Revision: 20808
http://sourceforge.net/p/jmol/code/20808
Author: hansonr
Date: 2015-10-06 04:55:57 +0000 (Tue, 06 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.10.05"
new feature: load =aflow/AgAu
-- easy access to binary metal alloy CIF files
bug fix: braceless if/for fix from 10.04
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shape/MeshCollection.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-04
04:28:59 UTC (rev 20807)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-06
04:55:57 UTC (rev 20808)
@@ -753,9 +753,8 @@
break;
case 'p':
case 'm':
- bondOrder = Edge.getBondOrderNumberFromOrder(
- bond.getCovalentOrder()).charAt(0)
- - '0' + (type == 'p' ? 1 : -1);
+ bondOrder = Edge.getBondOrderNumberFromOrder(bond.getCovalentOrder())
+ .charAt(0) - '0' + (type == 'p' ? 1 : -1);
if (bondOrder > 3)
bondOrder = 1;
else if (bondOrder < 0)
@@ -775,8 +774,11 @@
return bsAtoms;
}
bond.setOrder(bondOrder | Edge.BOND_NEW);
- removeUnnecessaryBonds(bond.atom1, false);
- removeUnnecessaryBonds(bond.atom2, false);
+ if (bond.atom1.getElementNumber() != 1
+ && bond.atom2.getElementNumber() != 1) {
+ removeUnnecessaryBonds(bond.atom1, false);
+ removeUnnecessaryBonds(bond.atom2, false);
+ }
bsAtoms.set(bond.atom1.i);
bsAtoms.set(bond.atom2.i);
} catch (Exception e) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-04 04:28:59 UTC
(rev 20807)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-06 04:55:57 UTC
(rev 20808)
@@ -783,21 +783,22 @@
}
if (endOfLine) {
if (flowContext != null && flowContext.checkForceEndIf(-1)) {
+ boolean isOneLine = (flowContext.addLine == 0); // if (....) xxxxx;
if (isComment) {
- if (flowContext.addLine > 0) {
+ if (!isOneLine) {
flowContext.addLine++;
flowContext.forceEndIf = true;
}
- } else if (n > 0) {
+ } else if (n > 0 || isOneLine) {
forceFlowEnd(flowContext.token);
- if (lastFlowContext.addLine > 0) {
+ if (!isOneLine) {
lastFlowContext.forceEndIf = true;
}
}
isEndOfCommand = true;
cchToken = 0;
ichCurrentCommand = ichToken;
- if (n > 0)
+ if (n > 0 || isOneLine)
lineCurrent--;
return CONTINUE;
}
@@ -902,15 +903,15 @@
atokenInfix = ltoken.toArray(new T[size = ltoken.size()]);
- if (logMessages) {
- Logger.debug("token list:");
- for (int i = 0; i < atokenInfix.length; i++)
- Logger.debug(i + ": " + atokenInfix[i]);
- Logger.debug("vBraces list:");
- for (int i = 0; i < vBraces.size(); i++)
- Logger.debug(i + ": " + vBraces.get(i));
- Logger.debug("-------------------------------------");
- }
+// if (logMessages) {
+// Logger.debug("token list:");
+// for (int i = 0; i < atokenInfix.length; i++)
+// Logger.debug(i + ": " + atokenInfix[i]);
+// Logger.debug("vBraces list:");
+// for (int i = 0; i < vBraces.size(); i++)
+// Logger.debug(i + ": " + vBraces.get(i));
+// Logger.debug("-------------------------------------");
+// }
// compile expressions (ScriptCompilerTokenParser.java)
return compileExpressions();
@@ -1603,7 +1604,10 @@
lastToken = T.tokenOff;
ichCurrentCommand = ichEnd = ichToken;
setCommand(theToken);
- if (T.tokAttr(tokCommand, T.flowCommand)) {
+ if (logMessages)
+ Logger.info("compiling " + theToken);
+ boolean isFlowCmd = T.tokAttr(tokCommand, T.flowCommand);
+ if (isFlowCmd) {
