- updated to 2.2.0
- fixed testsuite - added strict perl version requirements (patch by Paul Howarth) - fixed some rpmlint warnings - merged a sed call into -rpm patch
This commit is contained in:
Dominik Mierzejewski
parent
e5a93508d3
commit
7ec9e5e5c4
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@ -1 +1 @@
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openbabel-2.2.0b7-20080627-r2628.tar.gz
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openbabel-2.2.0.tar.gz
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|
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@ -0,0 +1,12 @@
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diff -up openbabel-2.2.0b7/test/bond.cpp.chk openbabel-2.2.0b7/test/bond.cpp
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--- openbabel-2.2.0b7/test/bond.cpp.chk 2008-06-13 22:48:05.000000000 +0200
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+++ openbabel-2.2.0b7/test/bond.cpp 2008-07-06 14:05:26.000000000 +0200
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@@ -58,7 +58,7 @@ int main(int argc,char *argv[])
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bond1.SetBegin(&begin1);
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bond1.SetEnd(&end1);
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- cout << "ok 4\n";
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+ cout << "ok 3\n";
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return(0);
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}
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@ -1,348 +0,0 @@
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Index: scripts/openbabel-python2.i
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===================================================================
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--- scripts/openbabel-python2.i (revision 0)
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+++ scripts/openbabel-python2.i (revision 2535)
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@@ -0,0 +1,92 @@
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+%module obconversion
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+
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+%{
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+// used to set import/export for Cygwin DLLs
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+#ifdef WIN32
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+#define USING_OBDLL
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+#endif
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+
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+#include <openbabel/base.h>
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+
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+#include <openbabel/generic.h>
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+#include <openbabel/griddata.h>
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+#include <openbabel/math/vector3.h>
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+#include <openbabel/bitvec.h>
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+
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+#include <openbabel/mol.h>
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+#include <openbabel/obconversion.h>
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+#include <openbabel/oberror.h>
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+#include <openbabel/plugin.h>
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+#include <openbabel/fingerprint.h>
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+#include <openbabel/descriptor.h>
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+#include <openbabel/format.h>
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+#include <openbabel/forcefield.h>
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+#include <openbabel/op.h>
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+
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+%}
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+
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+// These methods are renamed to valid Python method names, as otherwise
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+// they cannot be used from Python
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+%rename(inc) *::operator++;
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+%rename(good) *::operator bool;
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+
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+%import <openbabel/babelconfig.h>
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+
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+%import <openbabel/base.h>
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+%import <openbabel/generic.h>
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+%import <openbabel/griddata.h>
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+
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+%import <openbabel/math/vector3.h>
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+%import <openbabel/bitvec.h>
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+
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+%import <openbabel/chains.h>
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+%import <openbabel/typer.h>
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+
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+%include <openbabel/plugin.h>
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+%include <openbabel/oberror.h>
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+%include <openbabel/format.h>
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+%include <openbabel/obconversion.h>
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+%import <openbabel/residue.h>
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+%import <openbabel/internalcoord.h>
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+%import <openbabel/atom.h>
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+%import <openbabel/bond.h>
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+%import <openbabel/mol.h>
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+%import <openbabel/ring.h>
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+%import <openbabel/parsmart.h>
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+
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+%include <openbabel/fingerprint.h>
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+%include <openbabel/descriptor.h>
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+%include <openbabel/forcefield.h>
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+
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+%include <openbabel/op.h>
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+%include <openbabel/bitvec.h>
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+
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+%ignore *::operator=;
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+
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+%include "carrays.i"
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+%array_class(double, doubleArray)
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+%pythoncode %{
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+def double_array(mylist):
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+ """Create a C array of doubles from a list."""
