* scripts/java/OBTest.java: Bring back test program.

* scripts/openbabel-java.i, scripts/openbabel-perl.i, scripts/openbabel-ruby.i: Fix script bindings. Now compile cleanly. Perl still needs work to pass tests. * include/openbabel/math/spacegroup.h, include/openbabel/plugin.h: Minor updates for SWIG compatibility.
2025-02-25 18:55:23 -06:00 · 2008-05-16 21:07:13 +00:00
parent 6d97fbc5bf
commit 889fba2d20
10 changed files with 83 additions and 12 deletions
--- a/16
+++ b/16
@@ -1,3 +1,19 @@
+2008-05-16  Geoffrey Hutchison  <babel@geoffhutchison.net>
+
+	* scripts/java/OBTest.java: Bring back test program.
+
+	* scripts/openbabel-java.i, scripts/openbabel-perl.i,
+	scripts/openbabel-ruby.i: Fix script bindings. Now compile
+	cleanly. Perl still needs work to pass tests.
+
+	* include/openbabel/math/spacegroup.h, include/openbabel/plugin.h:
+	Minor updates for SWIG compatibility.
+
+	* src/formats/Makefile.*: Add xtcformat.cpp.
+
+	* src/formats/xtcformat.cpp: Add rpc/types.h for Mac
+	compatibility.
+
 2008-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

 	* include/openbabel/forcefield.h, src/forcefield.cpp: Added functions
--- a/include/openbabel/math/spacegroup.h
+++ b/include/openbabel/math/spacegroup.h
@@ -64,7 +64,12 @@ namespace OpenBabel
        static const SpaceGroup * Find (SpaceGroup* group);
        /* Use it if the space group is unknown (might happen if no database has
         been loaded or if the HM name is not usual. */
+        // Unfortunately, this seems to confuse the SWIG parser
+        // Fortunately, it's not needed for the scripting bindings, 
+        // since this is internal code
+#ifndef SWIG
        void RegisterSpaceGroup (int nb = 0, ...);
+#endif

        bool operator ==(const SpaceGroup &) const;
        int operator!=(const SpaceGroup &other) const
--- a/include/openbabel/plugin.h
+++ b/include/openbabel/plugin.h
@@ -57,7 +57,7 @@ public:
  virtual ~OBPlugin(){};

  ///Required description of a sub-type
-  virtual const char* Description() =0;
+  virtual const char* Description() { return NULL;} ;

  ///Write information on a plugin class to the string txt.
  ///Return false if not written.
--- a/scripts/java/OBTest.java
+++ b/scripts/java/OBTest.java
@@ -0,0 +1,21 @@
+public class OBTest
+{
+  public OBTest()
+  {
+    System.loadLibrary("openbabel");
+  }
+
+  public void run()
+  {
+    OBConversion c = new OBConversion();
+  }
+
+  public static void main(String[] args)
+  {
+    System.out.println("Running OBTest...");
+
+    OBTest test = new OBTest();
+
+    test.run();
+  }
+}
--- a/scripts/openbabel-java.i
+++ b/scripts/openbabel-java.i
@@ -11,7 +11,11 @@
 #include <openbabel/rand.h>
 #include <openbabel/math/vector3.h>
 #include <openbabel/math/matrix3x3.h>
+#include <openbabel/math/transform3d.h>
+#include <openbabel/math/spacegroup.h>
+
 #include <openbabel/generic.h>
+#include <openbabel/griddata.h>

 #include <openbabel/base.h>
 #include <openbabel/mol.h>
@@ -90,14 +94,16 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %include <openbabel/obutil.h>
 %include <openbabel/math/vector3.h>
 %include <openbabel/math/matrix3x3.h>
+%include <openbabel/math/transform3d.h>
+%include <openbabel/math/spacegroup.h>

-%import <openbabel/math/spacegroup.h>
 %include <openbabel/base.h>
 %include <openbabel/generic.h>
+%include <openbabel/griddata.h>

-%import <openbabel/chains.h>
-%import <openbabel/bitvec.h>
-%import <openbabel/typer.h>
+%include <openbabel/chains.h>
+%include <openbabel/bitvec.h>
+%include <openbabel/typer.h>

 %include <openbabel/plugin.h>

@@ -139,6 +145,6 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %ignore OBResidueIter(OBMol &);
 %ignore OBResidueAtomIter(OBResidue &);

-
+%ignore SpaceGroup::RegisterSpaceGroup;

