Revision: 18248
http://sourceforge.net/p/jmol/code/18248
Author: hansonr
Date: 2013-05-24 02:59:39 +0000 (Fri, 24 May 2013)
Log Message:
-----------
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
2013-05-24 02:50:58 UTC (rev 18247)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-24 02:59:39 UTC (rev 18248)
@@ -1563,6 +1563,9 @@
/**
* PyMOL does not display cartoons or traces for single-residue runs.
+ * This two-pass routine first sets bits in a residue bitset,
+ * then it clears out all singletons, and in a second pass
+ * all atom bits for not-represented residues are cleared.
*
* @param atoms
* @param bs
@@ -1572,12 +1575,11 @@
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 = 0; i < n; i++) {
- if (nextChain(atoms, i, iPrev))
+ for (int i = 0, offset = 0,
+ iPrev = Integer.MIN_VALUE,
+ iSeqLast = Integer.MIN_VALUE,
+ iSeq = Integer.MIN_VALUE; i < n; i++) {
+ if (iPrev < 0 || atoms[iPrev].chainID != atoms[i].chainID)
offset++;
iSeq = atoms[i].sequenceNumber;
if (iSeq != iSeqLast) {
@@ -1601,14 +1603,6 @@
}
}
- private static boolean nextChain(Atom[] atoms, int i, int iPrev) {
- if (i == 0 || iPrev < 0)
- return true;
- Atom a = atoms[iPrev];
- Atom b = atoms[i];
- return a.chainID != b.chainID;
- }
-
/**
* Create JmolObjects for each shape.
*
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