Public Member Functions | Static Public Member Functions | Protected Attributes

OBReaction Class Reference

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

#include <reaction.h>

Inheritance diagram for OBReaction:
Inheritance graph
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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.

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 OBMol::AddAtom(), OBDepict::DrawMolecule(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), OBMol::operator=(), OBMoleculeFormat::ReadChemObjectImpl(), 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 OBMol::AddAtom(), OBMol::BeginModify(), OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OBMol::EndModify(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::NewAtom(), OBMol::RenumberAtoms(), and OBForceField::Setup().

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 OBMol::AddBond(), OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DoTransformations(), OBAtom::Duplicate(), AliasData::Expand(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::operator=(), OBDescriptor::PredictAndSave(), OBMol::SetEnergies(), and OBMol::SetFormula().

void CloneData ( OBGenericData *  d  )  [inherited]

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

Since:
version 2.2

Referenced by OBMol::AddBond().

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(), AliasData::Expand(), 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::BeginModify(), OBMol::DoTransformations(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBMol::SetEnergies(), and OBMol::SetFormula().

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 OBMol::AddAtom(), OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::NewAtom(), and OBMol::operator=().

OBDataIterator EndData (  )  [inline, inherited]
Returns:
An iterator pointing to the end of the data

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

Member Data Documentation

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

Custom data.

Referenced by OBBase::Clear(), OBBase::CloneData(), OBBase::DeleteData(), OBAtom::Duplicate(), OBBase::GetAllData(), OBBase::GetData(), OBBase::HasData(), OBBond::OBBond(), OBMol::OBMol(), and OBResidue::OBResidue().

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