Revision: 21588
http://sourceforge.net/p/jmol/code/21588
Author: hansonr
Date: 2017-05-09 20:03:13 +0000 (Tue, 09 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.4"
bug fix: CIP Rule 1b modification to ensure aromatic rings do not result in
false positive for R/S (binap2)
-- specifically that the duplicate atom is given the root distance of its
parent, not its duplicated atom
bug fix: CIP chiral bridgehead N designations missing
bug fix: Assignment of auxiliary r/s not functional (AY-236.201,202)
new feature: set debugHigh
-- same as set loglevel 6 - debugging only
-- debugging only; not considered significant enough to increment minor
version
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/awt/Mouse.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/util/Node.java
trunk/Jmol/src/org/jmol/viewer/ActionManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/awt/Mouse.java
===================================================================
--- trunk/Jmol/src/org/jmol/awt/Mouse.java 2017-05-08 20:59:30 UTC (rev
21587)
+++ trunk/Jmol/src/org/jmol/awt/Mouse.java 2017-05-09 20:03:13 UTC (rev
21588)
@@ -180,8 +180,8 @@
int modifiers = ke.getModifiers();
// for whatever reason, CTRL may also drop the 6- and 7-bits,
// so we are in the ASCII non-printable region 1-31
- if (Logger.debuggingHigh)
- Logger.debug("MouseManager keyTyped: " + ch + " " + (0+ch) + " " +
modifiers);
+// if (Logger.debuggingHigh && vwr.getBoolean(T.testflag1))
+// Logger.debug("MouseManager keyTyped: " + ch + " " + (0+ch) + " " +
modifiers);
if (modifiers != 0 && modifiers != Event.SHIFT_MASK) {
switch (ch) {
case (char) 11:
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-05-08 20:59:30 UTC (rev
21587)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-05-09 20:03:13 UTC (rev
21588)
@@ -1422,7 +1422,16 @@
| (c << CIP_CHIRALITY_OFFSET);
}
+ /**
+ *
+ * @param c [0:unknown; 1: R; 2: S; 4: Z, 8: E, 3: none, 12: none]
+ */
@Override
+ public int getCIPChiralityCode() {
+ return (formalChargeAndFlags & CIP_CHIRALITY_MASK) >> CIP_CHIRALITY_OFFSET;
+ }
+
+ @Override
public char getInsertionCode() {
return group.getInsertionCode();
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-05-08 20:59:30 UTC
(rev 21587)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-05-09 20:03:13 UTC
(rev 21588)
@@ -4097,8 +4097,5 @@
at[i].setCIPChirality(0);
Interface.getSymmetry(vwr, "ms").calculateCIPChiralityForAtoms(vwr,
bsAtoms);
}
-
-
-
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-05-08 20:59:30 UTC
(rev 21587)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-05-09 20:03:13 UTC
(rev 21588)
@@ -6782,10 +6782,11 @@
setBooleanProperty("bondModeOr", b);
return;
case T.debug:
+ case T.debughigh:
if (chk)
return;
int iLevel = (tokAt(2) == T.off || tokAt(2) == T.integer
- && intParameter(2) == 0 ? 4 : 5);
+ && intParameter(2) == 0 ? 4 : (tok == T.debughigh ? 6 : 5));
Logger.setLogLevel(iLevel);
setIntProperty("logLevel", iLevel);
if (iLevel == 4) {
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2017-05-08 20:59:30 UTC (rev
21587)
+++ trunk/Jmol/src/org/jmol/script/T.java 2017-05-09 20:03:13 UTC (rev
21588)
@@ -788,6 +788,7 @@
public final static int backgroundmodel = setparam | 2;
public final static int debug = setparam | 4;
+ public final static int debughigh = setparam | 5;
public final static int defaultlattice = setparam | 6;
public final static int highlight = setparam | 8;// 12.0.RC14
public final static int showscript = setparam | 10;
@@ -2339,6 +2340,7 @@
"celShading",
"celShadingPower",
"debug",
+ "debugHigh",
"defaultLattice",
"measurements",
"measurement",
@@ -3387,6 +3389,7 @@
celshading, // "celShading"
celshadingpower, // "celShadingPower"
debug, // "debug"
+ debughigh, // "debugHigh"
defaultlattice, // "defaultLattice"
measurements, // "measurements"
-1, // "measurement"
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2017-05-08 20:59:30 UTC
(rev 21587)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2017-05-09 20:03:13 UTC
(rev 21588)
@@ -869,6 +869,13 @@
}
@Override
+ public int getCIPChiralityCode() {
+ //n/a
+ return 0;
+ }
+
+
+ @Override
public P3 getXYZ() {
return this;
}
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-08 20:59:30 UTC
(rev 21587)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-09 20:03:13 UTC
(rev 21588)
@@ -252,6 +252,7 @@
final static int[] PRIORITY_SHIFT = new int[] { -1, 24, 20, 12, 9, 6, 3, 0 };
static final float TRIGONALITY_MIN = 0.2f;
+ //public static final int MAX_ROOT_DISTANCE = 10000;
/**
* incremental pointer providing a unique ID to every CIPAtom for debugging
@@ -334,8 +335,10 @@
this.bsAtropisomeric = bsAtropisomeric;
init();
- // using BSAtoms here because we need the entire graph, even starting with
an H atom.
