Revision: 21080
http://sourceforge.net/p/jmol/code/21080
Author: hansonr
Date: 2016-05-02 03:55:42 +0000 (Mon, 02 May 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.4_2016.05.01"
bug fix: Jmol SMILES directive /noaromatic/ should ignore ":" bond type
bug fix: Jmol SMILES directive /aromaticDouble/ not implemented for SMILES
buf fix; Jmol SMARTS measurements should be required to come after branches
bug fix: Jmol SMILES parser should require connection numbers to be placed
prior to branches
bug fix: Jmol SMILES should not allow (.t!50,60,70,80)
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-04-30
13:34:51 UTC (rev 21079)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-05-02
03:55:42 UTC (rev 21080)
@@ -1217,7 +1217,7 @@
float stddev = eval.getSmilesExt().getSmilesCorrelation(bsFrom, bsTo,
strSmiles, null, null, m4, null, false, null, center,
false, isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS);
- System.out.println("compare:\n" + m4);
+// System.out.println("compare:\n" + m4);
if (Float.isNaN(stddev)) {
showString("structures do not match");
return;
@@ -4205,21 +4205,20 @@
msg = SV.getVariable(info[1]).asString();
}
break;
- case T.nmr:
- if (eval.optParameterAsString(2).equalsIgnoreCase("1H")) {
- len = 3;
- if (!chk)
- msg = vwr.getNMRPredict(false);
- break;
- }
+ case T.nmr: {
+ String type = eval.optParameterAsString(2);
+ // switch to "H1" and "C13"
+ if (type.equals("1H") || type.equals("13C"))
+ type = type.substring(type.length() - 1) + type.substring(0,
type.length() - 1);
+ else if (type.equals("H"))
if (!chk)
- vwr.getNMRPredict(true);
+ vwr.getNMRPredict(type);
return;
+ }
case T.drawing:
case T.chemical:
case T.smiles:
-
- checkLength((tok == T.chemical || tok == T.smiles && tokAt(2) != T.nada
? len = 3
+ checkLength((tok == T.chemical || tok == T.smiles && tokAt(2) == T.on ?
len = 3
: 2)
+ filterLen);
if (chk)
@@ -4237,9 +4236,11 @@
}
} else if (eval.optParameterAsString(2).equalsIgnoreCase("true")) {
msg = vwr.getBioSmiles(null);
+ filter = null;
} else if (filter != null) {
msg = vwr.getSmilesOpt(null, -1, -1, JC.SMILES_TYPE_SMILES, filter
+ "///");
+ filter = null;
}
if (msg == null)
msg = (tok == T.smiles ? vwr.getSmiles(null) : vwr
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-04-30
13:34:51 UTC (rev 21079)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-05-02
03:55:42 UTC (rev 21080)
@@ -403,7 +403,8 @@
int pt = 0;
char ch;
SmilesBond bond = null;
-
+ boolean wasMeasure = false;
+ boolean wasBranch = false;
while (pattern != null && pattern.length() != 0) {
int index = 0;
if (currentAtom == null || bond != null
@@ -446,13 +447,17 @@
if (currentAtom == null)
throw new InvalidSmilesException("No previous atom for "
+ (isMeasure ? "measure" : "branch"));
+ wasMeasure = wasBranch = false;
if (subString.startsWith(".")) {
parseMeasure(molecule, subString.substring(1), currentAtom);
+ wasMeasure = true;
} else if (subString.length() == 0 && isBioSequence) {
+ // () can mean NOT crosslinked
currentAtom.notCrossLinked = true;
} else {
branchLevel++;
parseSmiles(molecule, subString, currentAtom, true);
+ wasBranch = true;
branchLevel--;
}
}
@@ -469,7 +474,6 @@
bond = parseBond(molecule, null, pattern.substring(pt, index), null,
currentAtom, false, isBranchAtom);
-
if (haveOpen && bond.order != SmilesBond.TYPE_UNKNOWN)
index = pt;
ch = getChar(pattern, index);
@@ -486,11 +490,14 @@
boolean isAtom = (!isRing && (ch == '_' || ch == '[' || ch == '*' || PT
