int i = mc; --i >= 0;)
if (am[i].isBioModel)
((BioModel) am[i]).getAtomicDSSRData(dssrData, dataType);
}
- public int getAtomicDSSRData(int i) {
- return (dssrData == null || dssrData.length <= i ? 0 : dssrData[i]);
+ public float getAtomicDSSRData(int i) {
+ return (dssrData == null || dssrData.length <= i ? Float.NaN :
dssrData[i]);
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2017-04-04 16:44:00 UTC
(rev 21481)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2017-04-04 23:09:31 UTC
(rev 21482)
@@ -438,7 +438,7 @@
getRasmolHydrogenBonds(bs, bs, null, false, Integer.MAX_VALUE, false,
null, dsspVersion);
}
- public void getAtomicDSSRData(int[] dssrData, String dataType) {
+ public void getAtomicDSSRData(float[] dssrData, String dataType) {
if (auxiliaryInfo.containsKey("dssr"))
vwr.getAnnotationParser(true).getAtomicDSSRData(ms, modelIndex,
dssrData, dataType);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2017-04-04 16:44:00 UTC
(rev 21481)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2017-04-04 23:09:31 UTC
(rev 21482)
@@ -1661,9 +1661,12 @@
bsAtom = BS.newN(ac);
tokenAtom = SV.newV(T.bitset, bsAtom);
break;
+ case T.dssr:
+ for (int j = fout.length; --j >= 0;)
+ fout[j] = Float.NaN;
+ //$FALL-THROUGH$
case T.straightness:
case T.surfacedistance:
- case T.dssr:
vwr.autoCalculate(tok, (String) tokenValue);
break;
case T.distance:
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2017-04-04 16:44:00 UTC (rev
21481)
+++ trunk/Jmol/src/org/jmol/script/T.java 2017-04-04 23:09:31 UTC (rev
21482)
@@ -583,7 +583,6 @@
public final static int strucno = intproperty | 23;
public final static int subsystem = intproperty | 24;
public final static int valence = intproperty | 25 | settable;
- public final static int dssr = intproperty | 26;
// float values must be multiplied by 100 prior to comparing to integer
values
@@ -615,6 +614,7 @@
public final static int mody = floatproperty | 24;
public final static int modz = floatproperty | 25;
public final static int modo = floatproperty | 26;
+ public final static int dssr = floatproperty | 27;
public final static int vectorscale = floatproperty | 1 | floatparam;
public final static int atomx = floatproperty | 1 | settable;
public final static int atomy = floatproperty | 2 | settable;
@@ -625,7 +625,7 @@
public final static int fux = floatproperty | 7 | settable;
public final static int fuy = floatproperty | 8 | settable;
public final static int fuz = floatproperty | 9 | settable;
- public final static int bondingradius = floatproperty | 10 |
settable;
+ public final static int bondingradius = floatproperty | 10 | settable;
public final static int partialcharge = floatproperty | 11 | settable;
public final static int temperature = floatproperty | 12 | settable;
public final static int vibx = floatproperty | 18 | settable;
@@ -636,7 +636,7 @@
public final static int z = floatproperty | 23 | settable;
public final static int vanderwaals = floatproperty | 24 | settable |
setparam;
public final static int property = floatproperty | 25 | settable |
setparam | mathproperty;
- public final static int hydrophobicity = floatproperty | 26 | settable |
predefinedset;
+ public final static int hydrophobicity = floatproperty | 26 | settable |
predefinedset;
public final static int selected = floatproperty | 27 | settable |
predefinedset;
public final static int backbone = floatproperty | shapeCommand | 1 |
predefinedset | defaultON | settable;
Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2017-04-04 16:44:00 UTC
(rev 21481)
+++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2017-04-04 23:09:31 UTC
(rev 21482)
@@ -134,8 +134,9 @@
// we need to use the byte form here for speed
switch (pid) {
case PAL.PALETTE_PROPERTY:
- return (colorData == null || atom.i >= colorData.length ? C.GRAY : ce
- .getColorIndex(colorData[atom.i]));
+ float c = colorData[atom.i];
+ return (colorData == null || Float.isNaN(c) || atom.i >=
colorData.length ? C.GRAY : ce
+ .getColorIndex(c));
case PAL.PALETTE_NONE:
case PAL.PALETTE_CPK:
// Note that CPK colors can be changed based upon user preference
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