+ // using BSAtoms here because we need the entire graph,
+ // including multiple molecular units (AY-236.93
BS bs = BSUtil.copy(bsAtoms);
+ lstSmallRings = new Lst<BS>();
while (!bs.isEmpty())
getSmallRings(atoms[bs.nextSetBit(0)], bs);
bsAromatic = getAromaticity(atoms);
@@ -352,12 +355,12 @@
// Jmol will clear this anyway prior to CALCULATE CHIRALITY, so this is
mute.
// But it is here in case we want to implement full molecular chirality
generation
// prior to any request for atom.chirality. Right now we don't do that.
- String c = atom.getCIPChirality(false);
- if (c.length() > 0) {
+ if (atom.getCIPChiralityCode() != 0) {
bsToDo.clear(i);
} else {
ptID = 0;
- atom.setCIPChirality(getAtomChiralityLimited(atom, null, null,
RULE_3));
+ int stereo = getAtomChiralityLimited(atom, null, null, RULE_3);
+ atom.setCIPChirality(stereo == NO_CHIRALITY ? STEREO_BOTH_RS : stereo);
}
}
@@ -380,7 +383,10 @@
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1)) {
Node a = atoms[i];
a.setCIPChirality(0);
- a.setCIPChirality(getAtomChiralityLimited(a, null, null, RULE_5));
+ int c = getAtomChiralityLimited(a, null, null, RULE_5);
+ if (c == 0)
+ c = JC.CIP_CHIRALITY_NONE;
+ a.setCIPChirality(c);
}
//
@@ -392,6 +398,9 @@
clearSmallRingEZ(atoms, lstEZ);
}
+ System.out.println("sp2-aromatic = " + bsAromatic);
+ System.out.println("smallRings = " + PT.toJSON(null,lstSmallRings));
+
}
private BS getAzacyclic(Node[] atoms, BS bsAtoms) {
@@ -401,18 +410,42 @@
if (atom.getElementNumber() != 7 || atom.getCovalentBondCount() != 3
|| bsAromatic != null && bsAromatic.get(i))
continue;
- int nr = 0;
+ // bridgehead N must be in two rings that have at least three atoms in
common.
