Revision: 5131
Author: hansonr
Date: 2006-05-17 06:24:49 -0700 (Wed, 17 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5131&view=rev
Log Message:
-----------
bob200603 adds support for REAL multiple file loading
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java
branches/bob200603/Jmol/src/org/jmol/viewer/Model.java
branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
Modified:
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2006-05-17 13:23:48 UTC (rev 5130)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2006-05-17 13:24:49 UTC (rev 5131)
@@ -37,7 +37,14 @@
Properties atomSetCollectionProperties = new Properties();
Hashtable atomSetCollectionAuxiliaryInfo = new Hashtable();
- final static String[] notionalUnitcellTags =
+ final static String[] globalBooleans =
{"someModelsHaveFractionalCoordinates",
+ "someModelsHaveSymmetry", "someModelsHaveUnitcells"};
+
+ final static int GLOBAL_FRACTCOORD = 0;
+ final static int GLOBAL_SYMMETRY = 1;
+ final static int GLOBAL_UNITCELLS = 2;
+
+ final static String[] notionalUnitcellTags =
{ "a", "b", "c", "alpha", "beta", "gamma" };
final static String[] dictRefUnitcellTags =
@@ -139,7 +146,11 @@
addNewBond(bond.atomIndex1 + existingAtomsCount, bond.atomIndex2
+ existingAtomsCount, bond.order);
}
-
+ // Set globals
+ for (int i = globalBooleans.length; --i >= 0;)
+ if ((Boolean) collection
+ .getAtomSetCollectionAuxiliaryInfo(globalBooleans[i]) ==
Boolean.TRUE)
+ setGlobalBoolean(i);
}
protected void finalize() {
@@ -338,8 +349,7 @@
setAtomSetAuxiliaryInfo("coordinatesAreFractional",
new Boolean(coordinatesAreFractional));
if (coordinatesAreFractional)
- setAtomSetCollectionAuxiliaryInfo("someModelsHaveFractionalCoordinates",
- Boolean.TRUE);
+ setGlobalBoolean(GLOBAL_FRACTCOORD);
}
boolean setNotionalUnitcell(float[] info, JmolAdapter.Logger logger) {
@@ -355,10 +365,14 @@
logger.log(notionalUnitcellTags[i] + " = " + info[i]);
}
setAtomSetAuxiliaryInfo("notionalUnitcell", notionalUnitcell);
- setAtomSetCollectionAuxiliaryInfo("someModelsHaveUnitcells", Boolean.TRUE);
+ setGlobalBoolean(GLOBAL_UNITCELLS);
return true;
}
+ void setGlobalBoolean(int globalIndex) {
+ setAtomSetCollectionAuxiliaryInfo(globalBooleans[globalIndex],
Boolean.TRUE);
+ }
+
boolean addSymmetry(String xyz) {
return addSymmetryWithLatt(xyz, Symmetry.ptNoLatt);
}
@@ -450,7 +464,7 @@
notionalUnitcell = new float[6];
iHaveSymmetry = false;
coordinatesAreFractional = false; //turn off global fractional conversion
-- this wil be model by model
- setAtomSetCollectionAuxiliaryInfo("someModelsHaveSymmetry", Boolean.TRUE);
+ setGlobalBoolean(GLOBAL_SYMMETRY);
}
void symmetryAddAtoms(int atomIndex, int count, boolean normalize, int
transX, int transY, int transZ) {
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-05-17 13:23:48 UTC (rev 5130)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-05-17 13:24:49 UTC (rev 5131)
@@ -42,7 +42,7 @@
// for now, just update this by hand
// perhaps use ant filter later ... but mth doesn't like it :-(
public final static String copyright = "(C) 2006 Jmol Development";
- public final static String version = "10.3.BH";
+ public final static String version = "10.x.01(branch bob200603)";
public final static String cvsDate = "$Date$";
public final static String date = cvsDate.substring(7, 23);
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java 2006-05-17
13:23:48 UTC (rev 5130)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java 2006-05-17
13:24:49 UTC (rev 5131)
@@ -241,7 +241,7 @@
for (int i = structureCount; --i >= 0;) {
Structure structure = structures[i];
- System.out.println("Mmset.propogate " +structure.modelIndex+"
"+structure.type +" "+ structure.startChainID +" "+ structure.startSeqcode + "
"+structure.endSeqcode);
+ //System.out.println("Mmset.propogate " +structure.modelIndex+"
"+structure.type +" "+ structure.startChainID +" "+ structure.startSeqcode + "
"+structure.endSeqcode);
for (int j = modelCount; --j >= 0;)
if (structure.modelIndex == j || structure.modelIndex == -1)
models[j].addSecondaryStructure(structure.type,
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Model.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Model.java 2006-05-17
13:23:48 UTC (rev 5130)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Model.java 2006-05-17
13:24:49 UTC (rev 5131)
@@ -68,7 +68,6 @@
void addSecondaryStructure(byte type,
char startChainID, int startSeqcode,
char endChainID, int endSeqcode) {
- System.out.println("MODEL addSecondary (from file) " + modelIndex+" "+type
+ startChainID + " "+startSeqcode + " " + endSeqcode);
for (int i = polymerCount; --i >= 0; ) {
Polymer polymer = polymers[i];
polymer.addSecondaryStructure(type, startChainID, startSeqcode,
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-05-17 13:23:48 UTC (rev 5130)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-05-17 13:24:49 UTC (rev 5131)
@@ -1391,14 +1391,12 @@
continue;
String altLocs = frame.getAltLocListInModel(i);
BitSet bsConformation = getModelAtomBitSet(i);
- System.out.println("\nmodelmanager.setconf. a "+i+" "+bsConformation);
if (conformationIndex >= 0)
for (int c = frame.getAltLocCountInModel(i); --c >= 0;)
if (c != conformationIndex)
bsConformation.andNot(frame.getSpecAlternate(altLocs.substring(c,
c + 1)));
if (bsConformation.length() > 0) {
- System.out.println("modelmanager.setconf. b "+i+" "+bsConformation);
frame.setConformation(i, bsConformation);
bsResult.or(bsConformation);
}
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