Revision: 21651
http://sourceforge.net/p/jmol/code/21651
Author: hansonr
Date: 2017-07-06 07:19:40 +0000 (Thu, 06 Jul 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.1"
new feature: BZ2 compressed file reader
-- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
-- Apache license
bug fix: ADF reader not accepting Xx.name atom ids
bug fix: ADF reader not accepting Xx.name atom ids
bug fix: SMILES generator can show wrong @/@@ or stereochemical type for some
allenes and cumulenes
bug fix: CIPChirality additional Rules 1b, 4b, and 4c fixes (substituted
cubanes; multiple branched branches; 841 lines)
Modified Paths:
--------------
trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/AdfReader.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/ActionManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
===================================================================
--- trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
2017-07-06 00:13:14 UTC (rev 21650)
+++ trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
2017-07-06 07:19:40 UTC (rev 21651)
@@ -116,6 +116,7 @@
* stream to be the first one after the magic. Thus callers have
* to skip the first two bytes. Otherwise this constructor will
* throw an exception. </p>
+ * @param in
*
* @throws IOException
* if the stream content is malformed or an I/O error occurs.
@@ -161,15 +162,13 @@
setupBlock();
}
- /** {@inheritDoc} */
- @Override
- public int read() throws IOException {
- if (this.in != null) {
- return read0();
- } else {
- throw new IOException("stream closed");
- }
- }
+ /** {@inheritDoc} */
+ @Override
+ public int read() throws IOException {
+ if (this.in == null)
+ throw new IOException("stream closed");
+ return read0();
+ }
/*
* (non-Javadoc)
@@ -267,17 +266,17 @@
throw new IOException("Empty InputStream");
}
} else {
- int magic0 = this.in.read();
+ int magic0 = readByteAsInt();
if (magic0 == -1) {
return false;
}
- int magic1 = this.in.read();
+ int magic1 = readByteAsInt();
if (magic0 != 'B' || magic1 != 'Z') {
throw new IOException("Garbage after a valid BZip2 stream");
}
}
- int magic2 = this.in.read();
+ int magic2 = readByteAsInt();
if (magic2 != 'h') {
throw new IOException(isFirstStream
? "Stream is not in the BZip2 format"
@@ -284,7 +283,7 @@
: "Garbage after a valid BZip2 stream");
}
- int blockSize = this.in.read();
+ int blockSize = readByteAsInt();
if ((blockSize < '1') || (blockSize > '9')) {
throw new IOException("Stream is not BZip2 formatted: illegal "
+ "blocksize " + (char) blockSize);
@@ -298,66 +297,76 @@
return true;
}
- private void initBlock() throws IOException {
- char magic0;
- char magic1;
- char magic2;
- char magic3;
- char magic4;
- char magic5;
+ public synchronized int readByteAsInt() throws IOException {
+ /**
+ * @j2sNative
+ *
+ * return(this.in.readByteAsInt());
+ */
+ {
+ return in.read();
+ }
+ }
- while (true) {
- // Get the block magic bytes.
- magic0 = bsGetUByte();
- magic1 = bsGetUByte();
- magic2 = bsGetUByte();
- magic3 = bsGetUByte();
- magic4 = bsGetUByte();
- magic5 = bsGetUByte();
+ private void initBlock() throws IOException {
+ char magic0;
+ char magic1;
+ char magic2;
+ char magic3;
+ char magic4;
+ char magic5;
- // If isn't end of stream magic, break out of the loop.
- if (magic0 != 0x17 || magic1 != 0x72 || magic2 != 0x45
- || magic3 != 0x38 || magic4 != 0x50 || magic5 != 0x90) {
- break;
- }
+ while (true) {
+ // Get the block magic bytes.
+ magic0 = bsGetUByte();
+ magic1 = bsGetUByte();
+ magic2 = bsGetUByte();
+ magic3 = bsGetUByte();
+ magic4 = bsGetUByte();
+ magic5 = bsGetUByte();
- // End of stream was reached. Check the combined CRC and
- // advance to the next .bz2 stream if decoding concatenated
- // streams.
- if (complete()) {
- return;
- }
- }
+ // If isn't end of stream magic, break out of the loop.
+ if (magic0 != 0x17 || magic1 != 0x72 || magic2 != 0x45 || magic3 != 0x38
+ || magic4 != 0x50 || magic5 != 0x90) {
+ break;
+ }
- if (magic0 != 0x31 || // '1'
- magic1 != 0x41 || // ')'
- magic2 != 0x59 || // 'Y'
- magic3 != 0x26 || // '&'
- magic4 != 0x53 || // 'S'
- magic5 != 0x59 // 'Y'
- ) {
- this.currentState = EOF;
- throw new IOException("bad block header");
- } else {
- this.storedBlockCRC = bsGetInt();
- this.blockRandomised = bsR(1) == 1;
+ // End of stream was reached. Check the combined CRC and
+ // advance to the next .bz2 stream if decoding concatenated
+ // streams.
+ if (complete()) {
+ return;
+ }
+ }
- /**
- * Allocate data here instead in constructor, so we do not
- * allocate it if the input file is empty.
- */
- if (this.data == null) {
- this.data = new Data(this.blockSize100k);
- }
+ if (magic0 != 0x31 || // '1'
+ magic1 != 0x41 || // ')'
+ magic2 != 0x59 || // 'Y'
+ magic3 != 0x26 || // '&'
+ magic4 != 0x53 || // 'S'
+ magic5 != 0x59 // 'Y'
+ ) {
+ this.currentState = EOF;
+ throw new IOException("bad block header");
+ }
+ this.storedBlockCRC = bsGetInt();
+ this.blockRandomised = bsR(1) == 1;
- // currBlockNo++;
- getAndMoveToFrontDecode();
-
- this.crc.initialiseCRC();
- this.currentState = START_BLOCK_STATE;
- }
+ /**
+ * Allocate data here instead in constructor, so we do not allocate it if
+ * the input file is empty.
+ */
+ if (this.data == null) {
+ this.data = new Data(this.blockSize100k);
}
+ // currBlockNo++;
+ getAndMoveToFrontDecode();
+
+ this.crc.initialiseCRC();
+ this.currentState = START_BLOCK_STATE;
+ }
+
private void endBlock() throws IOException {
this.computedBlockCRC = this.crc.getFinalCRC();
@@ -415,7 +424,7 @@
if (bsLiveShadow < n) {
final InputStream inShadow = this.in;
do {
- int thech = inShadow.read();
+ int thech = readByteAsInt();//inShadow.read();
if (thech < 0) {
throw new IOException("unexpected end of stream");
@@ -437,7 +446,7 @@
int bsBuffShadow = this.bsBuff;
if (bsLiveShadow < 1) {
- int thech = this.in.read();
+ int thech = readByteAsInt();
if (thech < 0) {
throw new IOException("unexpected end of stream");
@@ -462,6 +471,13 @@
/**
* Called by createHuffmanDecodingTables() exclusively.
+ * @param limit
+ * @param base
+ * @param perm
+ * @param length
+ * @param minLen
+ * @param maxLen
+ * @param alphaSize
*/
private static void hbCreateDecodeTables(final int[] limit,
final int[] base,
@@ -588,6 +604,8 @@
/**
* Called by recvDecodingTables() exclusively.
+ * @param alphaSize
+ * @param nGroups
*/
private void createHuffmanDecodingTables(final int alphaSize,
final int nGroups) {
@@ -617,226 +635,217 @@
}
}
- private void getAndMoveToFrontDecode() throws IOException {
- this.origPtr = bsR(24);
- recvDecodingTables();
+ private void getAndMoveToFrontDecode() throws IOException {
+ this.origPtr = bsR(24);
+ recvDecodingTables();
- final InputStream inShadow = this.in;
- final Data dataShadow = this.data;
- final byte[] ll8 = dataShadow.ll8;
- final int[] unzftab = dataShadow.unzftab;
- final byte[] selector = dataShadow.selector;
- final byte[] seqToUnseq = dataShadow.seqToUnseq;
- final char[] yy = dataShadow.getAndMoveToFrontDecode_yy;
- final int[] minLens = dataShadow.minLens;
- final int[][] limit = dataShadow.limit;
- final int[][] base = dataShadow.base;
- final int[][] perm = dataShadow.perm;
- final int limitLast = this.blockSize100k * 100000;
+ final InputStream inShadow = this.in;
+ final Data dataShadow = this.data;
+ final byte[] ll8 = dataShadow.ll8;
+ final int[] unzftab = dataShadow.unzftab;
+ final byte[] selector = dataShadow.selector;
+ final byte[] seqToUnseq = dataShadow.seqToUnseq;
+ final char[] yy = dataShadow.getAndMoveToFrontDecode_yy;
+ final int[] minLens = dataShadow.minLens;
+ final int[][] limit = dataShadow.limit;
+ final int[][] base = dataShadow.base;
+ final int[][] perm = dataShadow.perm;
+ final int limitLast = this.blockSize100k * 100000;
- /*
- Setting up the unzftab entries here is not strictly
- necessary, but it does save having to do it later
- in a separate pass, and so saves a block's worth of
- cache misses.
- */
- for (int i = 256; --i >= 0;) {
- yy[i] = (char) i;
- unzftab[i] = 0;
- }
+ /*
+ Setting up the unzftab entries here is not strictly
+ necessary, but it does save having to do it later
+ in a separate pass, and so saves a block's worth of
+ cache misses.
+ */
+ for (int i = 256; --i >= 0;) {
+ yy[i] = (char) i;
+ unzftab[i] = 0;
+ }
- int groupNo = 0;
- int groupPos = G_SIZE - 1;
- final int eob = this.nInUse + 1;
- int nextSym = getAndMoveToFrontDecode0(0);
- int bsBuffShadow = this.bsBuff;
- int bsLiveShadow = this.bsLive;
- int lastShadow = -1;
- int zt = selector[groupNo] & 0xff;
- int[] base_zt = base[zt];
- int[] limit_zt = limit[zt];
- int[] perm_zt = perm[zt];
- int minLens_zt = minLens[zt];
+ int groupNo = 0;
+ int groupPos = G_SIZE - 1;
+ final int eob = this.nInUse + 1;
+ int nextSym = getAndMoveToFrontDecode0(0);
+ int bsBuffShadow = this.bsBuff;
+ int bsLiveShadow = this.bsLive;
+ int lastShadow = -1;
+ int zt = selector[groupNo] & 0xff;
+ int[] base_zt = base[zt];
+ int[] limit_zt = limit[zt];
+ int[] perm_zt = perm[zt];
+ int minLens_zt = minLens[zt];
- while (nextSym != eob) {
- if ((nextSym == RUNA) || (nextSym == RUNB)) {
- int s = -1;
+ while (nextSym != eob) {
+ if ((nextSym == RUNA) || (nextSym == RUNB)) {
+ int s = -1;
- for (int n = 1; true; n <<= 1) {
- if (nextSym == RUNA) {
- s += n;
- } else if (nextSym == RUNB) {
- s += n << 1;
- } else {
- break;
- }
+ for (int n = 1; true; n <<= 1) {
+ if (nextSym == RUNA) {
+ s += n;
+ } else if (nextSym == RUNB) {
+ s += n << 1;
+ } else {
+ break;
+ }
- if (groupPos == 0) {
- groupPos = G_SIZE - 1;
- zt = selector[++groupNo] & 0xff;
- base_zt = base[zt];
- limit_zt = limit[zt];
- perm_zt = perm[zt];
- minLens_zt = minLens[zt];
- } else {
- groupPos--;
- }
+ if (groupPos == 0) {
+ groupPos = G_SIZE - 1;
+ zt = selector[++groupNo] & 0xff;
+ base_zt = base[zt];
+ limit_zt = limit[zt];
+ perm_zt = perm[zt];
+ minLens_zt = minLens[zt];
+ } else {
+ groupPos--;
+ }
- int zn = minLens_zt;
+ int zn = minLens_zt;
- // Inlined:
- // int zvec = bsR(zn);
- while (bsLiveShadow < zn) {
- final int thech = inShadow.read();
- if (thech >= 0) {
- bsBuffShadow = (bsBuffShadow << 8) | thech;
- bsLiveShadow += 8;
- continue;
- } else {
- throw new IOException("unexpected end of stream");
- }
- }
- int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 <<
zn) - 1);
- bsLiveShadow -= zn;
+ // Inlined:
+ // int zvec = bsR(zn);
+ while (bsLiveShadow < zn) {
+ final int thech = readByteAsInt();//inShadow.read();
+ if (thech < 0)
+ throw new IOException("unexpected end of stream");
- while (zvec > limit_zt[zn]) {
- zn++;
- while (bsLiveShadow < 1) {
- final int thech = inShadow.read();
- if (thech >= 0) {
- bsBuffShadow = (bsBuffShadow << 8) | thech;
- bsLiveShadow += 8;
- continue;
- } else {
- throw new IOException("unexpected end of
stream");
- }
- }
- bsLiveShadow--;
- zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) &
1);
- }
- nextSym = perm_zt[zvec - base_zt[zn]];
- }
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ }
+ int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 << zn) - 1);
+ bsLiveShadow -= zn;
- final byte ch = seqToUnseq[yy[0]];
- unzftab[ch & 0xff] += s + 1;
+ while (zvec > limit_zt[zn]) {
+ zn++;
+ while (bsLiveShadow < 1) {
+ final int thech = readByteAsInt();//inShadow.read();
+ if (thech < 0)
+ throw new IOException("unexpected end of stream");
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ }
+ bsLiveShadow--;
+ zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
+ }
+ nextSym = perm_zt[zvec - base_zt[zn]];
+ }
- while (s-- >= 0) {
- ll8[++lastShadow] = ch;
- }
+ final byte ch = seqToUnseq[yy[0]];
+ unzftab[ch & 0xff] += s + 1;
- if (lastShadow >= limitLast) {
- throw new IOException("block overrun");
- }
- } else {
- if (++lastShadow >= limitLast) {
- throw new IOException("block overrun");
- }
+ while (s-- >= 0) {
+ ll8[++lastShadow] = ch;
+ }
- final char tmp = yy[nextSym - 1];
- unzftab[seqToUnseq[tmp] & 0xff]++;
- ll8[lastShadow] = seqToUnseq[tmp];
+ if (lastShadow >= limitLast) {
+ throw new IOException("block overrun");
+ }
+ } else {
+ if (++lastShadow >= limitLast) {
+ throw new IOException("block overrun");
+ }
- /*
- This loop is hammered during decompression,
- hence avoid native method call overhead of
- System.arraycopy for very small ranges to copy.
- */
- if (nextSym <= 16) {
- for (int j = nextSym - 1; j > 0;) {
- yy[j] = yy[--j];
- }
- } else {
- System.arraycopy(yy, 0, yy, 1, nextSym - 1);
- }
+ final char tmp = yy[nextSym - 1];
+ unzftab[seqToUnseq[tmp] & 0xff]++;
+ ll8[lastShadow] = seqToUnseq[tmp];
- yy[0] = tmp;
+ /*
+ This loop is hammered during decompression,
+ hence avoid native method call overhead of
+ System.arraycopy for very small ranges to copy.
+ */
+ if (nextSym <= 16) {
+ for (int j = nextSym - 1; j > 0;) {
+ yy[j] = yy[--j];
+ }
+ } else {
+ System.arraycopy(yy, 0, yy, 1, nextSym - 1);
+ }
- if (groupPos == 0) {
- groupPos = G_SIZE - 1;
- zt = selector[++groupNo] & 0xff;
- base_zt = base[zt];
- limit_zt = limit[zt];
- perm_zt = perm[zt];
- minLens_zt = minLens[zt];
- } else {
- groupPos--;
- }
+ yy[0] = tmp;
- int zn = minLens_zt;
+ if (groupPos == 0) {
+ groupPos = G_SIZE - 1;
+ zt = selector[++groupNo] & 0xff;
+ base_zt = base[zt];
+ limit_zt = limit[zt];
+ perm_zt = perm[zt];
+ minLens_zt = minLens[zt];
+ } else {
+ groupPos--;
+ }
- // Inlined:
- // int zvec = bsR(zn);
- while (bsLiveShadow < zn) {
- final int thech = inShadow.read();
- if (thech >= 0) {
- bsBuffShadow = (bsBuffShadow << 8) | thech;
- bsLiveShadow += 8;
- continue;
- } else {
- throw new IOException("unexpected end of stream");
- }
- }
- int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 << zn)
- 1);
- bsLiveShadow -= zn;
+ int zn = minLens_zt;
- while (zvec > limit_zt[zn]) {
- zn++;
- while (bsLiveShadow < 1) {
- final int thech = inShadow.read();
- if (thech >= 0) {
- bsBuffShadow = (bsBuffShadow << 8) | thech;
- bsLiveShadow += 8;
- continue;
- } else {
- throw new IOException("unexpected end of stream");
- }
- }
- bsLiveShadow--;
- zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
- }
- nextSym = perm_zt[zvec - base_zt[zn]];
- }
+ // Inlined:
+ // int zvec = bsR(zn);
+ while (bsLiveShadow < zn) {
+ final int thech = readByteAsInt();//inShadow.read();
+ if (thech < 0)
+ throw new IOException("unexpected end of stream");
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
}
+ int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 << zn) - 1);
+ bsLiveShadow -= zn;
- this.last = lastShadow;
- this.bsLive = bsLiveShadow;
- this.bsBuff = bsBuffShadow;
+ while (zvec > limit_zt[zn]) {
+ zn++;
+ while (bsLiveShadow < 1) {
+ final int thech = readByteAsInt();//inShadow.read();
+ if (thech <0)
+ throw new IOException("unexpected end of stream");
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ }
+ bsLiveShadow--;
+ zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
+ }
+ nextSym = perm_zt[zvec - base_zt[zn]];
+ }
}
- private int getAndMoveToFrontDecode0(final int groupNo)
- throws IOException {
- final InputStream inShadow = this.in;
- final Data dataShadow = this.data;
- final int zt = dataShadow.selector[groupNo] & 0xff;
- final int[] limit_zt = dataShadow.limit[zt];
- int zn = dataShadow.minLens[zt];
- int zvec = bsR(zn);
- int bsLiveShadow = this.bsLive;
- int bsBuffShadow = this.bsBuff;
+ this.last = lastShadow;
+ this.bsLive = bsLiveShadow;
+ this.bsBuff = bsBuffShadow;
+ }
- while (zvec > limit_zt[zn]) {
- zn++;
- while (bsLiveShadow < 1) {
- final int thech = inShadow.read();
+ private int getAndMoveToFrontDecode0(final int groupNo) throws IOException {
+ final InputStream inShadow = this.in;
+ final Data dataShadow = this.data;
+ final int zt = dataShadow.selector[groupNo] & 0xff;
+ final int[] limit_zt = dataShadow.limit[zt];
+ int zn = dataShadow.minLens[zt];
+ int zvec = bsR(zn);
+ int bsLiveShadow = this.bsLive;
+ int bsBuffShadow = this.bsBuff;
- if (thech >= 0) {
- bsBuffShadow = (bsBuffShadow << 8) | thech;
- bsLiveShadow += 8;
- continue;
- } else {
- throw new IOException("unexpected end of stream");
- }
- }
- bsLiveShadow--;
- zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
- }
+ while (zvec > limit_zt[zn]) {
+ zn++;
+ while (bsLiveShadow < 1) {
+ final int thech = readByteAsInt();//inShadow.read();
- this.bsLive = bsLiveShadow;
- this.bsBuff = bsBuffShadow;
+ if (thech < 0)
+ throw new IOException("unexpected end of stream");
- return dataShadow.perm[zt][zvec - dataShadow.base[zt][zn]];
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ }
+ bsLiveShadow--;
+ zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
}
+ this.bsLive = bsLiveShadow;
+ this.bsBuff = bsBuffShadow;
+
+ return dataShadow.perm[zt][zvec - dataShadow.base[zt][zn]];
+ }
+
private void setupBlock() throws IOException {
if (this.data == null) {
return;
@@ -1033,6 +1042,8 @@
* is known. I don't initialize it at construction time to
* avoid unnecessary memory allocation when compressing small
* files.
+ * @param length
+ * @return int array
*/
final int[] initTT(int length) {
int[] ttShadow = this.tt;
@@ -1050,6 +1061,7 @@
}
+ @SuppressWarnings("unused")
private static void reportCRCError() throws IOException {
// The clean way would be to throw an exception.
//throw new IOException("crc error");
Modified: trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
===================================================================
--- trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
2017-07-06 00:13:14 UTC (rev 21650)
+++ trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
2017-07-06 07:19:40 UTC (rev 21651)
@@ -13,7 +13,7 @@
* @throws IOException
*/
public CBZip2InputStream getStream(InputStream is) throws IOException {
- is.read(new byte[2]);
+ is.read(new byte[2], 0, 2);
return new CBZip2InputStream(is);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/AdfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/AdfReader.java
2017-07-06 00:13:14 UTC (rev 21650)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/AdfReader.java
2017-07-06 07:19:40 UTC (rev 21651)
@@ -161,10 +161,15 @@
if (tokens.length < 5)
break;
String symbol = tokens[1];
+ String name = null;
+ if (symbol.indexOf(".") >= 0) {
+ name = symbol;
+ symbol = symbol.substring(0, symbol.indexOf("."));
+ }
if (JmolAdapter.getElementNumber(symbol) < 1)
nXX++;
else
- addAtomXYZSymName(tokens, pt0, symbol, null);
+ addAtomXYZSymName(tokens, pt0, symbol, name);
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-06 00:13:14 UTC
(rev 21650)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-06 07:19:40 UTC
(rev 21651)
@@ -1574,6 +1574,7 @@
* @param isParentBond
* @return this
*/
+ @SuppressWarnings("unchecked")
CIPAtom create(SimpleNode atom, CIPAtom parent, boolean isAlkene,
boolean isDuplicate, boolean isParentBond) {
this.id = ++ptID;
@@ -1599,9 +1600,9 @@
htPathPoints = new Hashtable<Integer, Integer>();
} else if (parent != null) {
rootSubstituent = parent.rootSubstituent;
- htPathPoints = rootSubstituent.htPathPoints;
+ htPathPoints = (Map<Integer, Integer>) ((Hashtable<Integer, Integer>)
parent.htPathPoints).clone();
}
- this.bsPath = (parent == null ? new BS() : BSUtil.copy(parent.bsPath));
+ bsPath = (parent == null ? new BS() : BSUtil.copy(parent.bsPath));
sp2Duplicate = isDuplicate;
@@ -1625,15 +1626,15 @@
rootSubstituent.spiroEnd = parent;
} else if (bsPath.get(atomIndex)) {
isDuplicate = true;
- rootDistance = (isParentBond ? parent.sphere :
rootSubstituent.htPathPoints.get(
+ rootDistance = (isParentBond ? parent.sphere : htPathPoints.get(
Integer.valueOf(atomIndex)).intValue());
} else {
bsPath.set(atomIndex);
- rootSubstituent.htPathPoints.put(Integer.valueOf(atomIndex),
+ htPathPoints.put(Integer.valueOf(atomIndex),
Integer.valueOf(rootDistance));
}
this.isDuplicate = isDuplicate;
- if (Logger.debuggingHigh) {
+ if (Logger.debugging) {
if (sphere < MAX_PATH) // Logger
myPath = (parent != null ? parent.myPath + "-" : "") + this; //
Logger
Logger.info("new CIPAtom " + myPath);
@@ -2026,6 +2027,7 @@
// Two duplicates of the same atom are always tied
// if they have the same root distance.
+// System.out.println("breaking tie for \n" + this.myPath + "\n" +
b.myPath);
if (isDuplicate && b.isDuplicate && atom == b.atom
&& rootDistance == b.rootDistance)
return TIED;
@@ -2066,8 +2068,9 @@
//
// The rules require that we first only look at just the atoms, so OOC
beats OOH.
- if ((score = compareShallowly(b, sphere)) != TIED)
+ if ((score = compareShallowly(b, sphere)) != TIED) {
return score;
+ }
// Phase II -- check deeply using breakTie
//
@@ -2537,7 +2540,7 @@
}
- if (score == A_WINS || score == B_WINS) // Logger
+ if (Logger.debugging && (score == A_WINS || score == B_WINS))
Logger.info((score == A_WINS ? a : b) + " > " + (score == A_WINS ? b :
a) + " by " + reason + "\n"); // Logger
// no tie-breaking for Rules 4b or 5
@@ -2547,26 +2550,31 @@
/**
* Combine all subpaths
- * @param ignore atom to ignore (parent)
+ *
+ * @param ignore
+ * atom to ignore (parent)
*/
void generateRule4Paths(CIPAtom ignore) {
-
+
getRule4PriorityPaths("", ignore.atom);
rootRule4Paths = new Lst<String[]>();
appendRule4Paths(this, new String[3]);
- getRule4Counts(rule4Count = new Object[] { null, zero, zero,
Integer.valueOf(10000)});
-
+ getRule4Counts(rule4Count = new Object[] { null, zero, zero,
+ Integer.valueOf(10000) });
+
if (Logger.debugging) {
Logger.info("Rule 4b paths for " + this + "=\n");
- for (int i = 0; i < rootRule4Paths.size(); i++) { // Logger
- String s = rootRule4Paths.get(i)[0].toString(); // Logger
- int prefixLen = rootRule4Paths.get(i)[1].length(); // Logger
- while (prefixString.length() < prefixLen) // Logger
- prefixString += prefixString; // Logger
- Logger.info(prefixString.substring(0, prefixLen) +
s.substring(prefixLen) + " " + priorityPath);
+ for (int i = 0; i < rootRule4Paths.size(); i++) { // Logger
+ String s = rootRule4Paths.get(i)[0].toString(); // Logger
+ int prefixLen = rootRule4Paths.get(i)[1].length(); // Logger
+ while (prefixString.length() < prefixLen)
+ // Logger
+ prefixString += prefixString; // Logger
+ Logger.info(prefixString.substring(0, prefixLen)
+ + s.substring(prefixLen) + " " + priorityPath);
+ }
+ Logger.info("");
}
- Logger.info("");
- }
}
/**
@@ -2650,8 +2658,7 @@
private String getRule4ReferenceDescriptor() {
if (rule4Count == null)
return ("RCM".indexOf(auxChirality) >= 0 ? "R" : "S");
- int nR = ((Integer) rule4Count[1]).intValue();
- int nS = ((Integer) rule4Count[2]).intValue();
+ int nR = ((Integer) rule4Count[1]).intValue(), nS = ((Integer)
rule4Count[2]).intValue();
return (nR > nS ? "R" : nR < nS ? "S" : "RS");
}
@@ -2739,9 +2746,8 @@
}
/**
- * Creates a list of downstream (higher-sphere)
- * auxiliary chirality designators, starting with
- * those furthest from the root.
+ * Creates a list of downstream (higher-sphere) auxiliary chirality
+ * designators, starting with those furthest from the root.
*
* @param node1
* first node; sphere 1
@@ -2783,10 +2789,10 @@
nRS++;
subRS = ssub;
prevIsChiral = true;
- } else if (!prevIsChiral && priorities[i] == priorities[i - 1]) {
- // two groups have the same priority, and neither has a
stereocenter
- return "~";
} else {
+ if (!prevIsChiral && priorities[i] == priorities[i - 1])
+ // two groups have the same priority, and neither has a
stereocenter
+ return "~";
prevIsChiral = false;
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2017-07-06 00:13:14 UTC
(rev 21650)
+++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2017-07-06 07:19:40 UTC
(rev 21651)
@@ -1819,12 +1819,14 @@
case PICKING_LABEL:
if (bnd(clickAction, ACTION_pickLabel)) {
runScript("set labeltoggle {atomindex=" + atomIndex + "}");
- vwr.setStatusAtomPicked(atomIndex, null, null);
+ vwr.setStatusAtomPicked(atomIndex, "label picked", null);
}
return;
case PICKING_INVERT_STEREO:
- if (bnd(clickAction, ACTION_assignNew))
+ if (bnd(clickAction, ACTION_assignNew)) {
vwr.invertRingAt(atomIndex, true);
+ vwr.setStatusAtomPicked(atomIndex, "invert stereo", null);
+ }
return;
case PICKING_DELETE_ATOM:
if (bnd(clickAction, ACTION_deleteAtom)) {
@@ -1991,6 +1993,8 @@
try {
BS bs = vwr.getAtomBitSetEval(null, s);
vwr.select(bs, false, 0, false);
+ vwr.setStatusAtomPicked(-1, "selected: " + Escape.eBS(bs), null);
+
vwr.refresh(3, "selections set");
} catch (Exception e) {
// ignore
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-06 00:13:14 UTC
(rev 21650)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-06 07:19:40 UTC
(rev 21651)
@@ -61,9 +61,13 @@
new feature: BZ2 compressed file reader
-- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
-- Apache license
+
+bug fix: ADF reader not accepting Xx.name atom ids
+bug fix: ADF reader not accepting Xx.name atom ids
+
bug fix: SMILES generator can show wrong @/@@ or stereochemical type for some
allenes and cumulenes
-bug fix: CIPChirality additional Rule 4b and 4c fixes
+bug fix: CIPChirality additional Rules 1b, 4b, and 4c fixes (substituted
cubanes; multiple branched branches; 841 lines)
JmolVersion="14.19.1" // 2017.06.25
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