.isLetter(ch)));
if (isRing) {
+ if (wasMeasure || wasBranch)
+ throw new InvalidSmilesException("connection number must
immediately follow its connecting atom");
index = getRingNumber(pattern, index, ch, ret);
int ringNumber = ret[0];
parseRing(molecule, ringNumber, currentAtom, bond);
bond = null;
} else if (isAtom) {
+ wasMeasure = wasBranch = false;
switch (ch) {
case '[':
case '_':
@@ -632,7 +639,7 @@
if (isNegative)
strMeasure = "-" + strMeasure;
String[] tokens = PT.split(strMeasure, ",");
- if(tokens.length % 2 == 1)
+ if(tokens.length % 2 == 1 || isNot && tokens.length != 2)
break;
float[] vals = new float[tokens.length];
int i = tokens.length;
@@ -803,10 +810,8 @@
throw new InvalidSmilesException("invalid '!'");
newAtom.not = isNot = true;
}
-
int biopt = pattern.indexOf('.');
- int chiralpt = pattern.indexOf('@');
- if (biopt >= 0 && (chiralpt < 0 || biopt < chiralpt)) {
+ if (biopt >= 0) {
newAtom.isBioResidue = true;
String name = pattern.substring(index, biopt);
pattern = pattern.substring(biopt + 1).toUpperCase();
@@ -880,19 +885,19 @@
else
newAtom.elementNumber = ret[0];
break;
-// does not work
-// case '(':
-// // JmolSMARTS, JmolSMILES reference to atom
-// String name = getSubPattern(pattern, index, '(');
-// index += 2 + name.length();
-// newAtom = checkReference(newAtom, name, ret);
-// isNewAtom = (ret[0] == 1); // we are done here
-// if (!isNewAtom) {
-// if (isNot)
-// index = 0; // triggers an error
-// isNot = true; // flags that this must be the end
-// }
-// break;
+ // does not work
+ // case '(':
+ // // JmolSMARTS, JmolSMILES reference to atom
+ // String name = getSubPattern(pattern, index, '(');
+ // index += 2 + name.length();
+ // newAtom = checkReference(newAtom, name, ret);
+ // isNewAtom = (ret[0] == 1); // we are done here
+ // if (!isNewAtom) {
+ // if (isNot)
+ // index = 0; // triggers an error
+ // isNot = true; // flags that this must be the end
+ // }
+ // break;
case '-':
case '+':
index = checkCharge(pattern, index, newAtom);
@@ -913,6 +918,8 @@
// "!H" is "not hydrogen" but "!H2" is "not two attached hydrogens"
// [Rh] could be rhodium or "Any ring atom with at least one
implicit H atom"
// [Ar] could be argon or "Any aliphatic ring atom"
+ // however it has been pointed out by a reviewer that [Cr3] must
be
+ // interpreted as chromium-3.
// There is no ambiguity, though, with [Rh3] or [Ar6] because
// in those cases the number forces the single-character property
// "h3" or "r6", thus forcing "R" or "A"
@@ -921,12 +928,12 @@
// the first two-letters of the expression could be interpreted
// as a symbol, AND the next character is not a digit, then it
WILL be interpreted as a symbol
char nextChar = getChar(pattern, index + 1);
- String sym2 = pattern.substring(
- index + 1,
- index
- + (PT.isLowerCase(nextChar)
- && (!isBracketed || !PT.isDigit(getChar(pattern,
- index + 2))) ? 2 : 1));
+ String sym2 = pattern.substring(index + 1,
+ index + (PT.isLowerCase(nextChar)
+ // 14.4.5: removed to require [C;r3] not [Cr3] for C in a
3-membered ring
+ // && (!isBracketed ||
!PT.isDigit(getChar(pattern, index + 2)))
+ ? 2
+ : 1));
String symbol = Character.toUpperCase(ch) + sym2;
boolean mustBeSymbol = true;
boolean checkForPrimitive = (isBracketed && PT.isLetter(ch));
@@ -1084,7 +1091,7 @@
return newAtom;
}
- private Map<String, SmilesAtom> atomRefs;
+// private Map<String, SmilesAtom> atomRefs;
// /**
// * allow for [(...)] to indicate a specific pattern atom
