OBReaction Class Reference
Used to store chemical reactions (i.e., reactants -> products). More...
#include <reaction.h>
Public Member Functions | |
| OBReaction () | |
| int | NumReactants () const |
| int | NumProducts () const |
| void | AddReactant (const std::tr1::shared_ptr< OBMol > sp) |
| void | AddProduct (const std::tr1::shared_ptr< OBMol > sp) |
| void | SetTransitionState (const std::tr1::shared_ptr< OBMol > sp) |
| void | AddAgent (const std::tr1::shared_ptr< OBMol > sp) |
| std::tr1::shared_ptr< OBMol > | GetReactant (const unsigned i) |
| std::tr1::shared_ptr< OBMol > | GetProduct (const unsigned i) |
| std::tr1::shared_ptr< OBMol > | GetTransitionState () const |
| std::tr1::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) |
| virtual bool | Clear () |
| virtual OBBase * | DoTransformations (const std::map< std::string, std::string > *) |
| template<class T> | |
| T * | CastAndClear (bool clear=true) |
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) |
| unsigned int | 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 std::tr1::shared_ptr< OBMol > | sp | ) | [inline] |
| void AddProduct | ( | const std::tr1::shared_ptr< OBMol > | sp | ) | [inline] |
| void SetTransitionState | ( | const std::tr1::shared_ptr< OBMol > | sp | ) | [inline] |
| void AddAgent | ( | const std::tr1::shared_ptr< OBMol > | sp | ) | [inline] |
| std::tr1::shared_ptr<OBMol> GetReactant | ( | const unsigned | i | ) | [inline] |
| std::tr1::shared_ptr<OBMol> GetProduct | ( | const unsigned | i | ) | [inline] |
| std::tr1::shared_ptr<OBMol> GetTransitionState | ( | ) | const [inline] |
| std::tr1::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 | ) | [virtual, inherited] |
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 in OBAtom, OBMol, and OBResidue.
Referenced by OBResidue::Clear(), OBMol::Clear(), and OBAtom::Clear().
| virtual OBBase* DoTransformations | ( | const std::map< std::string, std::string > * | ) | [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()
Reimplemented in OBMol.
| T* CastAndClear | ( | bool | clear = true |
) | [inline, inherited] |
By default clears the object. Called from ReadMolecule of most format classes.
| bool HasData | ( | const std::string & | s | ) | [inherited] |
- Returns:
- whether the generic attribute/value pair exists
Referenced by OBMol::AddAtom(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), 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 OBMol::AddAtom(), OBMol::BeginModify(), OBBuilder::CorrectStereoBonds(), OBDescriptor::DeleteProperties(), OBMol::FindSSSR(), OBMol::NewAtom(), 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(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetNextFragment(), 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
| unsigned int 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(), OBDescriptor::FilterCompare(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), 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(), OBMol::FindSSSR(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), 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
| OBDataIterator BeginData | ( | ) | [inline, inherited] |
- Returns:
- An iterator pointing to the beginning of the data
Referenced by OBMol::AddAtom(), 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(), 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:
