/usr/include/openbabel-2.0/openbabel/plugin.h is in libopenbabel-dev 2.3.2+dfsg-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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plugin.h - facilitates construction of plugin classes
Copyright (C) 2007 by Chris Morley
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
***********************************************************************/
#ifndef OB_PLUGIN_H
#define OB_PLUGIN_H
#include <openbabel/babelconfig.h>
#include <string>
#include <iostream>
#include <vector>
#include <map>
#include <sstream>
#include <cstring>
#ifndef OBERROR
#define OBERROR
#endif
namespace OpenBabel
{
///@addtogroup plugins Plugins
///@{
/// @brief Case insensitive string comparison for PluginMapType key.
struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
{
bool operator()(const char* p1,const char* p2) const
{ return strcasecmp(p1,p2)<0; }
};
/** \class OBPlugin plugin.h <openbabel/plugin.h>
\brief Base class for all types of dynamic classes discovered at runtime
\since version 2.2
\sa plugin.h
*/
class OBERROR OBPlugin
{
public:
//Maps of thistype are used to store
// (a)a list of the plugin types in OBPlugin, and
// (b)a list of the sub-types in each type class derived from OBPlugin.
typedef std::map<const char*, OBPlugin*, CharPtrLess> PluginMapType;
typedef PluginMapType::const_iterator PluginIterator;
///Virtual destructor necessary for classes with virtual functions
virtual ~OBPlugin(){};
///Required description of a sub-type
virtual const char* Description() { return NULL;} ;
///Redefined by each plugin type: "formats", "fingerprints", etc.
virtual const char* TypeID(){ return "plugins"; }
///Write information on a plugin class to the string txt.
///Return false if not written.
///The default implementation outputs:
/// the ID, a tab character, and the first line of the Description.
///The param string can be used in derived types to provide different outputs.
virtual bool Display(std::string&txt, const char* param, const char* ID=NULL);
///Make a new instance of the class.
///See OpTransform, OBGroupContrib, SmartsDescriptor classes for derived versions.
///Usually, the first parameter is the classname, the next three are
///parameters(ID, filename, description) for a constructor, and the rest data.
virtual OBPlugin* MakeInstance(const std::vector<std::string>&){return NULL;}
///Initialize the plugin.
///The default version does nothing.
virtual void Init(){};
///Get a pointer to a plugin from its type and ID. Return NULL if not found.
///If Type is NULL, search all types. Not cast to Type*
static OBPlugin* GetPlugin(const char* Type, const char* ID);
///Return the ID of the sub-type instance.
const char* GetID()const{return _id;};
///Output a list of sub-type classes of the the type PluginID,
///or, if PluginID is "plugins" or empty, a list of the base types.
///If PluginID is not recognized or is NULL, the base types are output and the return is false.
static bool ListAsVector(const char* PluginID, const char* param, std::vector<std::string>& vlist);
///As ListAsVector but sent to an ostream with a default of cout if not specified
static void List(const char* PluginID, const char* param=NULL, std::ostream* os=&std::cout);
///As ListAsVector but returns a string containing the list
static std::string ListAsString(const char* PluginID, const char* param=NULL);
///Utility function to return only the first line of a string
static std::string FirstLine(const char* txt);
///Return an iterator at the start of the map of the plugin types PluginID or,
/// if there is no such map, the end of the top level plugin map.
static PluginIterator Begin(const char* PluginID)
{
if( !strcmp(PluginID, "plugins") || GetTypeMap(PluginID)!=PluginMap())
return GetTypeMap(PluginID).begin();
else
return PluginMap().end();
}
static PluginIterator End(const char* PluginID)
{
return GetTypeMap(PluginID).end();
}
///Returns the map of the subtypes
virtual PluginMapType& GetMap() const =0;
protected:
///\brief Returns a reference to the map of the plugin types.
/// Is a function rather than a static member variable to avoid initialization problems.
static PluginMapType& PluginMap()
{
static PluginMapType m;
return m;
}
///Returns the map of a particular plugin type, e.g. GetMapType("fingerprints")
static PluginMapType& GetTypeMap(const char* PluginID);
///\brief Returns the type with the specified ID, or NULL if not found.