+ Lst<BS> nRings = new Lst<BS>();
for (int j = lstSmallRings.size(); --j >= 0;) {
BS bsRing = lstSmallRings.get(j);
if (bsRing.get(i))
- nr++;
+ nRings.addLast(bsRing);
}
- if (nr != 3)
+ int nr = nRings.size();
+ if (nr < 2)
continue;
- if (bsAza == null)
- bsAza = new BS();
- bsAza.set(i);
-
+ BS bsSubs = new BS();
+ Edge[] bonds = atom.getEdges();
+ for (int b = bonds.length; --b >= 0;)
+ if (bonds[b].isCovalent())
+ bsSubs.set(bonds[b].getOtherAtomNode(atom).getIndex());
+ BS bsBoth = new BS();
+ BS bsAll = new BS();
+ for (int j = 0; j < nr - 1 && bsAll != null; j++) {
+ BS bs1 = nRings.get(j);
+ for (int k = j + 1; k < nr && bsAll != null; k++) {
+ BS bs2 = nRings.get(k);
+ BSUtil.copy2(bs1, bsBoth);
+ bsBoth.and(bs2);
+ if (bsBoth.cardinality() > 2) {
+ BSUtil.copy2(bs1,bsAll);
+ bsAll.or(bs2);
+ bsAll.and(bsSubs);
+ if (bsAll.cardinality() == 3) {
+ if (bsAza == null)
+ bsAza = new BS();
+ bsAza.set(i);
+ bsAll = null;
+ }
+ }
+ }
+ }
}
return bsAza;
}
@@ -558,7 +591,6 @@
* @param bs tracks all atoms in this molecular unit
*/
private void getSmallRings(Node atom, BS bs) {
- lstSmallRings = new Lst<BS>();
root = new CIPAtom().create(atom, null, false, false);
addSmallRings(root, bs);
}
@@ -617,7 +649,7 @@
)
continue;
CIPAtom r = a.addAtom(pt++, atom2, false, false);
- if (r.isRingDuplicate)
+ if (r.isDuplicate)
r.updateRingList();
}
for (int i = 0; i < pt; i++) {
@@ -675,7 +707,8 @@
*/
public int getAtomChirality(Node atom) {
init();
- return getAtomChiralityLimited(atom, null, null, RULE_3);
+ int rs = getAtomChiralityLimited(atom, null, null, RULE_3);
+ return (rs == NO_CHIRALITY ? STEREO_BOTH_RS : rs);
}
/**
@@ -688,6 +721,7 @@
*/
public int getBondChirality(Edge bond) {
init();
+ lstSmallRings = new Lst<BS>();
getSmallRings(bond.getOtherAtomNode(null), null);
return (bond.getCovalentOrder() == 2 ? getBondChiralityLimited(bond, null,
RULE_3) : NO_CHIRALITY);
}
@@ -830,6 +864,8 @@
for (currentRule = RULE_1a; currentRule <= ruleMax; currentRule++) {
if (Logger.debugging)
Logger.info("-Rule " + getRuleName() + " CIPChirality for " +
cipAtom + "-----");
+// if (currentRule == RULE_1b)
+// System.out.println("rule 1b");
if (currentRule == RULE_4) {
//cipAtom.resetAuxiliaryChirality();// was resetting E/Z
cipAtom.createAuxiliaryRSCenters(null, null);
@@ -1223,10 +1259,12 @@
private boolean isTrigonalPyramidal;
- boolean isRingDuplicate;
+ boolean isAromatic;
+ boolean sp2Duplicate;
+
CIPAtom() {
// had a problem in JavaScript that the constructor of an inner function
cannot
// access this.b$ yet. That assignment is made after construction.
@@ -1276,7 +1314,7 @@
}
this.bsPath = (parent == null ? new BS() : BSUtil.copy(parent.bsPath));
- boolean wasDuplicate = isDuplicate;
+ sp2Duplicate = isDuplicate;
// The rootDistance for a nonDuplicate atom is just its sphere.
// The rootDistance for a duplicate atom is (by IUPAC) the sphere of its
duplicated atom.
// I argue that for aromatic compounds, this introduces a Kekule problem
and that for
@@ -1283,13 +1321,13 @@
// those cases, the rootDistance should be the sphere of the parent, not
the duplicated atom.
// This shows up in AV-360#215.
+ isAromatic = (bsAromatic != null && bsAromatic.get(atomIndex));
if (parent == null) {
// original atom
bsPath.set(atomIndex);
rootDistance = 0;
- } else if (wasDuplicate && bsAromatic != null
- && bsAromatic.get(atomIndex)) {
- rootDistance = parent.rootDistance;
+ } else if (sp2Duplicate && isAromatic) {
+ rootDistance = parent.rootDistance;//MAX_ROOT_DISTANCE;
} else if (atom == root.atom) {
// pointing to original atom
rootDistance = 0;
@@ -1308,7 +1346,6 @@
myPath = (parent != null ? parent.myPath + "-" : "") + this;
if (Logger.debugging)
Logger.info("new CIPAtom " + myPath);
- isRingDuplicate = (isDuplicate && !wasDuplicate);
return this;
}
@@ -1326,7 +1363,7 @@
* than 8.