|
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+ c = doubleArray(len(mylist))
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+ for i,v in enumerate(mylist):
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+ c[i] = v
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+ return c
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+%}
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+
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+# Functions to set the log file to std::cout and std::cerr
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+
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+%ignore OBForceField::SetLogFile(std::ostream *pos);
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+%extend OpenBabel::OBForceField {
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+ void SetLogToStdOut()
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+ {
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+ self->SetLogFile(&std::cout);
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+ }
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+
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+ void SetLogToStdErr()
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+ {
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+ self->SetLogFile(&std::cerr);
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+ }
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+};
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+
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+
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Index: scripts/openbabel-python3.i
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===================================================================
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--- scripts/openbabel-python3.i (revision 0)
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+++ scripts/openbabel-python3.i (revision 2535)
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@@ -0,0 +1,65 @@
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+%module obtemplate
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+
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+%{
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+// used to set import/export for Cygwin DLLs
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+#ifdef WIN32
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+#define USING_OBDLL
|
||||
+#endif
|
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+
|
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+#include <openbabel/base.h>
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+#include <openbabel/mol.h>
|
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+#include <openbabel/atom.h>
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+#include <openbabel/bond.h>
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+#include <openbabel/residue.h>
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+#include <openbabel/ring.h>
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+
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+%}
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+
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+%include "std_list.i"
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+%include "std_map.i"
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+%include "std_vector.i"
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+%include "std_string.i"
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+
|
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+namespace std {
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+%template (vectorInt) vector<int>;
|
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+%template (vectorUnsignedInt) vector<unsigned int>;
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+%template (vvInt) vector< vector<int> >;
|
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+%template (vectorDouble) vector<double>;
|
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+%template (vectorString) vector<std::string>;
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+%template (vVector3) vector<OpenBabel::vector3>;
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+
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+%template (vectorMol) vector<OpenBabel::OBMol>;
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+%template (vectorBond) vector<OpenBabel::OBBond>;
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+%template (vectorResidue) vector<OpenBabel::OBResidue>;
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+%template (vectorRing) vector<OpenBabel::OBRing>;
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+%template (vectorpRing) vector<OpenBabel::OBRing*>;
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+%template (vectorData) vector<OpenBabel::OBGenericData*>;
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+}
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+
|
||||
+// These methods are renamed to valid Python method names, as otherwise
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||||
+// they cannot be used from Python
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+%rename(inc) *::operator++;
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+%rename(good) *::operator bool;
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+
|
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+%import <openbabel/babelconfig.h>
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+
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+%import <openbabel/base.h>
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+%import <openbabel/residue.h>
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+%import <openbabel/atom.h>
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+%import <openbabel/bond.h>
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+%import <openbabel/mol.h>
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+%import <openbabel/ring.h>
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+
|
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+%ignore *::operator=;
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+
|
||||
+%include "carrays.i"
|
||||
+%array_class(double, doubleArray)
|
||||
+%pythoncode %{
|
||||
+def double_array(mylist):
|
||||
+ """Create a C array of doubles from a list."""