///Needs to be cast to the appropriate class in the calling routine.
static OBPlugin* BaseFindType(PluginMapType& Map, const char* ID);
protected:
const char* _id;
};
#if defined(__CYGWIN__) || defined(__MINGW32__)
//Macro to be added to definition of the base class
#define MAKE_PLUGIN(BaseClass)\
protected:\
static PluginMapType& Map();\
virtual PluginMapType& GetMap() const {\
return Map();\
}\
public:\
static BaseClass*& Default() {\
static BaseClass* d;\
return d;\
}\
BaseClass(const char* ID, bool IsDefault=false) {\
_id=ID;\
if (ID&&*ID) {\
if (IsDefault || Map().empty()) {\
Default() = this;\
}\
if (Map().count(ID) == 0) {\
Map()[ID] = this;\
PluginMap()[TypeID()] = this;\
}\
}\
}\
static BaseClass* FindType(const char* ID) {\
if (!ID || *ID==0 || *ID==' ') {\
return Default();\
}\
return static_cast<BaseClass*>(BaseFindType(Map(),ID));\
}
#define PLUGIN_CPP_FILE(BaseClass)\
OBPlugin::PluginMapType& BaseClass::Map() {\
static OBPlugin::PluginMapType map;\
return map;\
}
#else // __CYGWIN__ || __MINGW32__
//Macro to be added to definition of the base class
#define MAKE_PLUGIN(BaseClass)\
protected:\
static PluginMapType& Map() {\
static PluginMapType m;\
return m;\
}\
virtual PluginMapType& GetMap() const {\
return Map();\
}\
public:\
static BaseClass*& Default() {\
static BaseClass* d;\
return d;\
}\
BaseClass(const char* ID, bool IsDefault=false) {\
_id=ID;\
if (ID&&*ID) {\
if (IsDefault || Map().empty()) {\
Default() = this;\
}\
if (Map().count(ID) == 0) {\
Map()[ID] = this;\
PluginMap()[TypeID()] = this;\
}\
}\
}\
static BaseClass* FindType(const char* ID) {\
if (!ID || *ID==0 || *ID==' ') {\
return Default();\
}\
return static_cast<BaseClass*>(BaseFindType(Map(),ID));\
}
#endif // __CYGWIN__ || __MINGW32__
/** \file plugin.h
\brief Simplify 'plugin' classes to be discovered and/or loaded at runtime.
The code in this file makes it easy to make 'plugin' classes. These classes are
derived from a base class, like OBFingerprint. The derived classes
('sub-types' like fingerprint2) usually have a single instance. Plugin classes
are only discovered at runtime, so no existing code needs to be changed when
adding a new derived class. In some builds the new code can be added or removed
by just moving a DLL or so file. The plugin classes derived from any base class
(including new ones) type can be listed from the commandline.
<h2>Step-by-Step Instructions</h2>
1) In the header file for YourBaseClass (which handles whatsits).
Make sure to include the plugin.h header ,
derive the class from OBPlugin
and in its definition add
the MAKE_PLUGIN macro
and a function TypeID() containing a simple descriptor of the type
\code
#include <openbabel/plugin.h>
class YourBaseClass : public OBPlugin
{
MAKE_PLUGIN(YourBaseClass)
const char* TypeID()
{ return "whatsits"; };
...rest of implementation, probably involving virtual functions redefined
in the sub-type classes
};
\endcode
See below for what the macro contains.
2) Declare each sub-type in a class derived from the base class
and give it a constructor which calls OBPlugin constructor as shown:
\code
class YourSubType1 : public YourBaseClass
{
public:
YourSubtype1(const char* ID, bool IsDefault=false)
: YourBaseClass(ID, IsDefault){}
virtual string Description()
{ return "A description with one or more lines";};
...rest of implementation
};
\endcode
Only the first line of the description is used when the subclasses are listed.
3) Declare a global instance of the sub-type class which specifies its ID.
and, optionally, whether it is to be regarded as the default type of YourBaseClass.
