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[Jmol-commits] SF.net SVN: jmol:[19370] trunk/Jmol/src
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From: <ha...@us...> - 2014-02-21 17:44:33
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Revision: 19370
http://sourceforge.net/p/jmol/code/19370
Author: hansonr
Date: 2014-02-21 17:44:27 +0000 (Fri, 21 Feb 2014)
Log Message:
-----------
___JmolVersion="14.1.11_2014.02.21"
new feature: added simpler associative array notation: [key:value,...]
-- no quotes required
-- supplements {"key":value,...] where quotes are still required
due to conflict with atom set chain descriptors sucu as {a:b}.
code: faster CONNECT [{...}] process for specified bonds
bug fix: JSON of 4x4 matrix (M4) fails
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/M3.java
trunk/Jmol/src/javajs/util/M34.java
trunk/Jmol/src/javajs/util/M4.java
trunk/Jmol/src/javajs/util/PT.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/util/M3.java
===================================================================
--- trunk/Jmol/src/javajs/util/M3.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/javajs/util/M3.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -228,6 +228,7 @@
* @param v
* The array into which the matrix row values will be copied
*/
+ @Override
public void getRow(int row, float v[]) {
getRow33(row, v);
}
Modified: trunk/Jmol/src/javajs/util/M34.java
===================================================================
--- trunk/Jmol/src/javajs/util/M34.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/javajs/util/M34.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -7,7 +7,7 @@
*
* additions by Bob Hanson ha...@st... 9/30/2012 for unique
* constructor and method names for the optimization of compiled
- * JavaScript using Java2Script
+ * JavaScript using Java2Script and for subclassing to M3 and M4
*
*/
public abstract class M34 {
@@ -239,6 +239,8 @@
err();
}
}
+
+ public abstract void getRow(int row, float v[]);
protected void getRow33(int row, float v[]) {
switch (row) {
Modified: trunk/Jmol/src/javajs/util/M4.java
===================================================================
--- trunk/Jmol/src/javajs/util/M4.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/javajs/util/M4.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -423,6 +423,7 @@
* @param v
* The array into which the matrix row values will be copied
*/
+ @Override
public void getRow(int row, float v[]) {
if (row < 3)
getRow33(row, v);
Modified: trunk/Jmol/src/javajs/util/PT.java
===================================================================
--- trunk/Jmol/src/javajs/util/PT.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/javajs/util/PT.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -787,7 +787,7 @@
// M4 extends M3
int len = (info instanceof M4 ? 4 : 3);
float[] x = new float[len];
- M3 m = (M3) info;
+ M34 m = (M34) info;
sb.appendC('[');
for (int i = 0; i < len; i++) {
if (i > 0)
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -2162,61 +2162,73 @@
Atom atomB = null;
float dAB = 0;
float dABcalc = 0;
+ float distanceSquared;
+ char altloc = '\0';
short newOrder = (short) (order | JmolEdge.BOND_NEW);
- for (int iA = bsA.nextSetBit(0); iA >= 0; iA = bsA.nextSetBit(iA + 1)) {
- if (isBonds) {
- bondAB = bonds[iA];
- atomA = bondAB.atom1;
- atomB = bondAB.atom2;
- } else {
- atomA = atoms[iA];
- if (atomA.isDeleted())
- continue;