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-04-30
13:34:51 UTC (rev 21079)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-05-02
03:55:42 UTC (rev 21080)
@@ -142,13 +142,13 @@
else
flags |= INVERT_STEREOCHEMISTRY;
}
+ if (strFlags.indexOf("ATOMCOMMENT") >= 0)
+ flags |= JC.SMILES_GEN_ATOM_COMMENT;
if ((flags & JC.SMILES_GEN_BIO) == JC.SMILES_GEN_BIO) {
if (strFlags.indexOf("NOCOMMENT") >= 0)
flags |= JC.SMILES_GEN_BIO_NOCOMMENTS;
- if (strFlags.indexOf("ATOMCOMMENT") >= 0)
- flags |= JC.SMILES_GEN_ATOM_COMMENT;
if (strFlags.indexOf("UNMATCHED") >= 0)
flags |= JC.SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS;
if (strFlags.indexOf("COVALENT") >= 0)
@@ -1191,8 +1191,9 @@
boolean isAromatic1 = (!noAromatic && bsAromatic.get(iAtom1));
boolean isAromatic2 = (!noAromatic && bsAromatic.get(iAtom2));
int order = bond.getCovalentOrder();
+ int patternOrder = patternBond.order;
if (isAromatic1 && isAromatic2) {
- switch (patternBond.order) {
+ switch (patternOrder) {
case SmilesBond.TYPE_AROMATIC: // :
case SmilesBond.TYPE_RING:
bondFound = isRingBond(ringSets, iAtom1, iAtom2);
@@ -1214,7 +1215,7 @@
// distinction between single and double, as for example is necessary
to distinguish
// between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing
//
- bondFound = !isSmarts || aromaticDouble &&
+ bondFound = aromaticDouble &&
(order == Edge.BOND_COVALENT_DOUBLE || order ==
Edge.BOND_AROMATIC_DOUBLE);
break;
case SmilesBond.TYPE_ATROPISOMER_1:
@@ -1225,7 +1226,11 @@
break;
}
} else {
- switch (patternBond.order) {
+ switch (patternOrder) {
+ case SmilesBond.TYPE_AROMATIC: // :
+ if (!noAromatic)
+ break;
+ //$FALL-THROUGH$
case SmilesBond.TYPE_ANY:
case SmilesBond.TYPE_UNKNOWN:
bondFound = true;
@@ -1253,7 +1258,7 @@
case SmilesBond.TYPE_RING:
bondFound = isRingBond(ringSets, iAtom1, iAtom2);
break;
- }
+ }
}
return bondFound != patternBond.isNot;
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-04-30
13:34:51 UTC (rev 21079)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-05-02
03:55:42 UTC (rev 21080)
@@ -5,6 +5,14 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
+Jmol.___JmolVersion="14.4.4_2016.05.01"
+
+bug fix: Jmol SMILES directive /noaromatic/ should ignore ":" bond type
+bug fix: Jmol SMILES directive /aromaticDouble/ not implemented for SMILES
+buf fix; Jmol SMARTS measurements should be required to come after branches
+bug fix: Jmol SMILES parser should require connection numbers to be placed
prior to branches
+bug fix: Jmol SMILES should not allow (.t!50,60,70,80)
+
Jmol.___JmolVersion="14.4.4_2016.04.30"
new feature: 13C Simulated spectra (but without correlation yet)
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-04-30 13:34:51 UTC
(rev 21079)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-05-02 03:55:42 UTC
(rev 21080)
@@ -1217,7 +1217,7 @@
float stddev = eval.getSmilesExt().getSmilesCorrelation(bsFrom, bsTo,
strSmiles, null, null, m4, null, false, null, center,
false, isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS);
- System.out.println("compare:\n" + m4);
+// System.out.println("compare:\n" + m4);
if (Float.isNaN(stddev)) {
showString("structures do not match");
return;
@@ -4218,8 +4218,7 @@
case T.drawing:
case T.chemical:
case T.smiles:
-
- checkLength((tok == T.chemical || tok == T.smiles && tokAt(2) != T.nada
? len = 3
+ checkLength((tok == T.chemical || tok == T.smiles && tokAt(2) == T.on ?
