OBReaction Class Reference

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

#include <reaction.h>

Inheritance diagram for OBReaction:

List of all members.

Public Member Functions
	OBReaction ()
int	NumReactants () const
int	NumProducts () const
void	AddReactant (const shared_ptr< OBMol > sp)
void	AddProduct (const shared_ptr< OBMol > sp)
void	SetTransitionState (const shared_ptr< OBMol > sp)
void	AddAgent (const shared_ptr< OBMol > sp)
shared_ptr< OBMol >	GetReactant (const unsigned i)
shared_ptr< OBMol >	GetProduct (const unsigned i)
shared_ptr< OBMol >	GetTransitionState () const
shared_ptr< OBMol >	GetAgent () 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.

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Constructor & Destructor Documentation

OBReaction

(

)

[inline]

---

Member Function Documentation

int NumReactants

(

)

const [inline]

int NumProducts

(

)

const [inline]

void AddReactant

(

const shared_ptr< OBMol >

sp )

[inline]

void AddProduct

(

const shared_ptr< OBMol >

sp )

[inline]

void SetTransitionState

(

const shared_ptr< OBMol >

sp )

[inline]

void AddAgent

(

const shared_ptr< OBMol >

sp )

[inline]

shared_ptr<OBMol> GetReactant

(

const unsigned

i )

[inline]

shared_ptr<OBMol> GetProduct

(

const unsigned

i )

[inline]

shared_ptr<OBMol> GetTransitionState

(

)

const [inline]

shared_ptr<OBMol> GetAgent

(

)

const [inline]

std::string GetTitle

(

)

const [inline]

std::string GetComment

(

)

const [inline]

void SetTitle

(

const std::string &

title )

[inline]

void SetComment

(

const std::string &

comment )

[inline]

bool IsReversible

(

)

const [inline]

void SetReversible

(

bool

b = true )

[inline]

static const char* ClassDescription

(

)

[inline, static]

Returns:

A list of descriptions of command-line options for DoTransformations()

Reimplemented from OBBase.

bool Clear

(

void

)

[inline, virtual]

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.

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)		[inline, virtual, inherited]

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.

T* CastAndClear

(

bool

clear = true )

[inline, inherited]

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

virtual const char* GetTitle

(

bool

replaceNewlines = true )

const [inline, virtual, inherited]

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

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

virtual void SetTitle

(

const char *

)

[inline, virtual, inherited]

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

bool HasData

(

const std::string &

s )

[inherited]

Returns:

whether the generic attribute/value pair exists

Referenced by OBDepict::DrawMolecule(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMol::operator=(), and OBMol::SetEnergies().

bool HasData

(

const char *

s )

[inherited]

Returns:

whether the generic attribute/value pair exists

bool HasData

(

const unsigned int

type )

[inherited]

Returns:

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

void DeleteData

(

unsigned int

type )

[inherited]

Delete any data matching the given OBGenericDataType.

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

void DeleteData

(

OBGenericData *

gd )

[inherited]

Delete the given generic data from this object.

void DeleteData

(

std::vector< OBGenericData * > &

vg )

[inherited]

Delete all of the given generic data from this object.

bool DeleteData

(

const std::string &

s )

[inherited]

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

void SetData

(

OBGenericData *

d )

[inline, inherited]

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

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), and OBMol::SetEnergies().

void CloneData

(

OBGenericData *

d )

[inherited]

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

Since:

version 2.2

size_t DataSize

(

)

const [inline, inherited]

Returns:

the number of OBGenericData items attached to this molecule.

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 OpenBabel::CalcSignedVolume(), OpenBabel::CorrectChirality(), OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), OBMol::operator=(), and OBDescriptor::PredictAndSave().

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

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

std::vector<OBGenericData*>& GetData

(

)

[inline, inherited]

Returns:

all data, suitable for iterating

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

std::vector< OBGenericData * > GetData

(

DataOrigin

source )

[inherited]

Returns:

all data with a specific origin, suitable for iterating

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(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().

OBDataIterator BeginData

(

)

[inline, inherited]

Returns:

An iterator pointing to the beginning of the data

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

OBDataIterator EndData

(

)

[inline, inherited]

Returns:

An iterator pointing to the end of the data

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

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Member Data Documentation

std::vector<OBGenericData*> _vdata [protected, inherited]

Custom data.

Referenced by OBMol::OBMol().

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

• reaction.h