lastFlowCommand = tokenCommand;
}
// before processing this command, check to see if we have completed
@@ -1617,31 +1621,59 @@
cchToken = 0;
return CONTINUE;
}
- if (T.tokAttr(tokCommand, T.flowCommand)) {
- if (!checkFlowCommand((String) tokenCommand.value))
- return ERROR;
- theToken = tokenCommand;
- if (theTok == T.casecmd) {
- addTokenToPrefix(tokenCommand);
- theToken = T.tokenLeftParen;
- }
+ switch (theTok) {
+ case T.leftbrace:
break;
- }
- if (theTok == T.colon) {
+ case T.colon:
braceCount++;
isEndOfCommand = true;
- break;
- }
- if (theTok == T.rightbrace) {
- // if }, just push onto vBrace, but NOT onto ltoken
- vBraces.addLast(tokenCommand);
- iBrace++;
- tokCommand = T.nada;
- return CONTINUE;
- }
-
- if (theTok != T.leftbrace) {
- if (flowContext != null) {
+ return OK;
+ case T.elsecmd:
+ case T.elseif:
+ // unexpectedly allows if (x) { print x else print y}
+ fixFlowAddLine(flowContext);
+ if (lltoken.get(iCommand - 1)[0].tok == T.end
+ && lastFlowContext != null && lastFlowContext.forceEndIf
+ && lastFlowContext.addLine > 0
+ && isFlowIfContextOK(lastFlowContext, tokCommand)) {
+ flowContext = lastFlowContext;
+ flowContext.forceEndIf = true;
+ lltoken.remove(--iCommand);
+ } else if (flowContext != null && flowContext.addLine > 0) {
+ while (flowContext != null
+ && !isFlowIfContextOK(flowContext, tokCommand)) {
+ if (flowContext.checkForceEndIf(0)) {
+ forceFlowEnd(flowContext.token);
+ processTokenList(iLine, isFull);
+ fixFlowAddLine(flowContext);
+ setCommand(theToken);
+ theTok = theToken.tok;
+ } else {
+ break;
+ }
+ }
+ }
+ // why is this?
+ // if (lastFlowContext != null && lastFlowContext.forceEndIf
+ // && lastFlowContext.addLine > 0) {
+ // flowContext = lastFlowContext;
+ // flowContext.forceEndIf = true;
+ // if (isFlowIfContextOK(flowContext, tokCommand) &&
lltoken.get(iCommand - 1)[0].tok == T.end)
+ // lltoken.remove(--iCommand);
+ // }
+ //$FALL-THROUGH$
+ default:
+ if (isFlowCmd) {
+ if (!checkFlowCommand((String) tokenCommand.value))
+ return ERROR;
+ theToken = tokenCommand;
+ if (theTok == T.casecmd) {
+ addTokenToPrefix(tokenCommand);
+ theToken = T.tokenLeftParen;
+ }
+ return OK;
+ }
+ if (flowContext != null && flowContext.addLine > 0) {
fixFlowAddLine(flowContext);
while (flowContext != null) {
if (flowContext.checkForceEndIf(0)) {
@@ -1654,6 +1686,13 @@
}
}
}
+ if (theTok == T.rightbrace) {
+ // if }, just push onto vBrace, but NOT onto ltoken
+ vBraces.addLast(tokenCommand);
+ iBrace++;
+ tokCommand = T.nada;
+ return CONTINUE;
+ }
lastFlowCommand = null;
}
@@ -1803,11 +1842,11 @@
forPoint3 = nSemiSkip = 0;
nSemiSkip += 2;
break;
- }
+ }
if (nTokens == 3 && tokAt(2) == T.var) {
newContextVariable(ident);
break;
- }
+ }
if ((nTokens == 3 || nTokens == 4) && theTok == T.in) {
// for ( var x IN
// for ( x IN
@@ -1816,13 +1855,13 @@
addTokenToPrefix(theToken);
theToken = T.tokenLeftParen;
break;
- }
+ }
//$FALL-THROUGH$
case T.switchcmd:
case T.whilecmd:
case T.elseif:
case T.ifcmd:
- if (nTokens <= 2 ||braceCount != 0 || parenCount != 0)
+ if (nTokens <= 2 || braceCount != 0 || parenCount != 0)
break;
//$FALL-THROUGH$
case T.process:
@@ -1900,10 +1939,8 @@
return ERROR;
}
} else if (T.tokAttr(theTok, T.predefinedset)) {
