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Group :: Sciences/Chemistry
RPM: openbabel
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Patch: openbabel-2.0.0-gcc41.patch
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diff -uNr openbabel-2.0.0.old/src/fingerprint.h openbabel-2.0.0/src/fingerprint.h
--- openbabel-2.0.0.old/src/fingerprint.h 2005-11-26 23:19:45.000000000 +0100
+++ openbabel-2.0.0/src/fingerprint.h 2006-03-25 15:56:09.000000000 +0100
@@ -60,7 +60,7 @@
static double Tanimoto(const std::vector<unsigned int>& vec1, const std::vector<unsigned int>& vec2);
/// Inline version of Tanimoto() taking a pointer for the second vector
- static double OBFingerprint::Tanimoto(const std::vector<unsigned int>& vec1, const unsigned int* p2)
+ static double Tanimoto(const std::vector<unsigned int>& vec1, const unsigned int* p2)
{
///If used for two vectors, vec1 and vec2, call as Tanimoto(vec1, &vec2[0]);
int andbits=0, orbits=0;
diff -uNr openbabel-2.0.0.old/src/formats/copyformat.cpp openbabel-2.0.0/src/formats/copyformat.cpp
--- openbabel-2.0.0.old/src/formats/copyformat.cpp 2005-11-26 23:19:51.000000000 +0100
+++ openbabel-2.0.0/src/formats/copyformat.cpp 2006-03-25 15:54:08.000000000 +0100
@@ -41,7 +41,7 @@
};
/////////////////////////////////////////////////////////////////
- virtual bool CopyFormat::WriteChemObject(OBConversion* pConv)
+ virtual bool WriteChemObject(OBConversion* pConv)
{
pConv->GetChemObject();//needed to increment pConv->Index
diff -uNr openbabel-2.0.0.old/src/formats/crkformat.cpp openbabel-2.0.0/src/formats/crkformat.cpp
--- openbabel-2.0.0.old/src/formats/crkformat.cpp 2005-11-26 23:19:51.000000000 +0100
+++ openbabel-2.0.0/src/formats/crkformat.cpp 2006-03-25 15:55:07.000000000 +0100
@@ -61,8 +61,8 @@
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
- static bool CRK2DFormat::ReadCRK(std::istream &ifs,OBMol &mol,const char *classTag);
- static void CRK2DFormat::WriteCRK(std::ostream &ofs,OBMol &mol,bool GroupCharges);
+ static bool ReadCRK(std::istream &ifs,OBMol &mol,const char *classTag);
+ static void WriteCRK(std::ostream &ofs,OBMol &mol,bool GroupCharges);
};
diff -uNr openbabel-2.0.0.old/src/formats/xml/cmlreactlformat.cpp openbabel-2.0.0/src/formats/xml/cmlreactlformat.cpp
--- openbabel-2.0.0.old/src/formats/xml/cmlreactlformat.cpp 2005-11-26 23:19:57.000000000 +0100
+++ openbabel-2.0.0/src/formats/xml/cmlreactlformat.cpp 2006-03-25 15:51:06.000000000 +0100
@@ -51,7 +51,7 @@
\n";
}
- unsigned CMLReactFormat::Flags()
+ unsigned Flags()
{
return 0;
}
diff -uNr openbabel-2.0.0.old/src/formats/xml/xmlformat.cpp openbabel-2.0.0/src/formats/xml/xmlformat.cpp
--- openbabel-2.0.0.old/src/formats/xml/xmlformat.cpp 2005-11-26 23:19:57.000000000 +0100
+++ openbabel-2.0.0/src/formats/xml/xmlformat.cpp 2006-03-25 15:52:14.000000000 +0100
@@ -21,12 +21,12 @@
class XMLFormat : XMLBaseFormat
{
public:
- XMLFormat::XMLFormat()
+ XMLFormat()
{
OBConversion::RegisterFormat("xml",this);
}
- const char* XMLFormat::Description()
+ const char* Description()
{
return " \
General XML format\n \
@@ -40,7 +40,7 @@
const char* NamespaceURI()const{return "Undefined";};
- unsigned XMLFormat::Flags()
+ unsigned Flags()
{
return NOTWRITABLE;
}
diff -uNr openbabel-2.0.0.old/src/formats/xml/xml.h openbabel-2.0.0/src/formats/xml/xml.h
--- openbabel-2.0.0.old/src/formats/xml/xml.h 2005-11-26 23:19:57.000000000 +0100
+++ openbabel-2.0.0/src/formats/xml/xml.h 2006-03-25 15:50:31.000000000 +0100
@@ -41,8 +41,8 @@
///Frees reader and writer if necessary
~XMLConversion();
- bool XMLConversion::SetupReader();///< opens libxml2 reader
- bool XMLConversion::SetupWriter();///< opens libxml2 writer
+ bool SetupReader();///< opens libxml2 reader
+ bool SetupWriter();///< opens libxml2 writer
///Parses the input xml stream and sends each element to the format's callback routines
bool ReadXML(XMLBaseFormat* pFormat, OBBase* pOb);
@@ -57,7 +57,7 @@
return *nsm;
};
- static void XMLConversion::RegisterXMLFormat(XMLBaseFormat* pFormat,
+ static void RegisterXMLFormat(XMLBaseFormat* pFormat,
bool IsDefault=false, const char* uri=NULL);
///Returns the extended OBConversion class, making it if necessary
@@ -65,9 +65,9 @@
///Because OBConversion::Convert is still using the unextended OBConversion object
///we need to obtain the conversion paramters from it when requested
- bool XMLConversion::IsLast()
+ bool IsLast()
{ return _pConv->IsLast(); }
- int XMLConversion::GetOutputIndex()
+ int GetOutputIndex()
{ return _pConv->GetOutputIndex(); }
@@ -96,7 +96,7 @@
string GetAttribute(const char* attrname);
///Sets value to element content. Returns false if there is no content.
- string XMLConversion::GetContent();
+ string GetContent();
///Sets value to element content as an integer. Returns false if there is no content.
bool GetContentInt(int& value);
diff -uNr openbabel-2.0.0.old/src/zipstreamimpl.h openbabel-2.0.0/src/zipstreamimpl.h
--- openbabel-2.0.0.old/src/zipstreamimpl.h 2005-11-26 23:19:48.000000000 +0100
+++ openbabel-2.0.0/src/zipstreamimpl.h 2006-03-25 16:01:08.000000000 +0100
@@ -73,7 +73,7 @@
window_size, memory_level,
static_cast<int>(strategy));
- setp( &(_buffer[0]), &(_buffer[_buffer.size()-1]));
+ this->setp( &(_buffer[0]), &(_buffer[_buffer.size()-1]));
}
/** Destructor
@@ -123,7 +123,7 @@
}
if (zip_to_stream(this->pbase(), w))
{
- setp(this->pbase(), this->epptr() - 1);
+ this->setp(this->pbase(), this->epptr() - 1);
return c;
}
else