*
*/
- private void updateRingList() {
+ void updateRingList() {
BS bsRing = BSUtil.newAndSetBit(atomIndex);
CIPAtom p = this;
int index = -1;
@@ -1377,6 +1414,7 @@
knownAtomChirality = "~";
if (atom.getCovalentBondCount() == 2 && atom.getValence() == 4) {
parent.isAlkeneAtom2 = false;
+ parent.knownAtomChirality = "~";
} else {
isAlkeneAtom2 = true;
}
@@ -1383,6 +1421,7 @@
parent.alkeneChild = null;
alkeneParent = (parent.alkeneParent == null ? parent :
parent.alkeneParent);
alkeneParent.alkeneChild = this;
+ alkeneParent.knownAtomChirality = knownAtomChirality;
if (parent.alkeneParent == null)
parent.nextSP2 = this;
}
@@ -1424,12 +1463,9 @@
for (; pt < atoms.length; pt++)
atoms[pt] = new CIPAtom().create(null, this, true, false);
- // Do an initial atom-only shallow sort using a.compareTo(b)
+ // Do an initial very shallow atom-only Rule 1 sort using a.compareTo(b)
- int ruleNow = currentRule;
- currentRule = RULE_1a;
Arrays.sort(atoms);
- currentRule = ruleNow;
// pretty sure this next test cannot be true
if (isTerminal)
System.out.println("????");
@@ -1508,7 +1544,7 @@
: prevPriorities[j] < prevPriorities[i] ? B_WINS : A_WINS);
// note that a.compareTo(b) also down-scores duplicated atoms
relative to actual atoms.
if (score == TIED)
- score = (checkRule4List ? checkRule4And5(i, j) : a.compareTo(b));
+ score = (checkRule4List ? checkRule4And5(i, j) :
a.checkPriority(b));
if (Logger_debugHigh)
Logger.info(dots() + "ordering " + this.id + "." + i + "." + j + "
" + this + "-" + a + " vs " + b + " = " + score);
switch (score) {
@@ -1649,9 +1685,9 @@
// BECAUSE DUPLICATES LOSE IN THE NEXT SPHERE NOT THIS
// THE NEED FOR THIS TEST SHOWS THAT
// SUBRULE 1a MUST BE COMPLETED EXHAUSTIVELY PRIOR TO SUBRULE 1b.
- int score = checkNoSubs(b);
+ int score = checkIsDuplicate(b);
if (score != TIED)
- return score*(sphere+1); // TESTING sphere instead of sphere+1 here
+ return score*(sphere+1);
// return NO_CHIRALITY/TIED if:
// a) both are null
@@ -1702,12 +1738,13 @@
if (!(a1 = atoms[i]).isDuplicate)
continue;
for (int j = i + 1; j < 4; j++) {
- if (!(a2 = atoms[j]).isDuplicate
- || a1.elemNo != a2.elemNo
- || a1.rootDistance <= a2.rootDistance)
- continue;
- atoms[i] = a2;
- atoms[j] = a1;
+ if (!(a2 = atoms[j]).isDuplicate || a1.elemNo != a2.elemNo
+ || a1.rootDistance <= a2.rootDistance)
+ continue;
+ atoms[i] = a2;
+ atoms[j] = a1;
+ j = 4;
+ i = -1;
}
}
}
@@ -1772,7 +1809,7 @@
return finalScore;
}
/**
- * Used in Array.sort and sortSubstituents; includes a preliminary check
for
+ * Used in Array.sort when an atom is set; includes a preliminary check for
* duplicates, since we know that that atom will ultimately be lower
priority
* if all other rules are tied. This is just a convenience.