\code
YourSubType1 theType1("whatsit2",true);
\endcode
4) The following functions are available:
YourBaseClass* YourBaseClass::FindType(const char* ID);
This returns the default type when ID is NULL or empty.
To list the sub-types of any plugin class use the List which sends to cout
by default (or any other ostream if specified).
\code
OBPlugin::List("whatsits")
\endcode
The ListAsString and ListAsVector functions are alternatives, usable with scripting.
It is also possible to iterate through each sub-type by the following code:
\code
OBPlugin::PluginIterator itr;
for(itr=OBPlugin::Begin("whatsits");itr!=OBPlugin::End("whatsits");++itr)
{
itr is a std::map::const_iterator
itr->first is the ID of the subtype;
itr->second is The OBPlugin* which you will have to cast to your type
}
\endcode
Since this is not the most beautiful code, it is probably better to use the
List methods if possible.
YourBaseClass* MakeNewInstance();
<h2>How it works</h2>
MAKE_PLUGIN(YourBaseClass) inserts the following code into YourBaseClass:
\code
protected:
//The collection of sub-types is in a local static variable to avoid
//any difficulties with the order of initialization of static objects.
static PluginMapType& Map()
{
static PluginMapType m;
return m;
}
//Making the map accessible to the base class (Cannot be used during construction)
virtual PluginMapType& GetMap()const
{
return Map();
}
public:
static YourBaseClass*& Default()
{
static YourBaseClass* d;
return d;
}
//Constructor registers the sub-type
YourBaseClass(const char* ID, bool IsDefault=false)
{
_id = ID;
if(ID && *ID && *ID!=' ') //do not register if ID is empty or starts with a space
{
if(IsDefault || Map().empty())
Default() = this;
Map()[ID]=this;
//Ensure YourBaseClass is registered in OBPlugin so it can be accessed from the commandline
PluginMap()[TypeID()] =this;
}
}
///Returns the sub-type associated with the ID, or the default subtype if ID NULL or empty.
static YourBaseClass* FindType(const char* ID)
{
if(!ID || *ID==0)
return Default();
return static_cast<YourBaseClass*>(BaseFindType(Map(),ID));
}
\endcode
*/
/*\@}*/
#ifndef SWIG // Skipped by SWIG (for the moment)
#ifndef USING_DYNAMIC_LIBS
#define OB_STATIC_PLUGIN(className,instanceName) \
class className; \
OBAPI EXTERN className instanceName;
// formats
OB_STATIC_PLUGIN(AcesOutputFormat, theAcesOutputFormat)
OB_STATIC_PLUGIN(AcesInputFormat, theAcesInputFormat)
OB_STATIC_PLUGIN(ACRFormat, theACRFormat)
OB_STATIC_PLUGIN(ADFOutputFormat, theADFOutputFormat)
OB_STATIC_PLUGIN(ADFInputFormat, theADFInputFormat)
OB_STATIC_PLUGIN(AlchemyFormat, theAlchemyFormat)
OB_STATIC_PLUGIN(AmberPrepFormat, theAmberPrepFormat)
OB_STATIC_PLUGIN(OBAPIInterface, theOBAPIInterface)
OB_STATIC_PLUGIN(BallStickFormat, theBallStickFormat)
OB_STATIC_PLUGIN(BGFFormat, theBGFFormat)
OB_STATIC_PLUGIN(BoxFormat, theBoxFormat)
OB_STATIC_PLUGIN(CacaoFormat, theCacaoFormat)
OB_STATIC_PLUGIN(CacheFormat, theCacheFormat)
OB_STATIC_PLUGIN(CARFormat, theCARFormat)
OB_STATIC_PLUGIN(CCCFormat, theCCCFormat)
OB_STATIC_PLUGIN(CHEM3D1Format, theCHEM3D1Format)
OB_STATIC_PLUGIN(CHEM3D2Format, theCHEM3D2Format)
OB_STATIC_PLUGIN(ChemDrawBinaryFormat, theChemDrawBinaryFormat)
OB_STATIC_PLUGIN(ChemDrawFormat, theChemDrawFormat)
OB_STATIC_PLUGIN(ChemKinFormat, theChemKinFormat)
OB_STATIC_PLUGIN(CHTFormat, theCHTFormat)
OB_STATIC_PLUGIN(CIFFormat, theCIFFormat)
OB_STATIC_PLUGIN(CopyFormat, theCopyFormat)
OB_STATIC_PLUGIN(CRK2DFormat, theCRK2DFormat)
OB_STATIC_PLUGIN(CRK3DFormat, theCRK3DFormat)
OB_STATIC_PLUGIN(CSRFormat, theCSRFormat)
OB_STATIC_PLUGIN(CSSRFormat, theCSSRFormat)
OB_STATIC_PLUGIN(DlpolyConfigFormat, theDlpolyConfigFormat)
OB_STATIC_PLUGIN(DlpolyHISTORYFormat, theDlpolyHISTORYFormat)
OB_STATIC_PLUGIN(DMolFormat, theDMolFormat)
OB_STATIC_PLUGIN(FASTAFormat, theFASTAFormat)
OB_STATIC_PLUGIN(FastSearchFormat, theFastSearchFormat)
OB_STATIC_PLUGIN(FCHKFormat, theFCHKFormat)
OB_STATIC_PLUGIN(FEATFormat, theFEATFormat)
OB_STATIC_PLUGIN(FenskeZmatFormat, theFenskeZmatFormat)
OB_STATIC_PLUGIN(FHIaimsFormat,theFHIaimsFormat)
OB_STATIC_PLUGIN(FingerprintFormat, theFingerprintFormat)
OB_STATIC_PLUGIN(FreeFormFractionalFormat, theFreeFormFractionalFormat)
OB_STATIC_PLUGIN(GAMESSOutputFormat, theGAMESSOutputFormat)
OB_STATIC_PLUGIN(GAMESSInputFormat, theGAMESSInputFormat)
OB_STATIC_PLUGIN(OBGaussianCubeFormat, theGaussianCubeFormat)
OB_STATIC_PLUGIN(GaussianOutputFormat, theGaussianOutputFormat)
OB_STATIC_PLUGIN(GaussianInputFormat, theGaussianInputFormat)
OB_STATIC_PLUGIN(GaussianZMatrixInputFormat, theGaussianZMatrixInputFormat)
OB_STATIC_PLUGIN(GenBankFormat, theGenBankFormat)
OB_STATIC_PLUGIN(GhemicalFormat, theGhemicalFormat)
OB_STATIC_PLUGIN(GROMOS96Format, theGROMOS96Format)
OB_STATIC_PLUGIN(GULPFormat, theGULPFormat)
OB_STATIC_PLUGIN(HINFormat, theHINFormat)
OB_STATIC_PLUGIN(JaguarOutputFormat, theJaguarOutputFormat)
OB_STATIC_PLUGIN(JaguarInputFormat, theJaguarInputFormat)
OB_STATIC_PLUGIN(MCDLFormat, theMCDLFormat)
OB_STATIC_PLUGIN(MOLFormat, theMOLFormat)
OB_STATIC_PLUGIN(SDFormat, theSDFormat)
OB_STATIC_PLUGIN(OBT41Format, t41Format__)
OB_STATIC_PLUGIN(OBMoldenFormat, moldenFormat__)
OB_STATIC_PLUGIN(mmCIFFormat, themmCIFFormat)
OB_STATIC_PLUGIN(MacroModFormat, theMacroModFormat)