- Logger
- .warn("WARNING: predefined term '"
- + ident
- + "' has been redefined by the user until the next file
load.");
+ Logger.warn("WARNING: predefined term '" + ident
+ + "' has been redefined by the user until the next file
load.");
} else if (!isCheckOnly && ident.length() > 1) {
Logger
.warn("WARNING: redefining "
@@ -1928,21 +1965,21 @@
}
}
//$FALL-THROUGH$
-// case T.display:
-// case T.hide:
-// case T.restrict:
-// case T.select:
-// case T.delete:
-// if (bracketCount == 0 && theTok != T.identifier
-// && !T.tokAttr(theTok, T.expression) && !T.tokAttr(theTok, T.misc)
-// && (theTok & T.minmaxmask) != theTok)
-// return ERROR(ERROR_invalidExpressionToken, ident);
+ // case T.display:
+ // case T.hide:
+ // case T.restrict:
+ // case T.select:
+ // case T.delete:
+ // if (bracketCount == 0 && theTok != T.identifier
+ // && !T.tokAttr(theTok, T.expression) && !T.tokAttr(theTok,
T.misc)
+ // && (theTok & T.minmaxmask) != theTok)
+ // return ERROR(ERROR_invalidExpressionToken, ident);
break;
-// case T.center:
-// if (theTok != T.identifier && theTok != T.dollarsign
-// && !T.tokAttr(theTok, T.expression))
-// return ERROR(ERROR_invalidExpressionToken, ident);
-// break;
+ // case T.center:
+ // if (theTok != T.identifier && theTok != T.dollarsign
+ // && !T.tokAttr(theTok, T.expression))
+ // return ERROR(ERROR_invalidExpressionToken, ident);
+ // break;
case T.plot3d:
case T.pmesh:
case T.isosurface:
@@ -2108,14 +2145,6 @@
break;
case T.elseif:
case T.elsecmd:
- if (lastFlowContext != null && lastFlowContext.forceEndIf
- && lastFlowContext.addLine > 0) {
- flowContext = lastFlowContext;
- flowContext.forceEndIf = true;
- if (isFlowIfContextOK(flowContext, tokCommand)
- && lltoken.get(iCommand - 1)[0].tok == T.end)
- lltoken.remove(pt = --iCommand);
- }
if (flowContext != null && !isFlowIfContextOK(flowContext, tokCommand))
flowContext = flowContext.parent;
if (!isFlowIfContextOK(flowContext, tokCommand))
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-10-04 04:28:59 UTC
(rev 20807)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-10-06 04:55:57 UTC
(rev 20808)
@@ -3408,7 +3408,6 @@
ContextToken cmdToken = (ContextToken) theToken;
int pt = st[0].intValue;
SV[] forVars = cmdToken.forVars;
- pt = st[0].intValue;
int[] pts = new int[2];
Object bsOrList = null;
SV forVal = null;
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-10-04 04:28:59 UTC
(rev 20807)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-10-06 04:55:57 UTC
(rev 20808)
@@ -1120,6 +1120,7 @@
if (tokAt(1) == T.list && listIsosurface(iShape))
return;
int iptDisplayProperty = 0;
+ boolean isDisplay = false;
boolean isIsosurface = (iShape == JC.SHAPE_ISOSURFACE);
boolean isPmesh = (iShape == JC.SHAPE_PMESH);
boolean isPlot3d = (iShape == JC.SHAPE_PLOT3D);
@@ -1319,7 +1320,7 @@
break;
case T.display:
case T.within:
- boolean isDisplay = (eval.theTok == T.display);
+ isDisplay = (eval.theTok == T.display);
if (isDisplay) {
sbCommand.append(" display");
iptDisplayProperty = i;
@@ -2766,7 +2767,7 @@
setShapeProperty(iShape, "clear", null);
if (toCache)
setShapeProperty(iShape, "cache", null);
- if (iShape != JC.SHAPE_LCAOCARTOON)
+ if (iShape != JC.SHAPE_LCAOCARTOON && !isDisplay && !haveSlab)
