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[Jmol-commits] SF.net SVN: jmol:[13494] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2010-07-01 14:41:58
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Revision: 13494
http://jmol.svn.sourceforge.net/jmol/?rev=13494&view=rev
Author: hansonr
Date: 2010-07-01 14:41:51 +0000 (Thu, 01 Jul 2010)
Log Message:
-----------
version=12.0.RC23_dev # new feature: data map {from}.property1 {to}.property2 propertyKey
# Allows mapping of property data from one set of atoms to another
# based on a key such as regno or atomno. Property2 must be "settable".
# For example, creating a quaternion map, then mapping that data
# with straightness, and then selecting a very specific subset of
# the quaternion data and using that selection to select data
# in the original model:
#
# load 3cc2.pdb
# calculate straightness
# set quaternionframe "A"
# quaternion r difference
# display {rna}
# data map {1.1 and *.P}.straightness {2.1 and rna}.property_x resno
# select 2.1 and rna; color property_x;spacefill 0.1
# select 2.1 and rna and within(2.0,{1.7700001 -0.49 2.62})
# data map {2.1 and rna and selected}.selected {1.1 and *.P}.selected resno
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/LabelToken.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/Token.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2010-06-30 21:56:33 UTC (rev 13493)
+++ trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2010-07-01 14:41:51 UTC (rev 13494)
@@ -164,6 +164,7 @@
Token.polymer,
Token.property,
Token.radius,
+ Token.selected,
Token.sequence,
Token.spacefill,
Token.structure,
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2010-06-30 21:56:33 UTC (rev 13493)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2010-07-01 14:41:51 UTC (rev 13494)
@@ -591,10 +591,10 @@
public boolean deleteAtoms(int modelIndex, BitSet bsBonds, BitSet bsAtoms) {
//false return means delete this script
if (modelIndex == this.modelIndex)
+ return false;
+ if (modelIndex > this.modelIndex) {
+// this.modelIndex--;
return true;
- if (modelIndex < this.modelIndex) {
-// this.modelIndex--;
- return false;
}
BitSetUtil.deleteBits(this.bsBonds, bsBonds);
BitSetUtil.deleteBits(this.bsAtoms1, bsAtoms);
@@ -2186,7 +2186,7 @@
public BitSet getAtomsWithin(float distance, Point3f coord, BitSet bsResult,
int modelIndex) {
- if (bsResult == null)
+ if (bsResult == null)
bsResult = new BitSet();
if (distance < 0) { // just check all unitCell distances
@@ -2204,7 +2204,7 @@
return bsResult;
}
- BitSet bsCheck = getIterativeModels(false);
+ BitSet bsCheck = getIterativeModels(true);
AtomIndexIterator iter = getSelectedAtomIterator(null, false, false, false);
for (int iModel = modelCount; --iModel >= 0;) {
if (!bsCheck.get(iModel))
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-30 21:56:33 UTC (rev 13493)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-01 14:41:51 UTC (rev 13494)
@@ -3255,12 +3255,17 @@
case Token.opGT:
case Token.opEQ:
case Token.opNE:
+ if (pc + 1 == code.length)
+ error(ERROR_invalidArgument);
val = code[++pc].value;
int tokOperator = instruction.tok;
int tokWhat = instruction.intValue;
String property = (tokWhat == Token.property ? (String) val : null);
- if (property != null)
+ if (property != null) {
+ if (pc + 1 == code.length)
+ error(ERROR_invalidArgument);
val = code[++pc].value;
+ }
if (tokWhat == Token.configuration && tokOperator != Token.opEQ)
error(ERROR_invalidArgument);
if (isSyntaxCheck) {
@@ -7218,6 +7223,48 @@
String dataLabel = null;
boolean isOneValue = false;
int i;
+ if (tokAt(1) == Token.map) {
+ // {resno=x}.straightness = ({i}).straightness
+ // data map {1.1}.straightness {2.1}.property_x resno
+ BitSet bsFrom = atomExpression(2);
+ while (true) {
+ if (tokAt(++iToken) != Token.per
+ || !Token.tokAttr(tokAt(++iToken), Token.atomproperty))
+ break;
+ String property1 = parameterAsString(iToken);
+ BitSet bsTo = atomExpression(++iToken);
+ if (tokAt(++iToken) != Token.per
+ || !Token.tokAttr(tokAt(++iToken), Token.settable))
+ break;
+ String property2 = parameterAsString(iToken);
+ if (!Token.tokAttr(tokAt(++iToken), Token.atomproperty))
+ break;
+ String mapKey = parameterAsString(iToken);
+
+ if (isSyntaxCheck)
+ return;
+ String format = "{" + mapKey + "=%[" + mapKey + "]}." + property2
+ + " = %[" + property1 + "]";
+ String[] data = (String[]) getBitsetIdent(bsFrom, format, null, false,
+ Integer.MAX_VALUE, false);
+ StringBuffer sb = new StringBuffer();
+ for (i = 0; i < data.length; i++)
+ if (data[i].indexOf("null") < 0)
+ sb.append(data[i]).append('\n');
+ if (Logger.debugging)
+ Logger.info(sb.toString());
+ BitSet bsSubset = BitSetUtil.copy(viewer.getSelectionSubset());
+ viewer.setSelectionSubset(bsTo);
+ try {
+ runScript(sb.toString());
+ } catch (Exception e) {
+ Logger.error(e.getMessage());
+ }
+ viewer.setSelectionSubset(bsSubset);
+ return;
+ }
+ error(ERROR_invalidArgument);
+ }
switch (iToken = statementLength) {
case 5:
// parameters 3 and 4 are just for the ride: [end] and ["key"]
@@ -7945,6 +7992,7 @@
boolean isRamachandranRelative = false;
String stateScript = "";
int pt = statementLength - 1;
+ String qFrame = "";
String type = optParameterAsString(pt).toLowerCase();
switch (datatype) {
case JmolConstants.JMOL_DATA_RAMACHANDRAN:
@@ -7957,7 +8005,8 @@
+ (isDraw ? " draw" : "");
break;
case JmolConstants.JMOL_DATA_QUATERNION:
- stateScript = "set quaternionFrame " + Escape.escape("" + viewer.getQuaternionFrame()) + ";\n ";
+ qFrame = " \"" + viewer.getQuaternionFrame() + "\"";
+ stateScript = "set quaternionFrame" + qFrame + ";\n ";
isQuaternion = true;
// working backward this time:
if (type.equalsIgnoreCase("draw")) {
@@ -7986,6 +8035,7 @@
if (isSyntaxCheck) // just in case we later add parameter options to this
return;
// for now, just one frame visible
+ stateScript += type;
int modelIndex = viewer.getCurrentModelIndex();
if (modelIndex < 0)
error(ERROR_multipleModelsDisplayedNotOK, type);
@@ -7994,16 +8044,16 @@
runScript(viewer.getPdbData(modelIndex, type));
return;
}
- int ptDataFrame = viewer.getJmolDataFrameIndex(modelIndex, type);
+ int ptDataFrame = viewer.getJmolDataFrameIndex(modelIndex, stateScript);
if (ptDataFrame > 0) {
- viewer.deleteAtoms(viewer.getModelUndeletedAtomsBitSet(ptDataFrame), true);
+ // no -- this is that way we switch frames. viewer.deleteAtoms(viewer.getModelUndeletedAtomsBitSet(ptDataFrame), true);
// data frame can't be 0.
