#include <reaction.h>

Inheritance diagram for OBReaction:

Public Member Functions
	OBReaction ()

int	NumReactants () const

int	NumProducts () const

int	NumAgents () const

void	AddReactant (const obsharedptr< OBMol > sp)

void	AddProduct (const obsharedptr< OBMol > sp)

void	SetTransitionState (const obsharedptr< OBMol > sp)

void	AddAgent (const obsharedptr< OBMol > sp)

obsharedptr< OBMol >	GetReactant (const unsigned i)

obsharedptr< OBMol >	GetProduct (const unsigned i)

obsharedptr< OBMol >	GetAgent (const unsigned i)

obsharedptr< OBMol >	GetTransitionState () const

std::string	GetTitle () const

std::string	GetComment () const

void	SetTitle (const std::string &title)

void	SetComment (const std::string &comment)

bool	IsReversible () const

void	SetReversible (bool b=true)

bool	Clear ()

virtual OBBase *	DoTransformations (const std::map< std::string, std::string > , OBConversion )

template<class T >
T *	CastAndClear (bool clear=true)

virtual const char *	GetTitle (bool replaceNewlines=true) const

virtual void	SetTitle (const char *)

Generic data handling methods (via OBGenericData)
bool	HasData (const std::string &)

bool	HasData (const char *)

bool	HasData (const unsigned int type)

void	DeleteData (unsigned int type)

void	DeleteData (OBGenericData *)

void	DeleteData (std::vector< OBGenericData *> &)

bool	DeleteData (const std::string &s)

void	SetData (OBGenericData *d)

void	CloneData (OBGenericData *d)

size_t	DataSize () const

OBGenericData *	GetData (const unsigned int type)

OBGenericData *	GetData (const std::string &)

OBGenericData *	GetData (const char *)

std::vector< OBGenericData * > &	GetData ()

std::vector< OBGenericData * >	GetData (DataOrigin source)

std::vector< OBGenericData * >	GetAllData (const unsigned int type)

OBDataIterator	BeginData ()

OBDataIterator	EndData ()

Static Public Member Functions
static const char *	ClassDescription ()

Protected Attributes
std::vector< OBGenericData * >	_vdata

Detailed Description

Used to store chemical reactions (i.e., reactants -> products)

Reactants and products stored as smart pointers to molecules stored elsewhere.

For performing actual reaction transformations (i.e., deleting atoms, changing bonds, etc.) use the OBChemTsfm class.

Constructor & Destructor Documentation

◆ OBReaction()

OBReaction ( )

inline

Member Function Documentation

◆ NumReactants()

int NumReactants ( ) const

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ NumProducts()

int NumProducts ( ) const

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ NumAgents()

int NumAgents ( ) const

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ AddReactant()

void AddReactant ( const obsharedptr< OBMol > sp )

inline

◆ AddProduct()

void AddProduct ( const obsharedptr< OBMol > sp )

inline

◆ SetTransitionState()

void SetTransitionState ( const obsharedptr< OBMol > sp )

inline

◆ AddAgent()

void AddAgent ( const obsharedptr< OBMol > sp )

inline

◆ GetReactant()

obsharedptr<OBMol> GetReactant ( const unsigned i )

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ GetProduct()

obsharedptr<OBMol> GetProduct ( const unsigned i )

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ GetAgent()

obsharedptr<OBMol> GetAgent ( const unsigned i )

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ GetTransitionState()

obsharedptr<OBMol> GetTransitionState ( ) const

inline

Referenced by OBMoleculeFormat::DeleteDeferredMols().

◆ GetTitle() [1/2]

std::string GetTitle ( ) const

inline

◆ GetComment()

std::string GetComment ( ) const

inline

◆ SetTitle() [1/2]

void SetTitle ( const std::string & title )

inline

◆ SetComment()

void SetComment ( const std::string & comment )

inline

◆ IsReversible()

bool IsReversible ( ) const

inline

◆ SetReversible()

void SetReversible ( bool b = true )

inline

◆ ClassDescription()

static const char* ClassDescription ( )

inlinestatic

◆ Clear()

bool Clear ( void )

inlinevirtual

Clear any and all data associated with this object.

This method can be called by OBConversion::Read() before reading data. Derived classes should be sure to call OBBase::Clear() to remove inherited generic data.

Returns: Whether the call was successful.

Since: version 2.1.

Reimplemented from OBBase.

◆ DoTransformations()

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)

inlinevirtualinherited

Perform a set of transformations specified by the user

Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription() Base type does nothing

Reimplemented in OBMol.

◆ CastAndClear()

T* CastAndClear ( bool clear = true )

inlineinherited

By default clears the object. Called from ReadMolecule of most format classes.