|
||||
+ c = doubleArray(len(mylist))
|
||||
+ for i,v in enumerate(mylist):
|
||||
+ c[i] = v
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||||
+ return c
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+%}
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+
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Index: scripts/python/setup.py
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===================================================================
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--- scripts/python/setup.py (revision 2534)
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+++ scripts/python/setup.py (revision 2535)
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@@ -60,13 +60,27 @@
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OBinclude,OBlibrary = find_likely_directory()
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-obExtension = Extension('_openbabel',
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- ['openbabel_python.cpp'],
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- include_dirs=OBinclude,
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- library_dirs=OBlibrary,
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- libraries=['openbabel']
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- )
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+obCore = Extension('_obcore',
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+ ['obcore.cpp'],
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+ include_dirs=OBinclude,
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+ library_dirs=OBlibrary,
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+ libraries=['openbabel']
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+ )
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+obConversion = Extension('_obconversion',
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+ ['obconversion.cpp'],
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+ include_dirs=OBinclude,
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+ library_dirs=OBlibrary,
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+ libraries=['openbabel']
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+ )
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+
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+obTemplate = Extension('_obtemplate',
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+ ['obtemplate.cpp'],
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+ include_dirs=OBinclude,
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+ library_dirs=OBlibrary,
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+ libraries=['openbabel']
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+ )
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+
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setup(name='openbabel',
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version='1.3',
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author='Noel O\'Boyle',
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@@ -74,7 +88,7 @@
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url='http://openbabel.sourceforge.net/',
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license='http://www.gnu.org/copyleft/gpl.html',
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py_modules=['openbabel','pybel'],
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- ext_modules=[obExtension],
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+ ext_modules=[obCore, obConversion, obTemplate],
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description = 'openbabel: Python interface to the Open Babel chemistry library',
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classifiers=[
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'Development Status :: 5 - Production/Stable',
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Index: scripts/python/openbabel.py
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||||
===================================================================
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--- scripts/python/openbabel.py (revision 0)
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+++ scripts/python/openbabel.py (revision 2535)
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@@ -0,0 +1,11 @@
|
||||
+import sys
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||||
+if sys.platform.find("linux") != -1:
|
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+ try:
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||||
+ import dl
|
||||
+ except ImportError:
|
||||
+ import DLFCN as dl
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||||
+ sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
|
||||
+
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+import obcore
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+import obconversion
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||||
+import obtemplate
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||||
Index: scripts/Makefile.am
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||||
===================================================================
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||||
--- scripts/Makefile.am (revision 2534)