 %include <openbabel/obiter.h>
--- a/scripts/openbabel-perl.i
+++ b/scripts/openbabel-perl.i
@@ -13,6 +13,7 @@
 #include <openbabel/math/vector3.h>
 #include <openbabel/math/matrix3x3.h>
 #include <openbabel/generic.h>
+#include <openbabel/griddata.h>

 #include <openbabel/base.h>
 #include <openbabel/mol.h>
@@ -82,12 +83,13 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %import <openbabel/math/spacegroup.h>
 %include <openbabel/base.h>
 %include <openbabel/generic.h>
+%include <openbabel/griddata.h>

 %import <openbabel/chains.h>
 %import <openbabel/bitvec.h>
 %import <openbabel/typer.h>

-%include <openbabel/plugin.h>
+%import <openbabel/plugin.h>

 %include <openbabel/oberror.h>
 %include <openbabel/format.h>
--- a/scripts/openbabel-ruby.i
+++ b/scripts/openbabel-ruby.i
@@ -19,6 +19,7 @@
 #include <openbabel/rand.h>
 #include <openbabel/math/vector3.h>
 #include <openbabel/math/matrix3x3.h>
+#include <openbabel/griddata.h>
 #include <openbabel/generic.h>

 #include <openbabel/base.h>
@@ -89,6 +90,7 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %import <openbabel/math/spacegroup.h>
 %include <openbabel/base.h>
 %include <openbabel/generic.h>
+%include <openbabel/griddata.h>

 %import <openbabel/chains.h>
 %import <openbabel/bitvec.h>
--- a/src/formats/Makefile.am
+++ b/src/formats/Makefile.am
@@ -102,7 +102,7 @@ pkglib_LTLIBRARIES = \
 	shelxformat.la smilesformat.la thermoformat.la \
 	tinkerformat.la titleformat.la \
 	turbomoleformat.la unichemformat.la viewmolformat.la \
-	xedformat.la xyzformat.la yasaraformat.la zindoformat.la
+	xedformat.la xtcformat.la xyzformat.la yasaraformat.la zindoformat.la
 if HAVE_SHARED_POINTER
    pkglib_LTLIBRARIES += chemdrawcdxformat.la chemkinformat.la \
                          rxnformat.la rsmiformat.la
@@ -335,6 +335,9 @@ viewmolformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.
 xedformat_la_SOURCES = xedformat.cpp 
 xedformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 

+xtcformat_la_SOURCES = xtcformat.cpp 
+xtcformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 
+
 xyzformat_la_SOURCES = xyzformat.cpp 
 xyzformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 

