Merge of svn commits r2707, 2711, 2713, 2717 from 2.2 release branch.

include/openbabel/fingerprint.h

@@ -90,7 +90,11 @@ public:
       int andfp = vec1[i] & p2[i];
       int orfp = vec1[i] | p2[i];
       // Count bits
-#ifdef __GNUC__
+      /* GCC 3.4 supports a "population count" builtin, which on many targets is
+         implemented with a single instruction.  There is a fallback definition
+         in libgcc in case a target does not have one, which should be just as
+         good as the static function below.  */
+#if __GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
       andbits += __builtin_popcount(andfp);
       orbits += __builtin_popcount(orfp);
 #else

scripts/java/OBTest.java

@@ -1,3 +1,5 @@
+import org.openbabel.*
+
 public class OBTest
 {
   public OBTest()

scripts/java/README

@@ -1,9 +1,8 @@
-Open Babel for Java (JNI) 0.9
---------------------
+Open Babel for Java
+-------------------
 
 This directory contains a set of SWIG-generated interface classes for
-using the Open Babel C++ library from Java. It is currently
-experimental and has not been thoroughly tested.
+using the Open Babel C++ library from Java.
 
 The Open Babel wiki pages on Java give information on compiling and
 running Java programs with Open Babel:
@@ -11,21 +10,27 @@ http://openbabel.sourceforge.net/wiki/Java
 
 *** Linux Compilation
 
-To compile on Debian 4.0, run the following steps:
-$ export JAVA=/home/noel/Tools/jdk1.5.0_15
+  First of all, set some environment variables (remember to change the paths to correspond to your system):
+$ export JAVAHOME=/home/noel/Tools/jdk1.5.0_15
+$ export OB_JAVADIR=/home/noel/Tools/openbabel-2.2.0/scripts/java
+$ export OB_LIBDIR=/home/noel/tree/lib # The install location of libopenbabel.so
 
-I installed OB into /home/noel/tree (/lib)
-$ export tree=/home/noel/tree 
+  Next, compile the Java bindings:
+$ cd $OB_JAVADIR
+$ g++ -c -fpic openbabel_java.cpp -I../../include -I$JAVAHOME/include -I$JAVAHOME/include/linux
+$ export LD_LIBRARY_PATH=$OB_LIBDIR
+$ g++ -shared -L$OB_LIBDIR openbabel_java.o -lopenbabel -o libopenbabel.so
 
-$ cd /home/noel/Tools/openbabel/scripts/java
-$ $JAVA/bin/javac *.java
-$ g++ -c -fpic openbabel_java.cpp -I../../include -I$JAVA/include -I$JAVA/include/linux
-$ g++ -shared -L$tree/lib openbabel_java.o -lopenbabel -o libopenbabel.so
-$ export LD_LIBRARY_PATH=.:$tree/lib
-$ LD_PRELOAD=$tree/lib/libopenbabel.so $JAVA/bin/java OBTest
+  Compile and run the test program:
+$ export CLASSPATH=.:$OB_JAVADIR/openbabel.jar
+$ $JAVAHOME/bin/javac OBTest.java
+$ export LD_LIBRARY_PATH=$OB_JAVADIR:$OB_LIBDIR
+$ $JAVAHOME/bin/java OBTest
 
+  If you get the output "Benzene has 0 atoms", you need to preload the OpenBabel library as follows:
+$ LD_PRELOAD=$OB_LIBDIR/libopenbabel.so $JAVAHOME/bin/java OBTest
 
-*** Mac OS X Compliation
+*** Mac OS X Compilation
 
 % javac *.java
 % g++ -c -I/System/Library/Frameworks/JavaVM.framework/Headers \
@@ -33,9 +38,6 @@ openbabel_java.cpp
 % g++ -dynamiclib -o libopenbabel.jnilib openbabel_java.o \
 -framework JavaVM -L/usr/local/lib -lopenbabel
 
-
-*** Running Programs
-
 To run the OBTest program:
 % java OBTest
 

scripts/openbabel-ruby.i

@@ -79,6 +79,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %rename(inc)   *::operator++;
 %rename(good)  *::operator bool;
 %rename(deref) *::operator->;
+%ignore *::DescribeBits;
 %import <openbabel/babelconfig.h>
 
 %include <openbabel/data.h>
@@ -93,7 +94,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %include <openbabel/griddata.h>
 
 %import <openbabel/chains.h>
-%import <openbabel/bitvec.h>
+//# %import <openbabel/bitvec.h>
 %import <openbabel/typer.h>
 
 %include <openbabel/plugin.h>
@@ -109,7 +110,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %include <openbabel/ring.h>
 %include <openbabel/parsmart.h>
 
-#%include <openbabel/fingerprint.h>
+%include <openbabel/fingerprint.h>
 %include <openbabel/descriptor.h>
 %include <openbabel/forcefield.h>
 
@@ -127,8 +128,8 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %ignore OBAtomBondIter(OBAtom &);
 %ignore OBMolAngleIter(OBMol &);
 %ignore OBMolAtomIter(OBMol &);
-%ignore OBMolAtomBFSIter(OBMol &);
-%ignore OBMolAtomDFSIter(OBMol &);
+%ignore OBMolAtomBFSIter;
+%ignore OBMolAtomDFSIter;
 %ignore OBMolBondIter(OBMol &);
 %ignore OBMolPairIter(OBMol &);
 %ignore OBMolRingIter(OBMol &);

src/fingerprint.cpp

@@ -100,7 +100,11 @@ namespace OpenBabel
         int andfp = vec1[i] & vec2[i];
         int orfp = vec1[i] | vec2[i];
         //Count bits
-#ifdef __GNUC__
+      /* GCC 3.4 supports a "population count" builtin, which on many targets is
+         implemented with a single instruction.  There is a fallback definition
+         in libgcc in case a target does not have one, which should be just as
+         good as the static function below.  */
+#if __GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
         andbits += __builtin_popcount(andfp);
         orbits += __builtin_popcount(orfp);
 #else