Used to store chemical reactions (i.e., reactants -> products).
More...
#include <reaction.h>
List of all members.
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
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] |
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] |
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] |
virtual void SetTitle |
( |
const char * |
|
) |
[inline, virtual, inherited] |
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 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.
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().
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.
- 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().
- Returns:
- any data matching the given attribute name or NULL if nothing matches
-
the value given an attribute name
- Returns:
- any data matching the given attribute name or NULL if nothing matches
-
the value given an attribute name
- 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().
- Returns:
- all data with a specific origin, suitable for iterating
std::vector< OBGenericData * > GetAllData |
( |
const unsigned int |
type |
) |
[inherited] |
Member Data Documentation
The documentation for this class was generated from the following file: