Fix UNIX builds of SVN trunk:

* */Makefile.in: Regenerate UNIX build files.

  * src/plugin.cpp: Make sure to #include <iterator> to solve GCC
  compile problem. 

  * src/descriptor.cpp: Change _isnan to IsNan, as discussed on the
  list to solve GCC compile problem.

  * scripts/*: Updated to compile. May have removed functionality
  because of plugin changes.

  * tools/obminimize.cpp, tools/obgen.cpp, tools/obenergy.cpp:
  Switch to OBPlugin::List().

ChangeLog

@@ -1,3 +1,19 @@
+2007-05-22  Geoffrey Hutchison  <babel@geoffhutchison.net>
+
+	* */Makefile.in: Regenerate UNIX build files.
+
+	* src/plugin.cpp: Make sure to #include <iterator> to solve GCC
+	compile problem. 
+
+	* src/descriptor.cpp: Change _isnan to IsNan, as discussed on the
+	list to solve GCC compile problem.
+
+	* scripts/*: Updated to compile. May have removed functionality
+	because of plugin changes.
+
+	* tools/obminimize.cpp, tools/obgen.cpp, tools/obenergy.cpp:
+	Switch to OBPlugin::List().
+
 2007-05-17  Chris Morley
 
 	* tools/obprop.cpp: mods to use new versions of logP etc.
@@ -11,7 +27,6 @@
 	* include/openbabel/fingerprint.h:comment had become
 	uncommented.
 	
-	
 2007-05-16  Noel O'Boyle <baoilleach@gmail.com>
 
 	* Added Chris's header changes to Makefile.am

include/openbabel/Makefile.in

@@ -195,13 +195,13 @@ libopenbabelinclude_HEADERS = \
 		atom.h \
 		babelconfig.h base.h bitvec.h bond.h \
 		bondtyper.h canon.h \
-		chains.h chiral.h data.h \
-		dlhandler.h fingerprint.h forcefield.h \
+		chains.h chiral.h data.h descriptor.h \
+		dlhandler.h fingerprint.h forcefield.h format.h \
 		generic.h grid.h internalcoord.h kinetics.h \
 		lineend.h  matrix.h mol.h molchrg.h \
 		obconversion.h oberror.h obiter.h \
 		obmolecformat.h obutil.h \
-		parsmart.h patty.h phmodel.h pluginiter.h \
+		parsmart.h patty.h phmodel.h plugin.h \
 		groupcontrib.h \
 		rand.h reaction.h \
 		residue.h ring.h rotamer.h rotor.h typer.h \

scripts/openbabel-java.i

@@ -18,7 +18,7 @@
 #include <openbabel/ring.h>
 #include <openbabel/obconversion.h>
 #include <openbabel/oberror.h>
-#include <openbabel/pluginiter.h>
+#include <openbabel/plugin.h>
 #include <openbabel/fingerprint.h>
 
 #include <openbabel/forcefield.h>
@@ -76,9 +76,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %include <openbabel/bitvec.h>
 %include <openbabel/typer.h>
 
-%include <openbabel/pluginiter.h>
-%template (pluginiterFingerprint) OpenBabel::PluginIter<OpenBabel::OBFingerprint>;
-%template (pluginiterForceField) OpenBabel::PluginIter<OpenBabel::OBForceField>;
+%include <openbabel/plugin.h>
 
 %include <openbabel/oberror.h>
 %include <openbabel/obconversion.h>

scripts/openbabel-perl.i

@@ -24,7 +24,7 @@
 #include <openbabel/ring.h>
 #include <openbabel/obconversion.h>
 #include <openbabel/oberror.h>
-#include <openbabel/pluginiter.h>
+#include <openbabel/plugin.h>
 #include <openbabel/fingerprint.h>
 
 #include <openbabel/forcefield.h>
@@ -84,9 +84,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %import <openbabel/bitvec.h>
 %import <openbabel/typer.h>
 
-%include <openbabel/pluginiter.h>
-%template (pluginiterFingerprint) OpenBabel::PluginIter<OpenBabel::OBFingerprint>;
-%template (pluginiterForceField) OpenBabel::PluginIter<OpenBabel::OBForceField>;
+%include <openbabel/plugin.h>
 
 %include <openbabel/oberror.h>
 %include <openbabel/obconversion.h>

scripts/openbabel-ruby.i

@@ -33,7 +33,7 @@
 #include <openbabel/ring.h>
 #include <openbabel/obconversion.h>
 #include <openbabel/oberror.h>
-#include <openbabel/pluginiter.h>
+#include <openbabel/plugin.h>
 #include <openbabel/fingerprint.h>
 
 #include <openbabel/forcefield.h>
@@ -92,9 +92,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %import <openbabel/bitvec.h>
 %import <openbabel/typer.h>
 
-%include <openbabel/pluginiter.h>
-%template (pluginiterFingerprint) OpenBabel::PluginIter<OpenBabel::OBFingerprint>;
-%template (pluginiterForceField) OpenBabel::PluginIter<OpenBabel::OBForceField>;
+%include <openbabel/plugin.h>
 
 %include <openbabel/oberror.h>
 %include <openbabel/obconversion.h>

scripts/perl/META.yml

@@ -1,7 +1,7 @@
 # http://module-build.sourceforge.net/META-spec.html
 #XXXXXXX This is a prototype!!!  It will change in the future!!! XXXXX#
 name:         Chemistry-OpenBabel
-version:      1.2.0
+version:      1.2.1
 version_from: 
 installdirs:  site
 requires:

scripts/perl/Makefile.PL

@@ -14,7 +14,7 @@ $ldfrom = "\$(OBJECT) $srcdir/.libs/libopenbabel.a -lz"
 WriteMakefile(
     'NAME'	=>  'Chemistry::OpenBabel',
     'AUTHOR'    =>  'Geoffrey Hutchison <openbabel-scripting@lists.sourceforge.net>',
-    'VERSION'   => '1.2.0',
+    'VERSION'   => '1.2.1',
     'LDFROM'    => $ldfrom,
     'CC'        => $CC,
     'LD'        => '$(CC)',

src/Makefile.in

@@ -62,20 +62,22 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
 @BUILD_SHARED_TRUE@	forcefields/libforcefields.la @LTLIBOBJS@
 am__libopenbabel_la_SOURCES_DIST = atom.cpp base.cpp bitvec.cpp \
 	bond.cpp bondtyper.cpp canon.cpp chains.cpp chiral.cpp \
-	data.cpp fingerprint.cpp forcefield.cpp generic.cpp grid.cpp \
-	kekulize.cpp matrix.cpp mol.cpp molchrg.cpp obconversion.cpp \
-	oberror.cpp obiter.cpp obutil.cpp parsmart.cpp patty.cpp \
-	phmodel.cpp rand.cpp residue.cpp ring.cpp rotor.cpp \
-	rotamer.cpp tokenst.cpp typer.cpp transform.cpp \
-	groupcontrib.cpp dlhandler_unix.cpp
+	data.cpp descriptor.cpp filters.cpp fingerprint.cpp \
+	forcefield.cpp format.cpp generic.cpp grid.cpp kekulize.cpp \
+	matrix.cpp mol.cpp molchrg.cpp obconversion.cpp oberror.cpp \
+	obiter.cpp obutil.cpp parsmart.cpp patty.cpp phmodel.cpp \
+	plugin.cpp rand.cpp residue.cpp ring.cpp rotor.cpp rotamer.cpp \
+	tokenst.cpp typer.cpp transform.cpp groupcontrib.cpp \
+	dlhandler_unix.cpp
 @BUILD_SHARED_TRUE@am__objects_1 = dlhandler_unix.lo
 am_libopenbabel_la_OBJECTS = atom.lo base.lo bitvec.lo bond.lo \
 	bondtyper.lo canon.lo chains.lo chiral.lo data.lo \
-	fingerprint.lo forcefield.lo generic.lo grid.lo kekulize.lo \
-	matrix.lo mol.lo molchrg.lo obconversion.lo oberror.lo \
-	obiter.lo obutil.lo parsmart.lo patty.lo phmodel.lo rand.lo \
-	residue.lo ring.lo rotor.lo rotamer.lo tokenst.lo typer.lo \
-	transform.lo groupcontrib.lo $(am__objects_1)
+	descriptor.lo filters.lo fingerprint.lo forcefield.lo \
+	format.lo generic.lo grid.lo kekulize.lo matrix.lo mol.lo \
+	molchrg.lo obconversion.lo oberror.lo obiter.lo obutil.lo \
+	parsmart.lo patty.lo phmodel.lo plugin.lo rand.lo residue.lo \
+	ring.lo rotor.lo rotamer.lo tokenst.lo typer.lo transform.lo \
+	groupcontrib.lo $(am__objects_1)
 libopenbabel_la_OBJECTS = $(am_libopenbabel_la_OBJECTS)
 libopenbabel_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
 	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
@@ -250,13 +252,14 @@ lib_LTLIBRARIES = libopenbabel.la
 libopenbabel_la_SOURCES = \
 		atom.cpp base.cpp bitvec.cpp bond.cpp \
 		bondtyper.cpp canon.cpp \
-		chains.cpp chiral.cpp data.cpp \
-		fingerprint.cpp forcefield.cpp generic.cpp \
+		chains.cpp chiral.cpp data.cpp descriptor.cpp filters.cpp \
+		fingerprint.cpp forcefield.cpp format.cpp generic.cpp \
 		grid.cpp kekulize.cpp matrix.cpp mol.cpp \
 		molchrg.cpp \
 		obconversion.cpp oberror.cpp obiter.cpp \
 		obutil.cpp parsmart.cpp \
-		patty.cpp phmodel.cpp rand.cpp residue.cpp ring.cpp \
+		patty.cpp phmodel.cpp plugin.cpp \
+                rand.cpp residue.cpp ring.cpp \
 		rotor.cpp rotamer.cpp tokenst.cpp typer.cpp \
 		transform.cpp groupcontrib.cpp $(dlhandler)
 
@@ -369,9 +372,12 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chains.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chiral.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/data.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/descriptor.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dlhandler_unix.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/filters.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/fingerprint.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/forcefield.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/format.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/generic.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/grid.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/groupcontrib.Plo@am__quote@
@@ -386,6 +392,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/parsmart.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/patty.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/phmodel.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/plugin.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rand.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/residue.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ring.Plo@am__quote@

src/descriptor.cpp

@@ -22,6 +22,10 @@ GNU General Public License for more details.
 #include <openbabel/base.h>
 #include <openbabel/descriptor.h>
 
+#if defined(WIN32)
+#define IsNan _isnan
+#endif
+
 using namespace std;
 namespace OpenBabel
 {
@@ -227,7 +231,7 @@ bool OBDescriptor::GenericDataCompare(string& ID, OBBase* pOb, istream& optionTe
   }
   stringstream ss(sval);
   double val;
-  if((ss >> val) && _isnan(filterval))
+  if((ss >> val) && IsNan(filterval))
     //Do a string comparison if either the filter or the OBPair value is not a number
     return DoComparison(ch1, ch2, sval, sfilterval);
   else
@@ -366,7 +370,7 @@ bool OBDescriptor::CompareStringWithFilter(istream& optionText, string& sval, bo
 
   stringstream ss(sval);
   double val;
-  if((ss >> val) && !_isnan(filterval))
+  if((ss >> val) && !IsNan(filterval))
     //Do a numerical comparison if both values are numbers
     return DoComparison(ch1, ch2, val, filterval);
   else

src/plugin.cpp

@@ -18,6 +18,8 @@ General Public License for more details.
 #include <openbabel/babelconfig.h>
 #include <openbabel/plugin.h>
 
+#include <iterator>
+
 using namespace std;
 namespace OpenBabel
 {
@@ -73,7 +75,7 @@ void OBPlugin::List(const char* PluginID, const char* param, ostream* os)
   vector<string> vlist;
   if(!ListAsVector(PluginID,param, vlist))
     *os << PluginID << " is not a recognized plugin type. Those with instances of sub-types loaded are:" << endl;
-  copy(vlist.begin(), vlist.end(), ostream_iterator<string>(*os, "\n"));
+  copy(vlist.begin(), vlist.end(), std::ostream_iterator<string>(*os, "\n"));
 }
 
 string OBPlugin::ListAsString(const char* PluginID, const char* param)

tools/Makefile.am

@@ -1,5 +1,5 @@
 bin_PROGRAMS = babel obchiral obgrep obrotate obfit obprop obxyz obgen \
-		obenergy obminimize obmm obrotamer obfragment obdoc
+		obenergy obminimize obmm obrotamer obfragment # obdoc
 
 # obdoc is intended to be used for generating file format documentation
 # and is not a general end-user program
@@ -40,8 +40,8 @@ obrotamer_LDADD = ../src/libopenbabel.la @LIBDL@
 obxyz_SOURCES = obxyz.cpp
 obxyz_LDADD = ../src/libopenbabel.la @LIBDL@
 
-obdoc_SOURCES = obdoc.cpp
-obdoc_LDADD = ../src/libopenbabel.la @LIBDL@
+# obdoc_SOURCES = obdoc.cpp
+# obdoc_LDADD = ../src/libopenbabel.la @LIBDL@
 
 obfragment_SOURCES = obfragment.cpp
 obfragment_LDADD = ../src/libopenbabel.la @LIBDL@

tools/Makefile.in

@@ -36,7 +36,7 @@ bin_PROGRAMS = babel$(EXEEXT) obchiral$(EXEEXT) obgrep$(EXEEXT) \
 	obrotate$(EXEEXT) obfit$(EXEEXT) obprop$(EXEEXT) \
 	obxyz$(EXEEXT) obgen$(EXEEXT) obenergy$(EXEEXT) \
 	obminimize$(EXEEXT) obmm$(EXEEXT) obrotamer$(EXEEXT) \
-	obfragment$(EXEEXT) obdoc$(EXEEXT)
+	obfragment$(EXEEXT)
 subdir = tools
 DIST_COMMON = README $(srcdir)/Makefile.am $(srcdir)/Makefile.in
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -56,9 +56,6 @@ babel_DEPENDENCIES = ../src/libopenbabel.la
 am_obchiral_OBJECTS = obchiral.$(OBJEXT)
 obchiral_OBJECTS = $(am_obchiral_OBJECTS)
 obchiral_DEPENDENCIES = ../src/libopenbabel.la
-am_obdoc_OBJECTS = obdoc.$(OBJEXT)
-obdoc_OBJECTS = $(am_obdoc_OBJECTS)
-obdoc_DEPENDENCIES = ../src/libopenbabel.la
 am_obenergy_OBJECTS = obenergy.$(OBJEXT)
 obenergy_OBJECTS = $(am_obenergy_OBJECTS)
 obenergy_DEPENDENCIES = ../src/libopenbabel.la
@@ -104,12 +101,12 @@ CXXLD = $(CXX)
 CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
 	--mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
 	$(LDFLAGS) -o $@
-SOURCES = $(babel_SOURCES) $(obchiral_SOURCES) $(obdoc_SOURCES) \
-	$(obenergy_SOURCES) $(obfit_SOURCES) $(obfragment_SOURCES) \
-	$(obgen_SOURCES) $(obgrep_SOURCES) $(obminimize_SOURCES) \
-	$(obmm_SOURCES) $(obprop_SOURCES) $(obrotamer_SOURCES) \
-	$(obrotate_SOURCES) $(obxyz_SOURCES)
-DIST_SOURCES = $(babel_SOURCES) $(obchiral_SOURCES) $(obdoc_SOURCES) \
+SOURCES = $(babel_SOURCES) $(obchiral_SOURCES) $(obenergy_SOURCES) \
+	$(obfit_SOURCES) $(obfragment_SOURCES) $(obgen_SOURCES) \
+	$(obgrep_SOURCES) $(obminimize_SOURCES) $(obmm_SOURCES) \
+	$(obprop_SOURCES) $(obrotamer_SOURCES) $(obrotate_SOURCES) \
+	$(obxyz_SOURCES)
+DIST_SOURCES = $(babel_SOURCES) $(obchiral_SOURCES) \
 	$(obenergy_SOURCES) $(obfit_SOURCES) $(obfragment_SOURCES) \
 	$(obgen_SOURCES) $(obgrep_SOURCES) $(obminimize_SOURCES) \
 	$(obmm_SOURCES) $(obprop_SOURCES) $(obrotamer_SOURCES) \
@@ -266,8 +263,9 @@ obrotamer_SOURCES = obrotamer.cpp
 obrotamer_LDADD = ../src/libopenbabel.la @LIBDL@
 obxyz_SOURCES = obxyz.cpp
 obxyz_LDADD = ../src/libopenbabel.la @LIBDL@
-obdoc_SOURCES = obdoc.cpp
-obdoc_LDADD = ../src/libopenbabel.la @LIBDL@
+
+# obdoc_SOURCES = obdoc.cpp
+# obdoc_LDADD = ../src/libopenbabel.la @LIBDL@
 obfragment_SOURCES = obfragment.cpp
 obfragment_LDADD = ../src/libopenbabel.la @LIBDL@
 AM_CPPFLAGS = -I$(top_srcdir)/include
@@ -338,9 +336,6 @@ babel$(EXEEXT): $(babel_OBJECTS) $(babel_DEPENDENCIES)
 obchiral$(EXEEXT): $(obchiral_OBJECTS) $(obchiral_DEPENDENCIES) 
 	@rm -f obchiral$(EXEEXT)
 	$(CXXLINK) $(obchiral_OBJECTS) $(obchiral_LDADD) $(LIBS)
-obdoc$(EXEEXT): $(obdoc_OBJECTS) $(obdoc_DEPENDENCIES) 
-	@rm -f obdoc$(EXEEXT)
-	$(CXXLINK) $(obdoc_OBJECTS) $(obdoc_LDADD) $(LIBS)
 obenergy$(EXEEXT): $(obenergy_OBJECTS) $(obenergy_DEPENDENCIES) 
 	@rm -f obenergy$(EXEEXT)
 	$(CXXLINK) $(obenergy_OBJECTS) $(obenergy_LDADD) $(LIBS)
@@ -383,7 +378,6 @@ distclean-compile:
 