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+++ scripts/Makefile.am (revision 2535)
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||||
@@ -20,8 +20,9 @@
|
||||
|
||||
if MAINTAINER_MODE
|
||||
if BUILD_SWIG
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||||
-BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
|
||||
- java/openbabel_java.cpp
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||||
+BUILT_SOURCES = perl/openbabel_perl.cpp \
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+ java/openbabel_java.cpp \
|
||||
+ python/obcore.cpp python/obconversion.cpp python/obtemplate.cpp
|
||||
|
||||
script_includes = $(top_srcdir)/include/openbabel
|
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script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
|
||||
@@ -34,20 +35,18 @@
|
||||
sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
|
||||
mv perl/OpenBabel.new perl/OpenBabel.pm;
|
||||
|
||||
-python/openbabel_python.cpp: openbabel-python.i $(script_headers)
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||||
- $(SWIG) -python -modern -naturalvar -fastinit \
|
||||
+python/obconversion.cpp: openbabel-python2.i $(script_headers)
|
||||
+ $(SWIG) -small -O -python -templatereduce -naturalvar \
|
||||
-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
|
||||
- echo "import sys" >python/ob.py;
|
||||
- echo "if sys.platform.find(\"linux\") != -1:" >>python/ob.py;
|
||||
- echo " try:" >>python/ob.py;
|
||||
- echo " import dl" >>python/ob.py;
|
||||
- echo " except ImportError:" >>python/ob.py;
|
||||
- echo " import DLFCN as dl" >>python/ob.py;
|
||||
- echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
|
||||
- echo >>python/ob.py;
|
||||
- cat python/openbabel.py >>python/ob.py;
|
||||
- mv python/ob.py python/openbabel.py;
|
||||
|
||||
+python/obtemplate.cpp: openbabel-python3.i $(script_headers)
|
||||
+ $(SWIG) -small -O -python -templatereduce -naturalvar \
|
||||
+ -c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
|
||||
+
|
||||
+python/obcore.cpp: openbabel-python.i $(script_headers)
|
||||
+ $(SWIG) -small -O -python -templatereduce -naturalvar \
|
||||
+ -c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
|
||||
+
|
||||
java/openbabel_java.cpp: openbabel-java.i $(script_headers)
|
||||
$(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/include \
|
||||
-I$(top_builddir)/include $<;
|
||||
Index: scripts/openbabel-python.i
|
||||
===================================================================
|
||||
--- scripts/openbabel-python.i (revision 2534)
|
||||
+++ scripts/openbabel-python.i (revision 2535)
|
||||
@@ -1,4 +1,4 @@
|
||||
-%module openbabel
|
||||
+%module obcore
|
||||
|
||||
%{
|
||||
// used to set import/export for Cygwin DLLs
|
||||
@@ -41,28 +41,6 @@
|
||||
|
||||
%}
|
||||
|
||||
-%include "std_list.i"
|
||||
-%include "std_map.i"
|
||||
-%include "std_vector.i"
|
||||
-%include "std_string.i"
|
||||
-
|
||||
-namespace std {
|
||||
-%template (vectorInt) vector<int>;
|
||||
-%template (vectorUnsignedInt) vector<unsigned int>;
|
||||
-%template (vvInt) vector< vector<int> >;
|
||||
-%template (vectorDouble) vector<double>;
|
||||
-%template (vectorString) vector<std::string>;
|
||||
-%template (vVector3) vector<OpenBabel::vector3>;
|
||||
-
|
||||
-%template (vectorMol) vector<OpenBabel::OBMol>;
|
||||
-%template (vectorBond) vector<OpenBabel::OBBond>;
|
||||
-%template (vectorResidue) vector<OpenBabel::OBResidue>;
|
||||
-%template (vectorRing) vector<OpenBabel::OBRing>;
|
||||
-%template (vectorpRing) vector<OpenBabel::OBRing*>;
|
||||
-%template (vectorData) vector<OpenBabel::OBGenericData*>;
|
||||
-}
|
||||
-
|
||||
-
|
||||
%inline %{
|
||||
OpenBabel::OBPairData *toPairData(OpenBabel::OBGenericData *data) {
|
||||
return (OpenBabel::OBPairData *) data;
|
||||
@@ -95,11 +73,11 @@
|
||||
//# %import <openbabel/bitvec.h>
|
||||
%import <openbabel/typer.h>
|
||||
|
||||
-%include <openbabel/plugin.h>
|
||||
+%import <openbabel/plugin.h>
|
||||
|
||||
-%include <openbabel/oberror.h>
|
||||
-%include <openbabel/format.h>
|
||||
-%include <openbabel/obconversion.h>
|
||||
+%import <openbabel/oberror.h>
|
||||
+%import <openbabel/format.h>
|
||||
+%import <openbabel/obconversion.h>
|
||||
%include <openbabel/residue.h>
|
||||
%include <openbabel/internalcoord.h>
|
||||
%include <openbabel/atom.h>
|
||||
@@ -110,11 +88,11 @@
|
||||
%include <openbabel/alias.h>
|
||||
%include <openbabel/atomclass.h>
|
||||
|
||||
-%include <openbabel/fingerprint.h>
|
||||
-%include <openbabel/descriptor.h>
|
||||
-%include <openbabel/forcefield.h>
|
||||
+%import <openbabel/fingerprint.h>
|
||||
+%import <openbabel/descriptor.h>
|
||||
+%import <openbabel/forcefield.h>
|
||||
|
||||
-%include <openbabel/op.h>
|
||||
+%import <openbabel/op.h>
|
||||
|
||||
%include <openbabel/bitvec.h>
|
||||
|
||||
|
|
@ -1,9 +1,9 @@
|
|||
diff -up openbabel-2.2.0b3-20080215-r2249/scripts/Makefile.am.r openbabel-2.2.0b3-20080215-r2249/scripts/Makefile.am
|
||||
--- openbabel-2.2.0b3-20080215-r2249/scripts/Makefile.am.r 2008-01-24 21:43:42.000000000 +0100
|
||||
+++ openbabel-2.2.0b3-20080215-r2249/scripts/Makefile.am 2008-02-23 15:48:26.000000000 +0100
|
||||
@@ -58,8 +58,8 @@ ruby/openbabel_ruby.cpp: openbabel-ruby.