listIsosurface(iShape);
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-04 04:28:59 UTC
(rev 20807)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-06 04:55:57 UTC
(rev 20808)
@@ -2008,6 +2008,15 @@
(type + "D").toUpperCase().charAt(0), t456));
}
+ /**
+ * plane() or intersection()
+ *
+ * @param mp
+ * @param args
+ * @param tok
+ * @return
+ * @throws ScriptException
+ */
private boolean evaluatePlane(ScriptMathProcessor mp, SV[] args, int tok)
throws ScriptException {
if (tok == T.hkl && args.length != 3 || tok == T.intersection
@@ -2127,7 +2136,7 @@
norm = V3.newV(pt2);
if (pt3 == null) {
plane = new P4();
- if (args.length == 2 || !args[2].asBoolean()) {
+ if (args.length == 2 || args[2].tok != T.integer && args[2].tok !=
T.decimal && !args[2].asBoolean()) {
// plane(<point1>,<point2>) or
// plane(<point1>,<point2>,false)
pt3 = P3.newP(pt1);
Modified: trunk/Jmol/src/org/jmol/shape/MeshCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2015-10-04 04:28:59 UTC
(rev 20807)
+++ trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2015-10-06 04:55:57 UTC
(rev 20808)
@@ -457,10 +457,11 @@
if (property == "ID")
return (currentMesh == null ? null : currentMesh.thisID);
if (property.startsWith("list")) {
- clean();
- SB sb = new SB();
+ clean();
+ SB sb = new SB();
int k = 0;
- String id = (property.equals("list") ? null : property.substring(5));
+ boolean isNamed = property.length() > 5;
+ String id = (property.equals("list") ? null : isNamed ?
property.substring(5) : currentMesh == null ? null : currentMesh.thisID);
for (int i = 0; i < meshCount; i++) {
m = meshes[i];
if (id != null && !id.equalsIgnoreCase(m.thisID))
@@ -482,7 +483,7 @@
sb.append(s);
}
sb.appendC('\n');
- if (id != null) {
+ if (isNamed) {
Object info = getProperty("jvxlFileInfo", 0);
if (info != null)
sb.append((String) info).appendC('\n');
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-04 04:28:59 UTC (rev
20807)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-06 04:55:57 UTC (rev
20808)
@@ -65,7 +65,8 @@
"pdbe2", "http://www.ebi.ac.uk/pdbe/static/entry/%FILE_updated.cif";,
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";,
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
- "rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";
+ "rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
+ "aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";
};
public static String[] macros = {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-04 04:28:59 UTC
(rev 20807)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-06 04:55:57 UTC
(rev 20808)
@@ -61,8 +61,19 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.3.16_2015.10.03"
+Jmol.___JmolVersion="14.3.16_2015.10.05"
+
+new feature: load =aflow/AgAu
+ -- easy access to binary metal alloy CIF files
+
+bug fix: braceless if/for fix from 10.04
+
+JmolVersion="14.3.16_2015.10.04"
+
+bug fix: changing bond order of X-H using set picking assignBond_2 generates
error messages and removes atoms
+
+
new feature: if, for, and while can all operate using no braces for
single-line bodies
-- similar to JavaScript and Java
-- examples:
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