From: <ha...@us...> - 2017-06-04 02:57:08
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |