Revision: 18247
http://sourceforge.net/p/jmol/code/18247
Author: hansonr
Date: 2013-05-24 02:50:58 +0000 (Fri, 24 May 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.05.23a"
PyMOL: measurement font/offsets enabled
-- adds measure ID "xxx" FONT scale face style
-- adds measure ID "xxx" OFFSET [mode, sx, sy, sz, ax, ay, az]
-- adds measure ID "xxx" OFFSET {sx, sy, sz}
code: Text.java, Object2d.java moved from shapes to modelset
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-23 23:47:30 UTC (rev 18246)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-24 02:50:58 UTC (rev 18247)
@@ -1569,26 +1569,29 @@
*/
private static void cleanSingletons(Atom[] atoms, BS bs) {
BS bsr = new BS();
- for (int pass = 0; pass < 2; pass++) {
+ int n = bs.length();
+ int pass = 0;
+ while (true) {
int offset = 1;
int iPrev = Integer.MIN_VALUE;
int iSeqLast = Integer.MIN_VALUE;
int iSeq = Integer.MIN_VALUE;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- if (!isSequential(atoms, i, iPrev))
+ for (int i = 0; i < n; i++) {
+ if (nextChain(atoms, i, iPrev))
offset++;
iSeq = atoms[i].sequenceNumber;
if (iSeq != iSeqLast) {
iSeqLast = iSeq;
offset++;
}
- if (pass == 0)
- bsr.set(offset);
- else if (!bsr.get(offset))
+ if (pass == 0) {
+ if (bs.get(i))
+ bsr.set(offset);
+ } else if (!bsr.get(offset))
bs.clear(i);
iPrev = i;
}
- if (pass == 1)
+ if (++pass == 2)
break;
BS bsnot = new BS();
for (int i = bsr.nextSetBit(0); i >= 0; i = bsr.nextSetBit(i + 1))
@@ -1598,12 +1601,12 @@
}
}
- private static boolean isSequential(Atom[] atoms, int i, int iPrev) {
+ private static boolean nextChain(Atom[] atoms, int i, int iPrev) {
if (i == 0 || iPrev < 0)
- return false;
+ return true;
Atom a = atoms[iPrev];
Atom b = atoms[i];
- return a.chainID == b.chainID && a.atomSetIndex == b.atomSetIndex;
+ return a.chainID != b.chainID;
}
/**
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