OB_STATIC_PLUGIN(MNAFormat, theMNAFormat)
OB_STATIC_PLUGIN(MOL2Format, theMOL2Format)
OB_STATIC_PLUGIN(MolproOutputFormat, theMolproOutputFormat)
OB_STATIC_PLUGIN(MolproInputFormat, theMolproInputFormat)
OB_STATIC_PLUGIN(MolReportFormat, theMolReportFormat)
OB_STATIC_PLUGIN(MOPACFormat, theMOPACFormat)
OB_STATIC_PLUGIN(MOPACCARTFormat, theMOPACCARTFormat)
OB_STATIC_PLUGIN(MOPACINTFormat, theMOPACINTFormat)
OB_STATIC_PLUGIN(MPDFormat, theMPDFormat)
OB_STATIC_PLUGIN(MPQCFormat, theMPQCFormat)
OB_STATIC_PLUGIN(MPQCInputFormat, theMPQCInputFormat)
OB_STATIC_PLUGIN(MSIFormat, theMSIFormat)
OB_STATIC_PLUGIN(OBMSMSFormat, msmsFormat__)
OB_STATIC_PLUGIN(NulFormat, theNulFormat)
OB_STATIC_PLUGIN(NWChemOutputFormat, theNWChemOutputFormat)
OB_STATIC_PLUGIN(NWChemInputFormat, theNWChemInputFormat)
OB_STATIC_PLUGIN(OBOpenDXCubeFormat, theOpenDXCubeFormat)
OB_STATIC_PLUGIN(OutputFormat, theOutputFormat)
OB_STATIC_PLUGIN(PCModelFormat, thePCModelFormat)
OB_STATIC_PLUGIN(PDBFormat, thePDBFormat)
OB_STATIC_PLUGIN(PDBQTFormat, thePDBQTFormat)
#ifdef HAVE_LIBZ
OB_STATIC_PLUGIN(PNGFormat, thePNGFormat)
#endif
OB_STATIC_PLUGIN(PovrayFormat, thePovrayFormat)
OB_STATIC_PLUGIN(PQRFormat, thePQRFormat)
OB_STATIC_PLUGIN(PQSFormat, thePQSFormat)
OB_STATIC_PLUGIN(PWscfFormat, thePWscfFormat)
OB_STATIC_PLUGIN(QChemOutputFormat, theQChemOutputFormat)
OB_STATIC_PLUGIN(QChemInputFormat, theQChemInputFormat)
OB_STATIC_PLUGIN(ReportFormat, theReportFormat)
OB_STATIC_PLUGIN(SmiReactFormat, theSmiReactFormat)
OB_STATIC_PLUGIN(RXNFormat, theRXNFormat)
OB_STATIC_PLUGIN(ShelXFormat, theShelXFormat)
OB_STATIC_PLUGIN(SMIFormat, theSMIFormat)
OB_STATIC_PLUGIN(CANSMIFormat, theCANSMIFormat)
OB_STATIC_PLUGIN(FIXFormat, theFIXFormat)
OB_STATIC_PLUGIN(SVGFormat, theSVGFormat)
OB_STATIC_PLUGIN(TextFormat, theTextFormat)
OB_STATIC_PLUGIN(ThermoFormat, theThermoFormat)
OB_STATIC_PLUGIN(TinkerFormat, theTinkerFormat)
OB_STATIC_PLUGIN(TitleFormat, theTitleFormat)
OB_STATIC_PLUGIN(TurbomoleFormat, theTurbomoleFormat)
OB_STATIC_PLUGIN(UniChemFormat, theUniChemFormat)
OB_STATIC_PLUGIN(VASPFormat, theVASPFormat)
OB_STATIC_PLUGIN(ViewMolFormat, theViewMolFormat)
OB_STATIC_PLUGIN(XEDFormat, theXEDFormat)
OB_STATIC_PLUGIN(XYZFormat, theXYZFormat)
OB_STATIC_PLUGIN(YOBFormat, theYOBFormat)
OB_STATIC_PLUGIN(ZINDOFormat, theZINDOFormat)
#ifdef HAVE_STATIC_LIBXML
OB_STATIC_PLUGIN(ChemDrawXMLFormat, theChemDrawXMLFormat)
OB_STATIC_PLUGIN(CMLFormat, theCMLFormat)
OB_STATIC_PLUGIN(CMLReactFormat, theCMLReactFormat)
OB_STATIC_PLUGIN(PubChemFormat, thePubChemFormat)
OB_STATIC_PLUGIN(XMLFormat, theXMLFormat)
#endif
#ifdef HAVE_STATIC_INCHI