- }
- char altloc = (isModulated(iA) ? '\0' : atomA.altloc);
- for (int iB = (isBonds ? m : bsB.nextSetBit(0)); iB >= 0; iB = (isBonds ? iB - 1
- : bsB.nextSetBit(iB + 1))) {
- if (!isBonds) {
- if (iB == iA)
+ boolean checkDistance = (!isBonds || minDistance != JC.DEFAULT_MIN_CONNECT_DISTANCE || maxDistance != JC.DEFAULT_MAX_CONNECT_DISTANCE);
+ try {
+ for (int i = bsA.nextSetBit(0); i >= 0; i = bsA.nextSetBit(i + 1)) {
+ if (isBonds) {
+ bondAB = bonds[i];
+ atomA = bondAB.atom1;
+ atomB = bondAB.atom2;
+ } else {
+ atomA = atoms[i];
+ if (atomA.isDeleted())
continue;
- atomB = atoms[iB];
- if (atomA.modelIndex != atomB.modelIndex || atomB.isDeleted())
- continue;
- if (altloc != '\0' && altloc != atomB.altloc
- && atomB.altloc != '\0')
- continue;
- bondAB = atomA.getBond(atomB);
+ altloc = (isModulated(i) ? '\0' : atomA.altloc);
}
- if (bondAB == null && (identifyOnly || modifyOnly) || bondAB != null
- && createOnly)
- continue;
- float distanceSquared = atomA.distanceSquared(atomB);
- if (minDistanceIsFractionRadius || maxDistanceIsFractionRadius) {
- dAB = atomA.distance(atomB);
- dABcalc = atomA.getBondingRadiusFloat()
- + atomB.getBondingRadiusFloat();
- }
- if ((minDistanceIsFractionRadius ? dAB < dABcalc * minDistance
- : distanceSquared < minDistanceSquared)
- || (maxDistanceIsFractionRadius ? dAB > dABcalc * maxDistance
- : distanceSquared > maxDistanceSquared))
- continue;
- if (bondAB != null) {
- if (!identifyOnly && !matchAny) {
- bondAB.setOrder(order);
- bsAromatic.clear(bondAB.index);
+ for (int j = (isBonds ? m : bsB.nextSetBit(0)); j >= 0; j = bsB
+ .nextSetBit(j + 1)) {
+ if (isBonds) {
+ j = 2147483646; // Integer.MAX_VALUE - 1; one pass only
+ } else {
+ if (j == i)
+ continue;
+ atomB = atoms[j];
+ if (atomA.modelIndex != atomB.modelIndex || atomB.isDeleted())
+ continue;
+ if (altloc != '\0' && altloc != atomB.altloc
+ && atomB.altloc != '\0')
+ continue;
+ bondAB = atomA.getBond(atomB);
}
- if (!identifyOnly || matchAny || order == bondAB.order
- || newOrder == bondAB.order || matchHbond && bondAB.isHydrogen()) {
- bsBonds.set(bondAB.index);
- nModified++;
+ if (bondAB == null && (identifyOnly || modifyOnly) || bondAB != null
+ && createOnly)
+ continue;
+ if (checkDistance) {
+ if (minDistanceIsFractionRadius || maxDistanceIsFractionRadius) {
+ dAB = atomA.distance(atomB);
+ dABcalc = atomA.getBondingRadiusFloat()
+ + atomB.getBondingRadiusFloat();
+ }
+ distanceSquared = atomA.distanceSquared(atomB);
+ if ((minDistanceIsFractionRadius ? dAB < dABcalc * minDistance
+ : distanceSquared < minDistanceSquared)
+ || (maxDistanceIsFractionRadius ? dAB > dABcalc * maxDistance
+ : distanceSquared > maxDistanceSquared))
+ continue;
}
- } else {
- bsBonds.set(bondAtoms(atomA, atomB, order, mad, bsBonds, energy,
- addGroup, true).index);
- nNew++;
+ if (bondAB != null) {
+ if (!identifyOnly && !matchAny) {
+ bondAB.setOrder(order);
+ bsAromatic.clear(bondAB.index);
+ }
+ if (!identifyOnly || matchAny || order == bondAB.order
+ || newOrder == bondAB.order || matchHbond
+ && bondAB.isHydrogen()) {
+ bsBonds.set(bondAB.index);
+ nModified++;
+ }
+ } else {
+ bsBonds.set(bondAtoms(atomA, atomB, order, mad, bsBonds, energy,
+ addGroup, true).index);
+ nNew++;
+ }
}
}
+ } catch (Exception e) {
+ // well, we tried -- probably ran over
}
if (autoAromatize)
assignAromaticBondsBs(true, bsBonds);
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -693,22 +693,23 @@