len = 3
: 2)
+ filterLen);
if (chk)
@@ -4237,9 +4236,11 @@
}
} else if (eval.optParameterAsString(2).equalsIgnoreCase("true")) {
msg = vwr.getBioSmiles(null);
+ filter = null;
} else if (filter != null) {
msg = vwr.getSmilesOpt(null, -1, -1, JC.SMILES_TYPE_SMILES, filter
+ "///");
+ filter = null;
}
if (msg == null)
msg = (tok == T.smiles ? vwr.getSmiles(null) : vwr
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-04-30 13:34:51 UTC
(rev 21079)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-05-02 03:55:42 UTC
(rev 21080)
@@ -403,7 +403,8 @@
int pt = 0;
char ch;
SmilesBond bond = null;
-
+ boolean wasMeasure = false;
+ boolean wasBranch = false;
while (pattern != null && pattern.length() != 0) {
int index = 0;
if (currentAtom == null || bond != null
@@ -446,13 +447,17 @@
if (currentAtom == null)
throw new InvalidSmilesException("No previous atom for "
+ (isMeasure ? "measure" : "branch"));
+ wasMeasure = wasBranch = false;
if (subString.startsWith(".")) {
parseMeasure(molecule, subString.substring(1), currentAtom);
+ wasMeasure = true;
} else if (subString.length() == 0 && isBioSequence) {
+ // () can mean NOT crosslinked
currentAtom.notCrossLinked = true;
} else {
branchLevel++;
parseSmiles(molecule, subString, currentAtom, true);
+ wasBranch = true;
branchLevel--;
}
}
@@ -469,7 +474,6 @@
bond = parseBond(molecule, null, pattern.substring(pt, index), null,
currentAtom, false, isBranchAtom);
-
if (haveOpen && bond.order != SmilesBond.TYPE_UNKNOWN)
index = pt;
ch = getChar(pattern, index);
@@ -486,11 +490,14 @@
boolean isAtom = (!isRing && (ch == '_' || ch == '[' || ch == '*' || PT
.isLetter(ch)));
if (isRing) {
+ if (wasMeasure || wasBranch)
+ throw new InvalidSmilesException("connection number must
immediately follow its connecting atom");
index = getRingNumber(pattern, index, ch, ret);
int ringNumber = ret[0];
parseRing(molecule, ringNumber, currentAtom, bond);
bond = null;
} else if (isAtom) {
+ wasMeasure = wasBranch = false;
switch (ch) {
case '[':
case '_':
@@ -632,7 +639,7 @@
if (isNegative)
strMeasure = "-" + strMeasure;
String[] tokens = PT.split(strMeasure, ",");
- if(tokens.length % 2 == 1)
+ if(tokens.length % 2 == 1 || isNot && tokens.length != 2)
break;
float[] vals = new float[tokens.length];
int i = tokens.length;
@@ -803,10 +810,8 @@
throw new InvalidSmilesException("invalid '!'");
newAtom.not = isNot = true;
}
-
int biopt = pattern.indexOf('.');
- int chiralpt = pattern.indexOf('@');
- if (biopt >= 0 && (chiralpt < 0 || biopt < chiralpt)) {
+ if (biopt >= 0) {
newAtom.isBioResidue = true;
String name = pattern.substring(index, biopt);
pattern = pattern.substring(biopt + 1).toUpperCase();
@@ -880,19 +885,19 @@
else
newAtom.elementNumber = ret[0];
break;
-// does not work
-// case '(':
-// // JmolSMARTS, JmolSMILES reference to atom
-// String name = getSubPattern(pattern, index, '(');
-// index += 2 + name.length();
-// newAtom = checkReference(newAtom, name, ret);
-// isNewAtom = (ret[0] == 1); // we are done here
-// if (!isNewAtom) {
-// if (isNot)
-// index = 0; // triggers an error
-// isNot = true; // flags that this must be the end
-// }
-// break;
+ // does not work
+ // case '(':
+ // // JmolSMARTS, JmolSMILES reference to atom
+ // String name = getSubPattern(pattern, index, '(');
+ // index += 2 + name.length();
+ // newAtom = checkReference(newAtom, name, ret);
+ // isNewAtom = (ret[0] == 1); // we are done here
+ // if (!isNewAtom) {
+ // if (isNot)
+ // index = 0; // triggers an error
+ // isNot = true; // flags that this must be the end
+ // }
+ // break;
case '-':
case '+':
index = checkCharge(pattern, index, newAtom);
@@ -913,6 +918,8 @@
// "!H" is "not hydrogen" but "!H2" is "not two attached hydrogens"
// [Rh] could be rhodium or "Any ring atom with at least one
implicit H atom"
// [Ar] could be argon or "Any aliphatic ring atom"
+ // however it has been pointed out by a reviewer that [Cr3] must
be
+ // interpreted as chromium-3.