OB_STATIC_PLUGIN(InChIFormat, theInChIFormat)
#endif
#ifdef HAVE_REGEX_H
OB_STATIC_PLUGIN(GAMESSUKInputFormat, theGAMESSUKInputFormat)
OB_STATIC_PLUGIN(GAMESSUKOutputFormat, theGAMESSUKOutputFormat)
#endif
#ifdef HAVE_RPC_XDR_H
OB_STATIC_PLUGIN(XTCFormat, theXTCFormat)
#endif
// descriptors
OB_STATIC_PLUGIN(CanSmiles, theCanSmiles)
OB_STATIC_PLUGIN(CompoundFilter, dummyCmpFilter)
OB_STATIC_PLUGIN(MWFilter, theMWFilter)
OB_STATIC_PLUGIN(SmartsFilter, firstSmartsFilter)
OB_STATIC_PLUGIN(SmartsFilter, secondSmartsFilter)
OB_STATIC_PLUGIN(TitleFilter, theTitleFilter)
OB_STATIC_PLUGIN(FormulaDescriptor, TheFormulaDescriptor)
//OB_STATIC_PLUGIN(FPCount, theFPCount)
OB_STATIC_PLUGIN(InChIFilter, theInChIFilter)
// smarts descriptors
OB_STATIC_PLUGIN(SmartsDescriptor, theHBD)
OB_STATIC_PLUGIN(SmartsDescriptor, theHBA1)
OB_STATIC_PLUGIN(SmartsDescriptor, theHBA2)
OB_STATIC_PLUGIN(SmartsDescriptor, thenF)
// group contribution descriptors
OB_STATIC_PLUGIN(OBGroupContrib, thelogP)
OB_STATIC_PLUGIN(OBGroupContrib, theTPSA)
OB_STATIC_PLUGIN(OBGroupContrib, theMR)
// fingerprints
OB_STATIC_PLUGIN(fingerprint2, thefingerprint2)
OB_STATIC_PLUGIN(PatternFP, FP3PatternFP)
OB_STATIC_PLUGIN(PatternFP, FP4PatternFP)
// forcefields
OB_STATIC_PLUGIN(OBForceFieldGaff, theForceFieldGaff)
OB_STATIC_PLUGIN(OBForceFieldGhemical, theForceFieldGhemical)
OB_STATIC_PLUGIN(OBForceFieldMMFF94, theForceFieldMMFF94)
OB_STATIC_PLUGIN(OBForceFieldMMFF94, theForceFieldMMFF94s)
OB_STATIC_PLUGIN(OBForceFieldUFF, theForceFieldUFF)
// operations
OB_STATIC_PLUGIN(OpAddInIndex, theOpAddInIndex)
OB_STATIC_PLUGIN(OpAddPolarH, theOpAddPolarH)
OB_STATIC_PLUGIN(OpCanonical, theOpCanonical)
OB_STATIC_PLUGIN(OpFillUC, theOpFillUC)
OB_STATIC_PLUGIN(OpEnergy, theOpEnergy)
OB_STATIC_PLUGIN(OpMinimize, theOpMinimize)
OB_STATIC_PLUGIN(OpGen2D, theOpGen2D)
OB_STATIC_PLUGIN(OpGen3D, theOpGen3D)
OB_STATIC_PLUGIN(OpNewS, theOpNewS)
OB_STATIC_PLUGIN(OpPartialCharge, theOpPartialCharge)
OB_STATIC_PLUGIN(OpReadConformers, theOpReadConformers)
OB_STATIC_PLUGIN(OpSort, theOpSort)
OB_STATIC_PLUGIN(OpExtraOut, theOpExtraOut)
#ifdef HAVE_STATIC_INCHI
OB_STATIC_PLUGIN(OpUnique, theOpUnique)
#endif
#ifdef HAVE_EIGEN
OB_STATIC_PLUGIN(OpConformer, theOpConformer)
#endif
// charges
OB_STATIC_PLUGIN(GasteigerCharges, theGasteigerCharges)
OB_STATIC_PLUGIN(MMFF94Charges, theMMFF94Charges)
#ifdef HAVE_EIGEN
OB_STATIC_PLUGIN(QEqCharges, theQEqCharges)
OB_STATIC_PLUGIN(QTPIECharges, theQTPIECharges)
#endif
OBAPI std::vector<std::string> EnableStaticPlugins();
#endif // USING_DYNAMIC_LIBS
#endif // SWIG
} // end namespce
#endif
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