Revision: 21628
http://sourceforge.net/p/jmol/code/21628
Author: hansonr
Date: 2017-06-04 02:57:04 +0000 (Sun, 04 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.17.2"
bug fix: WRITE FILE not working when file has been cached.
bug fix: array.find("regex...","") does not reset RegExp each time it runs
RegExp.exec() so does not find all possibilities
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/OC.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/util/OC.java
===================================================================
--- trunk/Jmol/src/javajs/util/OC.java 2017-05-31 03:16:55 UTC (rev 21627)
+++ trunk/Jmol/src/javajs/util/OC.java 2017-06-04 02:57:04 UTC (rev 21628)
@@ -217,6 +217,8 @@
public void write(byte[] buf, int i, int len) {
if (os == null)
initOS();
+ if (len < 0)
+ len = buf.length - i;
try {
os.write(buf, i, len);
} catch (IOException e) {
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-31 03:16:55 UTC
(rev 21627)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-04 02:57:04 UTC
(rev 21628)
@@ -1486,7 +1486,8 @@
if (Logger.debugging) {
if (sphere < MAX_PATH) // Logger
myPath = (parent != null ? parent.myPath + "-" : "") + this; //
Logger
- Logger.info("new CIPAtom " + myPath);
+ if (Logger.debuggingHigh)
+ Logger.info("new CIPAtom " + myPath);
}
return this;
}
@@ -1681,7 +1682,7 @@
priorities[i] = 0;
}
- if (Logger.debugging) {
+ if (Logger.debuggingHigh) {
Logger.info(root + "---sortSubstituents---" + this);
for (int i = 0; i < 4; i++) { // Logger
Logger.info(getRuleName() + ": " + this + "[" + i + "]="
@@ -1816,7 +1817,7 @@
break;
}
}
- if ((Logger.debugging) && atoms[2].atom != null && atoms[2].elemNo != 1)
{
+ if ((Logger.debuggingHigh) && atoms[2].atom != null && atoms[2].elemNo
!= 1) {
Logger.info(dots() + atom + " nPriorities = " + nPriorities);
for (int i = 0; i < 4; i++) { // Logger
Logger.info(dots() + myPath + "[" + i + "]=" + atoms[i] + " "
@@ -1986,20 +1987,20 @@
int finalScore = (nAtoms == 0 ? B_WINS : TIED), absScore =
Integer.MAX_VALUE;
for (int i = 0; i < nAtoms; i++) {
CIPAtom ai = atoms[i], bi = b.atoms[i];
- if (Logger.debugging && ai.isHeavy() && bi.isHeavy())
+ if (Logger.debuggingHigh && ai.isHeavy() && bi.isHeavy())
Logger.info(ai.dots() + "compareDeep sub " + this + "." + ai + " " +
b + "." + bi);
int score = ai.breakTie(bi, sphere + 1);
if (score == TIED)
continue;
int abs = Math.abs(score);
- if (Logger.debugging && ai.isHeavy() && bi.isHeavy())
- Logger.info(ai.dots() + "compareDeep sub " + ai + " " + bi + ": " +
score + "/" + finalScore);
if (abs < absScore) {
+ if (Logger.debugging && ai.isHeavy() && bi.isHeavy())
+ Logger.info(ai.dots() + "compareDeep sub " + ai + " " + bi + ": "
+ score + "/" + finalScore);
absScore = abs;
finalScore = score;
}
}
- if (Logger.debugging)
+ if (Logger.debuggingHigh)
Logger.info(dots() + "compareDeep " + this + " " + b + ": " +
finalScore);
return finalScore;
}
@@ -2173,7 +2174,7 @@
auxEZ = STEREO_BOTH_EZ;
}
alkeneParent.auxEZ = auxEZ;
- if (Logger.debugging)
+ if (Logger.debuggingHigh)
Logger.info("getZaux " + alkeneParent + " " + auxEZ);
return auxEZ;
}
@@ -2227,7 +2228,7 @@
CIPAtom thisAtom = this, newSub, oldParent = fromAtom, oldSub =
newParent;
// create path back to root
while (oldParent.parent != null && oldParent.parent.atoms[0] != null) {
- if (Logger.debugging)
+ if (Logger.debuggingHigh)
Logger.info("path:" + oldParent.parent + "->" + oldParent);
path.addLast(oldParent = oldParent.parent);
}
@@ -2265,7 +2266,7 @@
CIPAtom newSub) {
for (int i = 0; i < 4; i++)
if (atoms[i] == oldSub || newParent == null && atoms[i].atom == null) {
- if (Logger.debugging)
+ if (Logger.debuggingHigh)
Logger.info("reversed: " + newParent + "->" + this + "->" +
newSub);
parent = newParent;
atoms[i] = newSub;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-31 03:16:55 UTC
(rev 21627)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-04 02:57:04 UTC
(rev 21628)
@@ -58,6 +58,9 @@
Jmol.___JmolVersion="14.17.2"
+bug fix: WRITE FILE not working when file has been cached.
+bug fix: array.find("regex...","") does not reset RegExp each time it runs
RegExp.exec() so does not find all possibilities
+
code: CIPChirality.java fully interfaced using SimpleNode and SimpleEdge
JmolVersion="14.17.1" // 2017.05.27
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