*
@@ -1783,10 +1820,24 @@
int score;
return (b == null ? A_WINS
: (atom == null) != (b.atom == null) ? (atom == null ? B_WINS
+ : A_WINS) : (score = checkRule1a(b)) != TIED ? score
+ : checkIsDuplicate(b));
+ }
+
+ /**
+ * Used in sortSubstituents
+ * @param b
+ *
+ * @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
+ */
+ public int checkPriority(CIPAtom b) {
+ int score;
+ return (b == null ? A_WINS
+ : (atom == null) != (b.atom == null) ? (atom == null ? B_WINS
: A_WINS) : (score = checkCurrentRule(b)) == IGNORE ? TIED
- : score != TIED ? score : checkNoSubs(b));
+ : score);
}
-
+
/**
* This check is not technically one of those listed in the rules, but it
is
* useful when preparing to check substituents because if one of the atoms
@@ -1796,7 +1847,7 @@
* @param b
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
- private int checkNoSubs(CIPAtom b) {
+ private int checkIsDuplicate(CIPAtom b) {
return b.isDuplicate == isDuplicate ? TIED : b.isDuplicate ?
A_WINS : B_WINS;
}
@@ -1851,10 +1902,10 @@
*/
private int checkRule1b(CIPAtom b) {
- return !b.isDuplicate || !isDuplicate ? TIED
- : b.rootDistance == rootDistance ? TIED
- : b.rootDistance > rootDistance ? A_WINS
- : B_WINS;
+ return b.isDuplicate != isDuplicate ? TIED
+ : b.rootDistance != rootDistance ? (b.rootDistance > rootDistance ?
+ A_WINS : B_WINS)
+ : TIED;
}
/**
@@ -2393,7 +2444,6 @@
isBranch = true;
s = "u";
subRS = "";
-// TODO: Why is this setting of ret to null?
if (ret != null)
ret[0] = null;
break;
@@ -2420,6 +2470,7 @@
if (!isBranch || adj == A_WINS || adj == B_WINS) {
if (isAlkene && alkeneChild != null) {
+ System.out.println("M/P seqCis Rule 4b not implemented!");
// we must check for seqCis or M/P
} else if (node1 != null
&& (bondCount == 4 && nPriorities >= 3 - Math.abs(adj) ||
isTrigonalPyramidal
@@ -2426,12 +2477,15 @@
&& nPriorities >= 2 - Math.abs(adj))) {
if (isBranch) {
// if here, adj is A_WINS (-1), or B_WINS (1)
+ // we check based on A winning, but then reverse it if B
actually won
switch (checkPseudoHandedness(mataList, null)) {
case STEREO_R:
- s = "r";
+ s = (adj == A_WINS ? "r" : "s");
+ System.out.println("for " + atoms[mataList[0]] +
atoms[mataList[1]] + " adj=" + adj + "R->rs=" + s);
break;
case STEREO_S:
- s = "s";
+ s = (adj == A_WINS ? "s" : "r");
+ System.out.println("for " + atoms[mataList[0]] +
atoms[mataList[1]] + " adj=" + adj + "S->rs=" + s);
break;
}
subRS = "";
@@ -2506,19 +2560,24 @@
if (n != rs2.length())
return NOT_RELEVANT; // TODO: ?? this may not be true -- paths with
and without O, N, C for example, that still have stereochemistry
if (rs1.equals(rs2))
- return TIED;
-
- System.out.println("testing ~RS here with " + rs1 + " and " + rs2);
+ return TIED;
+// System.out.println("testing ~RS here with " + rs1 + " and " + rs2);
return checkEnantiomer(rs1, rs2, 1, n, "~RS");
}
private int checkEnantiomer(String rs1, String rs2, int m, int n, String
rs) {
int finalScore = TIED;
+ System.out.println("???");
// "0~~R 0~~S"
for (int i = m; i < n; i++) {
+ // a score of 0 means ~ was present for both
+ // a score of 3 means one was R and one was S
+ // any other score indicates diasteriomeric
int i1 = rs.indexOf(rs1.charAt(i));
int score = i1 + rs.indexOf(rs2.charAt(i));
- if (score != 0 && score != STEREO_BOTH_RS)
+ if (score == 0)
+ continue;
+ if (score != STEREO_BOTH_RS)
return DIASTEREOMERIC;
if (finalScore == TIED)
finalScore = (i1 == STEREO_R ? A_WINS : B_WINS);
Modified: trunk/Jmol/src/org/jmol/util/Node.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Node.java 2017-05-08 20:59:30 UTC (rev