◆ GetTitle() [2/2]

virtual const char* GetTitle ( bool replaceNewlines = true ) const

inlinevirtualinherited

Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ SetTitle() [2/2]

virtual void SetTitle ( const char * )

inlinevirtualinherited

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ HasData() [1/3]

bool HasData ( const std::string & s )

inherited

Returns: whether the generic attribute/value pair exists

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

◆ HasData() [2/3]

bool HasData ( const char * s )

inherited

Returns: whether the generic attribute/value pair exists

◆ HasData() [3/3]

bool HasData ( const unsigned int type )

inherited

Returns: whether the generic attribute/value pair exists, for a given OBGenericDataType

◆ DeleteData() [1/4]

void DeleteData ( unsigned int type )

inherited

Delete any data matching the given OBGenericDataType.

Referenced by OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OpenBabel::DeleteStereoOnAtom(), and OBMol::RenumberAtoms().

◆ DeleteData() [2/4]

void DeleteData ( OBGenericData * gd )

inherited

Delete the given generic data from this object.

◆ DeleteData() [3/4]

void DeleteData ( std::vector< OBGenericData *> & vg )

inherited

Delete all of the given generic data from this object.

◆ DeleteData() [4/4]

bool DeleteData ( const std::string & s )

inherited

Deletes the generic data with the specified attribute, returning false if not found.

◆ SetData()

void SetData ( OBGenericData * d )

inlineinherited

Adds a data object; does nothing if d==NULL.

Referenced by OBGastChrg::AssignPartialCharges(), OBMol::CopySubstructure(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), AliasData::RevertToAliasForm(), and OBMol::SetEnergies().

◆ CloneData()

void CloneData ( OBGenericData * d )

inherited

Adds a copy of a data object; does nothing if d == NULL

Since: version 2.2

Referenced by AliasData::Expand().

◆ DataSize()

size_t DataSize ( ) const

inlineinherited

Returns: the number of OBGenericData items attached to this molecule.

◆ GetData() [1/5]

OBGenericData * GetData ( const unsigned int type )

inherited

Returns: the first matching data for a given type from OBGenericDataType or NULL if nothing matches

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OpenBabel::extract_thermochemistry(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OpenBabel::IsSuppressibleHydrogen(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), and OBDescriptor::PredictAndSave().

◆ GetData() [2/5]

OBGenericData * GetData ( const std::string & s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [3/5]

OBGenericData * GetData ( const char * s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [4/5]

std::vector<OBGenericData*>& GetData ( )

inlineinherited

Returns: all data, suitable for iterating

Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().

◆ GetData() [5/5]

std::vector< OBGenericData * > GetData ( DataOrigin source )

inherited

Returns: all data with a specific origin, suitable for iterating

◆ GetAllData()

std::vector< OBGenericData * > GetAllData ( const unsigned int type )

inherited

Returns: the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches

Since: version 2.2

Referenced by OpenBabel::CanonicalLabels(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), OpenBabel::DeleteStereoOnAtom(), and OBMol::operator+=().

◆ BeginData()

OBDataIterator BeginData ( )

inlineinherited

Returns: An iterator pointing to the beginning of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

◆ EndData()

OBDataIterator EndData ( )

inlineinherited

Returns: An iterator pointing to the end of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

Member Data Documentation

◆ _vdata

std::vector<OBGenericData*> _vdata

protectedinherited

Custom data.

Referenced by OBMol::OBMol().

The documentation for this class was generated from the following file:

reaction.h

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OBReaction()

Member Function Documentation

◆ NumReactants()

◆ NumProducts()

◆ NumAgents()

◆ AddReactant()

◆ AddProduct()

◆ SetTransitionState()

◆ AddAgent()

◆ GetReactant()

◆ GetProduct()

◆ GetAgent()

◆ GetTransitionState()

◆ GetTitle() [1/2]

◆ GetComment()

◆ SetTitle() [1/2]

◆ SetComment()

◆ IsReversible()

◆ SetReversible()

◆ ClassDescription()

◆ Clear()

◆ DoTransformations()

◆ CastAndClear()

◆ GetTitle() [2/2]

◆ SetTitle() [2/2]

◆ HasData() [1/3]

◆ HasData() [2/3]

◆ HasData() [3/3]

◆ DeleteData() [1/4]

◆ DeleteData() [2/4]

◆ DeleteData() [3/4]

◆ DeleteData() [4/4]

◆ SetData()

◆ CloneData()

◆ DataSize()

◆ GetData() [1/5]

◆ GetData() [2/5]

◆ GetData() [3/5]

◆ GetData() [4/5]

◆ GetData() [5/5]

◆ GetAllData()

◆ BeginData()

◆ EndData()

Member Data Documentation

◆ _vdata