Revision: 21010
http://sourceforge.net/p/jmol/code/21010
Author: hansonr
Date: 2016-03-21 17:30:06 +0000 (Mon, 21 Mar 2016)
Log Message:
-----------
SmilesAromatic.java
SmilesSearch.java
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAromatic.java
trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAromatic.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-03-21
17:15:38 UTC (rev 21009)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-03-21
17:30:06 UTC (rev 21010)
@@ -552,11 +552,10 @@
private static void removeBridgingRings(Lst<BS> lstAromatic, Lst<SmilesRing>
lstSP2) {
BS bs = new BS();
BS bsBad = new BS();
- checkBridges(lstAromatic, bsBad, null, null, bs);
BS bsBad2 = new BS();
- checkBridges(lstSP2, bsBad2, null, null, bs);
+ checkBridges(lstAromatic, bsBad, lstAromatic, bsBad, bs);
+ checkBridges(lstSP2, bsBad2, lstSP2, bsBad2, bs);
checkBridges(lstAromatic, bsBad, lstSP2, bsBad2, bs);
-
for (int i = lstAromatic.size(); --i >= 0;)
if (bsBad.get(i))
lstAromatic.remove(i);
@@ -567,22 +566,10 @@
private static void checkBridges(Lst<?> lst, BS bsBad, Lst<?> lst2,
BS bsBad2, BS bs) {
+ boolean isSameList = (lst == lst2);
for (int i = lst.size(); --i >= 0;) {
BS bs1 = (BS) lst.get(i);
- if (lst2 == null)
- for (int j = lst.size(); --j > i;) {
- BS bs2 = (BS) lst.get(j);
- bs.clearAll();
- bs.or(bs1);
- bs.and(bs2);
- int n = bs.cardinality();
- if (n > 2) {
- bsBad.set(i);
- bsBad.set(j);
- }
- }
- else
- for (int j = lst2.size(); --j >= 0;) {
+ for (int j0 = (isSameList ? i + 1 : 0), j = lst2.size(); --j >= j0;) {
BS bs2 = (BS) lst2.get(j);
if (bs2.equals(bs1))
continue;
@@ -592,9 +579,8 @@
int n = bs.cardinality();
if (n > 2) {
bsBad.set(i);
- bsBad2.set(i);
+ bsBad2.set(j);
}
-
}
}
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-03-21 17:15:38 UTC
(rev 21009)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2016-03-21 17:30:06 UTC
(rev 21010)
@@ -552,11 +552,10 @@
private static void removeBridgingRings(Lst<BS> lstAromatic, Lst<SmilesRing>
lstSP2) {
BS bs = new BS();
BS bsBad = new BS();
- checkBridges(lstAromatic, bsBad, null, null, bs);
BS bsBad2 = new BS();
- checkBridges(lstSP2, bsBad2, null, null, bs);
+ checkBridges(lstAromatic, bsBad, lstAromatic, bsBad, bs);
+ checkBridges(lstSP2, bsBad2, lstSP2, bsBad2, bs);
checkBridges(lstAromatic, bsBad, lstSP2, bsBad2, bs);
-
for (int i = lstAromatic.size(); --i >= 0;)
if (bsBad.get(i))
lstAromatic.remove(i);
@@ -567,22 +566,10 @@
private static void checkBridges(Lst<?> lst, BS bsBad, Lst<?> lst2,
BS bsBad2, BS bs) {
+ boolean isSameList = (lst == lst2);
for (int i = lst.size(); --i >= 0;) {
BS bs1 = (BS) lst.get(i);
- if (lst2 == null)
- for (int j = lst.size(); --j > i;) {
- BS bs2 = (BS) lst.get(j);
- bs.clearAll();
- bs.or(bs1);
- bs.and(bs2);
- int n = bs.cardinality();
- if (n > 2) {
- bsBad.set(i);
- bsBad.set(j);
- }
- }
- else
- for (int j = lst2.size(); --j >= 0;) {
+ for (int j0 = (isSameList ? i + 1 : 0), j = lst2.size(); --j >= j0;) {
BS bs2 = (BS) lst2.get(j);
if (bs2.equals(bs1))
continue;
@@ -592,9 +579,8 @@
int n = bs.cardinality();
if (n > 2) {
bsBad.set(i);
- bsBad2.set(i);
+ bsBad2.set(j);
}
-
}
}
}
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