- // viewer.setCurrentModelIndex(ptDataFrame, true);
+ viewer.setCurrentModelIndex(ptDataFrame, true);
// BitSet bs2 = viewer.getModelAtomBitSet(ptDataFrame);
// bs2.and(bs);
// need to be able to set data directly as well.
// viewer.display(BitSetUtil.setAll(viewer.getAtomCount()), bs2, tQuiet);
- // return;
+ return;
}
String[] savedFileInfo = viewer.getFileInfo();
boolean oldAppendNew = viewer.getAppendNew();
@@ -8014,14 +8064,14 @@
viewer.setFileInfo(savedFileInfo);
if (!isOK)
return;
- StateScript ss = viewer.addStateScript(stateScript + type, true, false);
+ StateScript ss = viewer.addStateScript(stateScript, true, false);
int modelCount = viewer.getModelCount();
- viewer.setJmolDataFrame(type, modelIndex, modelCount - 1);
+ viewer.setJmolDataFrame(stateScript, modelIndex, modelCount - 1);
String script;
switch (datatype) {
case JmolConstants.JMOL_DATA_RAMACHANDRAN:
default:
- viewer.setFrameTitle(modelCount - 1, type + " plot for model "
+ viewer.setFrameTitle(modelCount - 1, " plot for model "
+ viewer.getModelNumberDotted(modelIndex));
script = "frame 0.0; frame last; reset;"
+ "select visible; color structure; spacefill 3.0; wireframe 0;"
@@ -8032,7 +8082,8 @@
;
break;
case JmolConstants.JMOL_DATA_QUATERNION:
- viewer.setFrameTitle(modelCount - 1, type + " for model "
+ viewer.setFrameTitle(modelCount - 1,
+ type.replace('w', ' ') + qFrame + " for model "
+ viewer.getModelNumberDotted(modelIndex));
String color = (Graphics3D
.getHexCode(viewer.getColixBackgroundContrast()));
@@ -8053,7 +8104,7 @@
viewer.setRotationRadius(isQuaternion ? 12.5f : 260f, true);
loadShape(JmolConstants.SHAPE_ECHO);
showString("frame " + viewer.getModelNumberDotted(modelCount - 1)
- + " created: " + type);
+ + " created: " + type + (isQuaternion ? qFrame : ""));
}
private void measure() throws ScriptException {
Modified: trunk/Jmol/src/org/jmol/script/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/Token.java 2010-06-30 21:56:33 UTC (rev 13493)
+++ trunk/Jmol/src/org/jmol/script/Token.java 2010-07-01 14:41:51 UTC (rev 13494)
@@ -132,7 +132,7 @@
* x x shapeCommand
* x noArgs
* x defaultON
- * xxxxxxxxxxxx uniqueID (may include math flags)
+ * xxxxxxxxxxx uniqueID (may include math flags)
*
*
* math bit flags:
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-06-30 21:56:33 UTC (rev 13493)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-07-01 14:41:51 UTC (rev 13494)
@@ -3,6 +3,24 @@
version=12.0.RC23_dev
+# new feature: data map {from}.property1 {to}.property2 propertyKey
+# Allows mapping of property data from one set of atoms to another
+# based on a key such as regno or atomno. Property2 must be "settable".
+# For example, creating a quaternion map, then mapping that data
+# with straightness, and then selecting a very specific subset of
+# the quaternion data and using that selection to select data
+# in the original model:
+#
+# load 3cc2.pdb
+# calculate straightness
+# set quaternionframe "A"
+# quaternion r difference
+# display {rna}
+# data map {1.1 and *.P}.straightness {2.1 and rna}.property_x resno
+# select 2.1 and rna; color property_x;spacefill 0.1
+# select 2.1 and rna and within(2.0,{1.7700001 -0.49 2.62})
+# data map {2.1 and rna and selected}.selected {1.1 and *.P}.selected resno
+
# bug fix: state save for quaternion/ramachandran data frames fails
# bug fix: Spartan reader not reading MOs when there is only one atom (AOs, that is)
# --------------------------------------------------------------
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