|
||||
$(SWIG) -ruby -naturalvar -autorename -c++ -o $@ -I$(top_srcdir)/include \
|
||||
-I$(top_builddir)/include $<;
|
||||
diff -up openbabel-2.2.0/scripts/Makefile.am.r openbabel-2.2.0/scripts/Makefile.am
|
||||
--- openbabel-2.2.0/scripts/Makefile.am.r 2008-07-03 20:25:54.000000000 +0200
|
||||
+++ openbabel-2.2.0/scripts/Makefile.am 2008-07-06 15:59:23.000000000 +0200
|
||||
@@ -63,8 +63,8 @@ ruby/openbabel_ruby.cpp: openbabel-ruby.
|
||||
$(SWIG) -small -O -ruby -naturalvar -autorename -c++ -o $@ \
|
||||
-templatereduce -I$(top_srcdir)/include -I$(top_builddir)/include $<;
|
||||
(cd ruby; ruby extconf.rb \
|
||||
- --with-openbabel-include=$(includedir)/openbabel-2.0 \
|
||||
- --with-openbabel-lib=$(libdir) )
|
||||
|
|
@ -12,3 +12,17 @@ diff -up openbabel-2.2.0b3-20080215-r2249/scripts/Makefile.am.r openbabel-2.2.0b
|
|||
sed -e 's/rb_define_module(\"Openbabel\")/rb_define_module(\"OpenBabel\")/' -e 's/void Init_OpenBabel/void Init_openbabel/' <ruby/openbabel_ruby.cpp >ruby/openbabel_ruby.new
|
||||
mv ruby/openbabel_ruby.new ruby/openbabel_ruby.cpp
|
||||
endif # BUILD_RUBY
|
||||
diff -up openbabel-2.2.0/scripts/perl/Makefile.PL.r openbabel-2.2.0/scripts/perl/Makefile.PL
|
||||
--- openbabel-2.2.0/scripts/perl/Makefile.PL.r 2008-07-06 16:16:45.000000000 +0200
|
||||
+++ openbabel-2.2.0/scripts/perl/Makefile.PL 2008-07-06 16:48:59.000000000 +0200
|
||||
@@ -3,8 +3,8 @@ use ExtUtils::MakeMaker;
|
||||
use lib 'inc';
|
||||
use Devel::CheckLib;
|
||||
|
||||
-check_lib_or_exit( lib => 'openbabel' , libpath =>
|
||||
-@ENV{"LD_LIBRARY_PATH"});
|
||||
+#check_lib_or_exit( lib => 'openbabel' , libpath =>
|
||||
+#@ENV{"LD_LIBRARY_PATH"});
|
||||
|
||||
$CC = 'g++';
|
||||
$srcdir = '../../src';
|
||||
|
|
|
|||
|
|
@ -4,12 +4,12 @@
|
|||
%{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
|
||||
%define ruby_sitearch %(ruby -rrbconfig -e 'puts Config::CONFIG["sitearchdir"]')
|
||||
|
||||
%define beta_ver b7
|
||||
%define beta_str b7-20080627-r2628
|
||||
%define beta_ver %{nil}
|
||||
%define beta_str %{nil}
|
||||
|
||||
Name: openbabel
|
||||
Version: 2.2.0
|
||||
Release: 0.5.%{beta_ver}%{?dist}
|
||||
Release: 1%{?dist}
|
||||
Summary: Chemistry software file format converter
|
||||
License: GPLv2
|
||||
Group: Applications/File
|
||||
|
|
@ -17,6 +17,7 @@ URL: http://openbabel.org/
|
|||
Source: http://dl.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz
|
||||
Patch: %{name}-gcc43.patch
|
||||
Patch1: %{name}-rpm.patch
|
||||
Patch2: %{name}-check.patch
|
||||
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
|
||||
BuildRequires: inchi-devel
|
||||
BuildRequires: libtool
|
||||
|
|
@ -62,8 +63,9 @@ you should install %{name}-devel. You'll also need to have the
|
|||
%package -n perl-%{name}
|
||||
Group: System Environment/Libraries
|
||||
Summary: Perl wrapper for the Open Babel library
|
||||
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
|
||||
Obsoletes: %{name}-perl < 2.2.0
|
||||
Provides: %{name}-perl
|
||||
Provides: %{name}-perl = %{version}-%{release}
|
||||
|
||||
%description -n perl-%{name}
|
||||
Perl wrapper for the Open Babel library.
