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[Jmol-commits] SF.net SVN: jmol: [9137] branches/bob-deleteatoms/Jmol/src/org/jmol
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From: <ha...@us...> - 2008-03-16 11:57:45
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Revision: 9137
http://jmol.svn.sourceforge.net/jmol/?rev=9137&view=rev
Author: hansonr
Date: 2008-03-16 04:57:42 -0700 (Sun, 16 Mar 2008)
Log Message:
-----------
bob-deleteatoms merge
Modified Paths:
--------------
branches/bob-deleteatoms/Jmol/src/org/jmol/atomdata/AtomData.java
branches/bob-deleteatoms/Jmol/src/org/jmol/geodesic/EnvelopeCalculation.java
branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/BondCollection.java
branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/ModelSet.java
branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Dots.java
branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Sticks.java
branches/bob-deleteatoms/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/atomdata/AtomData.java
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/atomdata/AtomData.java 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/atomdata/AtomData.java 2008-03-16 11:57:42 UTC (rev 9137)
@@ -152,7 +152,5 @@
public Point3f[][] hAtoms;
public int atomCount;
public int hydrogenAtomCount;
-
-
}
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/geodesic/EnvelopeCalculation.java
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/geodesic/EnvelopeCalculation.java 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/geodesic/EnvelopeCalculation.java 2008-03-16 11:57:42 UTC (rev 9137)
@@ -568,8 +568,15 @@
bitmap[i] = 0;
}
- public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted) {
+ public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted, BitSet bsAtoms) {
dotsConvexMaps = (int[][]) ArrayUtil.deleteElements(dotsConvexMaps, firstAtomDeleted, nAtomsDeleted);
dotsConvexMax = dotsConvexMaps.length;
+ if (mads != null)
+ mads = (short[]) ArrayUtil.deleteElements(mads, firstAtomDeleted, nAtomsDeleted);
+ atomData.atomRadius = (float[]) ArrayUtil.deleteElements(atomData.atomRadius, firstAtomDeleted, nAtomsDeleted);
+ atomData.atomXyz = (Point3f[]) ArrayUtil.deleteElements(atomData.atomXyz, firstAtomDeleted, nAtomsDeleted);
+ atomData.atomCount -= nAtomsDeleted;
+ atomCount = atomData.atomCount;
+
}
}
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/BondCollection.java 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/BondCollection.java 2008-03-16 11:57:42 UTC (rev 9137)
@@ -115,8 +115,11 @@
}
public BitSet getBondsForSelectedAtoms(BitSet bsAtoms) {
+ return getBondsForSelectedAtoms(bsAtoms, viewer.getBondSelectionModeOr());
+ }
+
+ protected BitSet getBondsForSelectedAtoms(BitSet bsAtoms, boolean bondSelectionModeOr) {
BitSet bs = new BitSet();
- boolean bondSelectionModeOr = viewer.getBondSelectionModeOr();
for (int iBond = 0; iBond < bondCount; ++iBond) {
Bond bond = bonds[iBond];
boolean isSelected1 = bsAtoms.get(bond.atom1.atomIndex);
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/ModelSet.java 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/modelset/ModelSet.java 2008-03-16 11:57:42 UTC (rev 9137)
@@ -638,6 +638,8 @@
public int deleteAtoms(BitSet bsAtoms) {
BitSet bs = BitSetUtil.copy(bsAtoms);
BitSet bsModels = getModelBitSet(bs);
+ System.out.println(bsAtoms.cardinality());
+ System.out.println("bsModels: " + bs);
includeAllRelatedFrames(bsModels);
int nAtomsDeleted = 0;
@@ -654,9 +656,6 @@
bspf = null;
molecules = null;
-
- // delete bonds
- deleteBonds(getBondsForSelectedAtoms(bs));
// create a new models array,
// and pre-calculate Model.bsAtoms and Model.atomCount
@@ -665,13 +664,17 @@
for (int i = 0, mpt = 0; i < modelCount; i++)
if (bsModels.get(i)) { // get a good count now
getAtomCountInModel(i);
- getModelAtomBitSet(i, false);
+ bs.or(getModelAtomBitSet(i, false));
} else {
models[i].modelIndex = mpt;
newModels[mpt++] = models[i];
}
models = newModels;
int oldModelCount = modelCount;
+
+ // delete bonds
+ deleteBonds(getBondsForSelectedAtoms(bs, true));
+
// main deletion cycle
for (int i = 0, mpt = 0; i < oldModelCount; i++) {
if (!bsModels.get(i)) {
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Dots.java
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Dots.java 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Dots.java 2008-03-16 11:57:42 UTC (rev 9137)
@@ -141,7 +141,7 @@
int firstAtomDeleted = ((int[])((Object[])value)[2])[1];
int nAtomsDeleted = ((int[])((Object[])value)[2])[2];
BitSetUtil.deleteBits(bsOn, bs);
- ec.deleteAtoms(firstAtomDeleted, nAtomsDeleted);
+ ec.deleteAtoms(firstAtomDeleted, nAtomsDeleted, bs);
// pass to AtomShape via super
}
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Sticks.java
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Sticks.java 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/shape/Sticks.java 2008-03-16 11:57:42 UTC (rev 9137)
@@ -163,7 +163,11 @@
BitSetUtil.deleteBits(bsOrderSet, bs);
return;
}
-
+
+ if ("deleteModelAtoms" == propertyName) {
+ return;
+ }
+
super.setProperty(propertyName, value, bsSelected);
}
@@ -205,12 +209,9 @@
else
setStateInfo(temp, i, getColorCommand("bonds", colix));
-
-
-
-
}
}
+
return getShapeCommands(temp, null, -1, "select BONDS") + "\n";
}
}
Modified: branches/bob-deleteatoms/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/bob-deleteatoms/Jmol/src/org/jmol/viewer/Jmol.properties 2008-03-15 20:37:23 UTC (rev 9136)
+++ branches/bob-deleteatoms/Jmol/src/org/jmol/viewer/Jmol.properties 2008-03-16 11:57:42 UTC (rev 9137)
@@ -1,5 +1,12 @@
-version=11.5.16_dev
+version=11.5.17_dev
+# bug fix: zap x.y for dots
+# bug fix: zap {atom expression} for not including all atoms in a model in the selection
+
+# -----------------------------------------------------------------------------
+
+#version=11.5.16
+
# new feature: zap {atom expression} # zaps models associated with given atoms.
# use "show models" to see what models are present, then zap them with their
# file.model number:
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