// There is no ambiguity, though, with [Rh3] or [Ar6] because
// in those cases the number forces the single-character property
// "h3" or "r6", thus forcing "R" or "A"
@@ -921,12 +928,12 @@
// the first two-letters of the expression could be interpreted
// as a symbol, AND the next character is not a digit, then it
WILL be interpreted as a symbol
char nextChar = getChar(pattern, index + 1);
- String sym2 = pattern.substring(
- index + 1,
- index
- + (PT.isLowerCase(nextChar)
- && (!isBracketed || !PT.isDigit(getChar(pattern,
- index + 2))) ? 2 : 1));
+ String sym2 = pattern.substring(index + 1,
+ index + (PT.isLowerCase(nextChar)
+ // 14.4.5: removed to require [C;r3] not [Cr3] for C in a
3-membered ring
+ // && (!isBracketed ||
!PT.isDigit(getChar(pattern, index + 2)))
+ ? 2
+ : 1));
String symbol = Character.toUpperCase(ch) + sym2;
boolean mustBeSymbol = true;
boolean checkForPrimitive = (isBracketed && PT.isLetter(ch));
@@ -1084,7 +1091,7 @@
return newAtom;
}
- private Map<String, SmilesAtom> atomRefs;
+// private Map<String, SmilesAtom> atomRefs;
// /**
// * allow for [(...)] to indicate a specific pattern atom
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-04-30 13:34:51 UTC
(rev 21079)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-05-02 03:55:42 UTC
(rev 21080)
@@ -142,13 +142,13 @@
else
flags |= INVERT_STEREOCHEMISTRY;
}
+ if (strFlags.indexOf("ATOMCOMMENT") >= 0)
+ flags |= JC.SMILES_GEN_ATOM_COMMENT;
if ((flags & JC.SMILES_GEN_BIO) == JC.SMILES_GEN_BIO) {
if (strFlags.indexOf("NOCOMMENT") >= 0)
flags |= JC.SMILES_GEN_BIO_NOCOMMENTS;
- if (strFlags.indexOf("ATOMCOMMENT") >= 0)
- flags |= JC.SMILES_GEN_ATOM_COMMENT;
if (strFlags.indexOf("UNMATCHED") >= 0)
flags |= JC.SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS;
if (strFlags.indexOf("COVALENT") >= 0)
@@ -1191,8 +1191,9 @@
boolean isAromatic1 = (!noAromatic && bsAromatic.get(iAtom1));
boolean isAromatic2 = (!noAromatic && bsAromatic.get(iAtom2));
int order = bond.getCovalentOrder();
+ int patternOrder = patternBond.order;
if (isAromatic1 && isAromatic2) {
- switch (patternBond.order) {
+ switch (patternOrder) {
case SmilesBond.TYPE_AROMATIC: // :
case SmilesBond.TYPE_RING:
bondFound = isRingBond(ringSets, iAtom1, iAtom2);
@@ -1214,7 +1215,7 @@
// distinction between single and double, as for example is necessary
to distinguish
// between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing
//
- bondFound = !isSmarts || aromaticDouble &&
+ bondFound = aromaticDouble &&
(order == Edge.BOND_COVALENT_DOUBLE || order ==
Edge.BOND_AROMATIC_DOUBLE);
break;
case SmilesBond.TYPE_ATROPISOMER_1:
@@ -1225,7 +1226,11 @@
break;
}
} else {
- switch (patternBond.order) {
+ switch (patternOrder) {
+ case SmilesBond.TYPE_AROMATIC: // :
+ if (!noAromatic)
+ break;
+ //$FALL-THROUGH$
case SmilesBond.TYPE_ANY:
case SmilesBond.TYPE_UNKNOWN:
bondFound = true;
@@ -1253,7 +1258,7 @@
case SmilesBond.TYPE_RING:
bondFound = isRingBond(ringSets, iAtom1, iAtom2);
break;
- }
+ }
}
return bondFound != patternBond.isNot;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-04-30 13:34:51 UTC
(rev 21079)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-05-02 03:55:42 UTC
(rev 21080)
@@ -42,6 +42,15 @@
TODO: slightly stronger unitcell lines for near point?
+Jmol.___JmolVersion="14.5.4_2016.05.01"
+
+bug fix: Jmol SMILES directive /noaromatic/ should ignore ":" bond type
+bug fix: Jmol SMILES directive /aromaticDouble/ not implemented for SMILES
+buf fix; Jmol SMARTS measurements should be required to come after branches
+bug fix: Jmol SMILES parser should require connection numbers to be placed
prior to branches
+bug fix: Jmol SMILES should not allow (.t!50,60,70,80)
+
+
Jmol.___JmolVersion="14.5.4_2016.04.30"
new feature: 13C Simulated spectra (but without correlation yet)
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