21587)
+++ trunk/Jmol/src/org/jmol/util/Node.java 2017-05-09 20:03:13 UTC (rev
21588)
@@ -98,6 +98,7 @@
public boolean isDeleted();
char getBioSmilesType();
String getCIPChirality(boolean doCalculate);
+ int getCIPChiralityCode();
void setCIPChirality(int c);
public P3 getXYZ();
Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2017-05-08 20:59:30 UTC
(rev 21587)
+++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2017-05-09 20:03:13 UTC
(rev 21588)
@@ -880,7 +880,7 @@
int buttonMods) {
if (!vwr.getMouseEnabled())
return;
- if (Logger.debuggingHigh && mode != Event.MOVED)
+ if (Logger.debuggingHigh && mode != Event.MOVED &&
vwr.getBoolean(T.testflag1))
vwr.showString("mouse action: " + mode + " " + buttonMods + " " +
Binding.getMouseActionName(Binding.getMouseAction(count, buttonMods, mode),
false), false);
if (vwr.tm.stereoDoubleDTI)
x = x << 1;
@@ -980,7 +980,7 @@
buttonMods = Binding.getButtonMods(pressAction);
}
setMouseActions(pressedCount, buttonMods, false);
- if (Logger.debuggingHigh)
+ if (Logger.debuggingHigh && vwr.getBoolean(T.testflag1))
Logger.debug(Binding.getMouseActionName(pressAction, false));
if (isDrawOrLabelAction(dragAction)) {
@@ -1264,7 +1264,7 @@
private void checkReleaseAction(int x, int y, long time, boolean
dragRelease) {
- if (Logger.debuggingHigh)
+ if (Logger.debuggingHigh && vwr.getBoolean(T.testflag1))
Logger.debug(Binding.getMouseActionName(pressAction, false));
vwr.checkInMotion(0);
vwr.setInMotion(false);
@@ -1331,7 +1331,7 @@
if (clickAction == 0)
return;
}
- if (Logger.debuggingHigh)
+ if (Logger.debuggingHigh && vwr.getBoolean(T.testflag1))
Logger.debug(Binding.getMouseActionName(clickAction, false));
if (bnd(clickAction, ACTION_clickFrank)) {
if (vwr.frankClicked(x, y)) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-08 20:59:30 UTC
(rev 21587)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-09 20:03:13 UTC
(rev 21588)
@@ -55,8 +55,19 @@
# instead of the occupancies I tried to assign in jmol.
-Jmol.___JmolVersion="14.15.3" // 2017-05-08
+Jmol.___JmolVersion="14.15.4"
+bug fix: CIP Rule 1b modification to ensure aromatic rings do not result in
false positive for R/S (binap2)
+ -- specifically that the duplicate atom is given the root distance of its
parent, not its duplicated atom
+bug fix: CIP chiral bridgehead N designations missing
+bug fix: Assignment of auxiliary r/s not functional (AY-236.201,202)
+
+new feature: set debugHigh
+ -- same as set loglevel 6 - debugging only
+ -- debugging only; not considered significant enough to increment minor
version
+
+JmolVersion="14.15.3" // 2017-05-08
+
bug fix: SMARTS search for atropisomeric bond that is in an alicyclic ring
fails (Fred Ziegler)
- used for M/P chirality check
- for example:
@@ -96,7 +107,9 @@
One structure awaiting full implementation of Rule 4b across all chirality
types, R/S, M/P, and seqCis/seqTrans
,"170":"Spp" // Jmol is missing the S -- mix of R/S and M/P for Rule 4b
-
+
+ - 939 lines
+
JmolVersion="14.15.2" // 4/29/17
bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for
cumulenes
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-05-08 20:59:30 UTC (rev
21587)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-05-09 20:03:13 UTC (rev
21588)
@@ -5268,6 +5268,7 @@
return g.strutsMultiple;
case T.testflag1:
// no PNGJ caching
+ // debug mouse actions
return g.testFlag1;
case T.testflag2:
// passed to MOCalcuation, but not used
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