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/babel.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/obchiral.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/obdoc.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/obenergy.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/obfit.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/obfragment.Po@am__quote@

tools/obenergy.cpp

@@ -49,10 +49,7 @@ int main(int argc,char **argv)
     cout << endl;
     cout << "              available forcefields:" << endl;
     cout << endl;
-    FOR_EACH(OBForceField, iter) {
-      //cout << "              " << iter.ID() << " - " << iter.Description() << endl;
-      cout << "              " << iter.ID() << endl;
-    }
+    OBPlugin::List("forcefields", "verbose");
     exit(-1);
   } else {
     int ifile = 1;

tools/obgen.cpp

@@ -51,10 +51,7 @@ int main(int argc,char **argv)
     cout << endl;
     cout << "  -ff         select a forcefield" << endl;
     cout << endl;
-    FOR_EACH(OBForceField, iter) {
-      //cout << "              " << iter.ID() << " - " << iter.Description() << endl;
-      cout << "              " << iter.ID() << endl;
-    }
+    OBPlugin::List("forcefields", "verbose");
     exit(-1);
   } else {
     basename = filename = argv[1];

tools/obminimize.cpp

@@ -56,10 +56,7 @@ int main(int argc,char **argv)
     cout << endl;
     cout << "  -ff ffid    select a forcefield:" << endl;
     cout << endl;
-    FOR_EACH(OBForceField, iter) {
-      //cout << "              " << iter.ID() << " - " << iter.Description() << endl;
-      cout << "              " << iter.ID() << endl;
-    }
+    OBPlugin::List("forcefields", "verbose");
     exit(-1);
   } else {
     int ifile = 1;