--- a/src/formats/Makefile.in
+++ b/src/formats/Makefile.in
@@ -718,6 +718,14 @@ xedformat_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
 	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
 	$(CXXFLAGS) $(xedformat_la_LDFLAGS) $(LDFLAGS) -o $@
@BUILD_SHARED_TRUE@am_xedformat_la_rpath = -rpath $(pkglibdir)
+xtcformat_la_LIBADD =
+am__xtcformat_la_SOURCES_DIST = xtcformat.cpp
+@BUILD_SHARED_TRUE@am_xtcformat_la_OBJECTS = xtcformat.lo
+xtcformat_la_OBJECTS = $(am_xtcformat_la_OBJECTS)
+xtcformat_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
+	$(CXXFLAGS) $(xtcformat_la_LDFLAGS) $(LDFLAGS) -o $@
+@BUILD_SHARED_TRUE@am_xtcformat_la_rpath = -rpath $(pkglibdir)
 xyzformat_la_LIBADD =
 am__xyzformat_la_SOURCES_DIST = xyzformat.cpp
@BUILD_SHARED_TRUE@am_xyzformat_la_OBJECTS = xyzformat.lo
@@ -791,8 +799,9 @@ SOURCES = $(APIInterface_la_SOURCES) $(CSRformat_la_SOURCES) \
 	$(thermoformat_la_SOURCES) $(tinkerformat_la_SOURCES) \
 	$(titleformat_la_SOURCES) $(turbomoleformat_la_SOURCES) \
 	$(unichemformat_la_SOURCES) $(viewmolformat_la_SOURCES) \
-	$(xedformat_la_SOURCES) $(xyzformat_la_SOURCES) \
-	$(yasaraformat_la_SOURCES) $(zindoformat_la_SOURCES)
+	$(xedformat_la_SOURCES) $(xtcformat_la_SOURCES) \
+	$(xyzformat_la_SOURCES) $(yasaraformat_la_SOURCES) \
+	$(zindoformat_la_SOURCES)
 DIST_SOURCES = $(am__APIInterface_la_SOURCES_DIST) \
 	$(am__CSRformat_la_SOURCES_DIST) \
 	$(am__MCDLformat_la_SOURCES_DIST) \
@@ -868,6 +877,7 @@ DIST_SOURCES = $(am__APIInterface_la_SOURCES_DIST) \
 	$(am__unichemformat_la_SOURCES_DIST) \
 	$(am__viewmolformat_la_SOURCES_DIST) \
 	$(am__xedformat_la_SOURCES_DIST) \
+	$(am__xtcformat_la_SOURCES_DIST) \
 	$(am__xyzformat_la_SOURCES_DIST) \
 	$(am__yasaraformat_la_SOURCES_DIST) \
 	$(am__zindoformat_la_SOURCES_DIST)
@@ -1091,8 +1101,8 @@ SUBDIRS = $(am__append_1) $(am__append_2)
@BUILD_SHARED_TRUE@	smilesformat.la thermoformat.la \
@BUILD_SHARED_TRUE@	tinkerformat.la titleformat.la \
@BUILD_SHARED_TRUE@	turbomoleformat.la unichemformat.la \
-@BUILD_SHARED_TRUE@	viewmolformat.la xedformat.la xyzformat.la \
-@BUILD_SHARED_TRUE@	yasaraformat.la zindoformat.la \
+@BUILD_SHARED_TRUE@	viewmolformat.la xedformat.la xtcformat.la \
+@BUILD_SHARED_TRUE@	xyzformat.la yasaraformat.la zindoformat.la \
@BUILD_SHARED_TRUE@	$(am__append_3)
@BUILD_SHARED_TRUE@APIInterface_la_SOURCES = APIInterface.cpp
@BUILD_SHARED_TRUE@APIInterface_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la
@@ -1244,6 +1254,8 @@ SUBDIRS = $(am__append_1) $(am__append_2)
@BUILD_SHARED_TRUE@viewmolformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 
@BUILD_SHARED_TRUE@xedformat_la_SOURCES = xedformat.cpp 
@BUILD_SHARED_TRUE@xedformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 
+@BUILD_SHARED_TRUE@xtcformat_la_SOURCES = xtcformat.cpp 
+@BUILD_SHARED_TRUE@xtcformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 
@BUILD_SHARED_TRUE@xyzformat_la_SOURCES = xyzformat.cpp 
@BUILD_SHARED_TRUE@xyzformat_la_LDFLAGS = -module -avoid-version -no-undefined ../libopenbabel.la 
@BUILD_SHARED_TRUE@yasaraformat_la_SOURCES = yasaraformat.cpp 
@@ -1470,6 +1482,8 @@ viewmolformat.la: $(viewmolformat_la_OBJECTS) $(viewmolformat_la_DEPENDENCIES)
 	$(viewmolformat_la_LINK) $(am_viewmolformat_la_rpath) $(viewmolformat_la_OBJECTS) $(viewmolformat_la_LIBADD) $(LIBS)
 xedformat.la: $(xedformat_la_OBJECTS) $(xedformat_la_DEPENDENCIES) 
 	$(xedformat_la_LINK) $(am_xedformat_la_rpath) $(xedformat_la_OBJECTS) $(xedformat_la_LIBADD) $(LIBS)
+xtcformat.la: $(xtcformat_la_OBJECTS) $(xtcformat_la_DEPENDENCIES) 
+	$(xtcformat_la_LINK) $(am_xtcformat_la_rpath) $(xtcformat_la_OBJECTS) $(xtcformat_la_LIBADD) $(LIBS)
 xyzformat.la: $(xyzformat_la_OBJECTS) $(xyzformat_la_DEPENDENCIES) 
 	$(xyzformat_la_LINK) $(am_xyzformat_la_rpath) $(xyzformat_la_OBJECTS) $(xyzformat_la_LIBADD) $(LIBS)
 yasaraformat.la: $(yasaraformat_la_OBJECTS) $(yasaraformat_la_DEPENDENCIES) 
@@ -1560,6 +1574,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/unichemformat.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/viewmolformat.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/xedformat.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/xtcformat.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/xyzformat.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/yasaraformat.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/zindoformat.Plo@am__quote@
--- a/src/formats/xtcformat.cpp
+++ b/src/formats/xtcformat.cpp
@@ -24,6 +24,7 @@
 //#include <malloc.h>
 //#include <math.h>
 //#include <rpc/rpc.h>
+#include <rpc/types.h>
 #include <rpc/xdr.h>
 //#include <stdio.h>
 //#include <stdlib.h>