String[] keys = ht.keySet().toArray(new String[keyset.size()]);
Arrays.sort(keys);
if (isEscaped) {
- sb.append("{ ");
+ sb.append("[");
String sep = "";
for (int i = 0; i < keys.length; i++) {
String key = keys[i];
sb.append(sep).append(PT.esc(key)).appendC(':');
sValueArray(sb, ht.get(key), map, level + 1, true);
- sep = ", ";
+ sep = ",";
}
- sb.append(" }");
+ sb.append("]");
return;
}
for (int i = 0; i < keys.length; i++) {
- sb.append(keys[i]).append("\t:");
- SV v = ht.get(keys[i]);
+ String key = keys[i];
+ sb.append(key).append("\t:");
SB sb2 = new SB();
- sValueArray(sb2, v, map, level + 1, isEscaped);
+ SV v = ht.get(key);
+ sValueArray(sb2, v, map, level + 1, v.tok == T.string);
String value = sb2.toString();
sb.append(value.indexOf("\n") >= 0 ? "\n" : "\t");
sb.append(value).append("\n");
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2014-02-21 17:44:27 UTC (rev 19370)
@@ -845,6 +845,16 @@
}
}
switch (tok) {
+ case T.rightsquare:
+ case T.rightbrace:
+ if (!ignoreComma && nParen == 0 && nSquare == 0)
+ break out;
+ if (tok == T.rightbrace)
+ invArg();
+ break;
+ }
+
+ switch (tok) {
case T.define:
// @{@x} or @{@{x}} or @{@1} -- also userFunction(@1)
if (tokAt(++i) == T.expressionBegin) {
@@ -1038,7 +1048,7 @@
i += 2;
break;
}
- v = getHash(i);
+ v = getAssocArray(i);
} else {
v = getPointOrPlane(i, false, true, true, false, 3, 4);
}
@@ -1071,11 +1081,6 @@
case T.expressionEnd:
i++;
break out;
- case T.rightbrace:
- if (!ignoreComma && nParen == 0 && nSquare == 0)
- break out;
- invArg();
- break;
case T.comma: // ignore commas
if (!ignoreComma && nParen == 0 && nSquare == 0) {
break out;
@@ -1120,6 +1125,11 @@
}
break;
default:
+ if (theTok == T.leftsquare && tokAt(i + 2) == T.colon) {
+ v = getAssocArray(i);
+ i = iToken;
+ break;
+ }
if (T.tokAttr(theTok, T.mathop) || T.tokAttr(theTok, T.mathfunc)
&& tokAt(iToken + 1) == T.leftparen) {
if (!rpn.addOp(theToken)) {
@@ -1218,12 +1228,13 @@
}
@SuppressWarnings("unchecked")
- private Map<String, Object> getHash(int i) throws ScriptException {
+ private Map<String, Object> getAssocArray(int i) throws ScriptException {
Map<String, Object> ht = new Hashtable<String, Object>();
+ int closer = (tokAt(i) == T.leftbrace ? T.rightbrace : T.rightsquare);
for (i = i + 1; i < slen; i++) {
- if (tokAt(i) == T.rightbrace)
+ if (tokAt(i) == closer)
break;
- String key = stringParameter(i++);
+ String key = optParameterAsString(i++);
if (tokAt(i++) != T.colon)
invArg();
List<SV> v = (List<SV>) parameterExpression(i, 0, null, false, true, -1,
@@ -1234,7 +1245,7 @@
break;
}
iToken = i;
- if (tokAt(i) != T.rightbrace)
+ if (tokAt(i) != closer)
invArg();
return ht;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-20 23:02:09 UTC (rev 19369)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-21 17:44:27 UTC (rev 19370)
@@ -13,8 +13,16 @@
___JmolVersion="14.1.11_2014.02.21"
-bug fix:modelkitmode broken for Java in 14.1.10
+new feature: added simpler associative array notation: [key:value,...]
+ -- no quotes required
+ -- supplements {"key":value,...] where quotes are still required
+ due to conflict with atom set chain descriptors sucu as {a:b}.
+code: faster CONNECT [{...}] process for specified bonds
+
+bug fix: JSON of 4x4 matrix (M4) fails
+bug fix: modelkitmode broken for Java in 14.1.10
+
new feature: catchable THROW
-- as in Java or JavaScript, allows a way of jumping
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