|
||||
|
|
@ -72,7 +74,7 @@ Perl wrapper for the Open Babel library.
|
|||
Group: System Environment/Libraries
|
||||
Summary: Python wrapper for the Open Babel library
|
||||
Obsoletes: %{name}-python < 2.2.0
|
||||
Provides: %{name}-python
|
||||
Provides: %{name}-python = %{version}-%{release}
|
||||
|
||||
%description -n python-%{name}
|
||||
Python wrapper for the Open Babel library.
|
||||
|
|
@ -90,7 +92,8 @@ Ruby wrapper for the Open Babel library.
|
|||
%setup -q -n %{name}-%{version}%{beta_ver}
|
||||
%patch -p1 -b .gcc43
|
||||
%patch1 -p1 -b .r
|
||||
find . -name "._*" | xargs rm
|
||||
%patch2 -p1 -b .chk
|
||||
chmod 644 src/formats/{mmcif,fchk}format.cpp
|
||||
|
||||
%build
|
||||
# don't reference m4 include directory which isn't shipped in the tarball
|
||||
|
|
@ -101,9 +104,6 @@ autoreconf --force --install
|
|||
%{__make} %{?_smp_mflags}
|
||||
|
||||
pushd scripts/perl
|
||||
# disable the check for the installed library, the library isn't installed yet
|
||||
# at this point and isn't expected to
|
||||
sed -i -e 's/check_lib_or_exit/#check_lib_or_exit/g' Makefile.PL
|
||||
perl Makefile.PL INSTALLDIRS="vendor"
|
||||
%{__make} %{?_smp_mflags} OPTIMIZE="$RPM_OPT_FLAGS"
|
||||
popd
|
||||
|
|
@ -134,6 +134,7 @@ pushd scripts/python
|
|||
%{__python} setup.py install --skip-build --root $RPM_BUILD_ROOT
|
||||
%{__python} setup.py install -O1 --skip-build --root $RPM_BUILD_ROOT
|
||||
popd
|
||||
chmod 755 $RPM_BUILD_ROOT%{python_sitearch}/_openbabel.so
|
||||
|
||||
pushd scripts/ruby
|
||||
%{__make} install DESTDIR=$RPM_BUILD_ROOT
|
||||
|
|
@ -187,11 +188,14 @@ popd
|
|||
%{ruby_sitearch}/openbabel.so
|
||||
|
||||
%changelog
|
||||
* Wed Jul 02 2008 Dominik Mierzejewski <rpm@greysector.net> 2.2.0-0.6.b7
|
||||
- updated to 2.2.0 beta7
|
||||
* Sun Jul 06 2008 Dominik Mierzejewski <rpm@greysector.net> 2.2.0-1
|
||||
- updated to 2.2.0
|
||||
- new URL
|
||||
- dropped Python binding split patch (broken, reverted upstream)
|
||||
- removed weird Macintosh files
|
||||
- fixed testsuite and disabled inchi tests temporarily
|
||||
- added strict perl version requirements (patch by Paul Howarth)
|
||||
- fixed some rpmlint warnings
|
||||
- merged a sed call into -rpm patch
|
||||
|
||||
* Fri Jun 06 2008 Kevin Kofler <Kevin@tigcc.ticalc.org> 2.2.0-0.5.b5
|
||||
- backport upstream patch to split Python binding (should fix #427700 for good)
|
||||
|
|
|
|||
Loading…
Reference in New Issue