Develop Biology
The language of life
Public Member Functions | List of all members
bio::chemical::Structure Class Reference

#include <Structure.h>

+ Inheritance diagram for bio::chemical::Structure:
+ Collaboration diagram for bio::chemical::Structure:

Public Member Functions

 Structure ()
 
virtual ~Structure ()
 
- Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
 UnorderedStructureInterface ()
 
virtual ~UnorderedStructureInterface ()
 
template<typename T >
T Add (const T t)
 
template<typename T >
void Clear ()
 
template<typename T >
Container * GetAll ()
 
template<typename T >
const Container * GetAll () const
 
template<typename T >
std::vector< T > GetAllAsVector ()
 
template<typename T >
const std::vector< T > GetAllAsVector () const
 
template<typename T >
unsigned long GetCount () const
 
template<typename T >
unsigned int GetNumMatching (const Container *other) const
 
template<typename T >
std::string GetStringFrom (std::string separator=", ")
 
template<typename T >
bool Has (T content) const
 
template<typename T >
bool HasAll (const Container *contents) const
 
template<typename T >
void Import (const std::vector< T > &other)
 
template<typename T >
void Import (const UnorderedMotif< T > *other)
 
Code ImportAll (const physical::Wave *other)
 
template<typename T >
T Remove (const T t)
 
- Public Member Functions inherited from bio::ThreadSafe
 ThreadSafe ()
 
 ThreadSafe (const ThreadSafe &toCopy)
 
virtual ~ThreadSafe ()
 
void LockThread () const
 
void UnlockThread () const
 
- Public Member Functions inherited from bio::chemical::Atom
 Atom (const Atom &other)
 
virtual ~Atom ()
 
template<typename T >
T As ()
 
template<typename T >
const T As () const
 
template<typename T >
T AsBonded ()
 
template<typename T >
const T AsBonded () const
 
template<typename T >
T AsBondedQuantum ()
 
template<typename T >
const T AsBondedQuantum () const
 
virtual Code Attenuate (const Wave *other)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Atom) explicit Atom()
 
template<typename T >
bool BreakBond (T toDisassociate, BondType type=bond_type::Unknown())
 
virtual Code Disattenuate (const Wave *other)
 
template<typename T >
bool FormBond (T toBond, BondType type=bond_type::Unknown())
 
Bonds * GetAllBonds ()
 
const Bonds * GetAllBonds () const
 
Wave * GetBonded (Valence position)
 
const Wave * GetBonded (Valence position) const
 
template<typename T >
Valence GetBondPosition () const
 
Valence GetBondPosition (AtomicNumber bondedId) const
 
Valence GetBondPosition (Name typeName) const
 
template<typename T >
BondType GetBondType () const
 
BondType GetBondType (Valence position) const
 
template<typename T >
 operator T ()
 
virtual Code Reify (physical::Symmetry *symmetry)
 
virtual physical::Symmetry * Spin () const
 
- Public Member Functions inherited from bio::physical::Class< Atom >
 Class (Atom *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual Wave * AsWave ()
 
virtual const Wave * AsWave () const
 
virtual Wave * Clone () const
 
Atom * Convert (Wave *wave)
 
virtual operator Atom * ()
 
virtual operator Wave * ()
 
- Public Member Functions inherited from bio::physical::Wave
 Wave (Symmetry *symmetry=NULL)
 
virtual ~Wave ()
 
virtual chemical::Atom * AsAtom ()
 
virtual const chemical::Atom * AsAtom () const
 
virtual Wave * AsWave ()
 
virtual const Wave * AsWave () const
 
virtual Code Attenuate (const Wave *other)
 
virtual Wave * Clone () const
 
virtual Wave * Demodulate ()
 
virtual const Wave * Demodulate () const
 
virtual Code Disattenuate (const Wave *other)
 
virtual Properties GetProperties () const
 
virtual Wave * Modulate (Wave *signal)
 
virtual Wave * operator* ()
 
virtual const Wave * operator* () const
 
virtual Wave * operator* (Wave *signal)
 
virtual void operator+ (const Wave *other)
 
virtual void operator- (const Wave *other)
 
virtual void operator| (Symmetry *symmetry)
 
virtual Code Reify (Symmetry *symmetry)
 
virtual Symmetry * Spin () const
 
- Public Member Functions inherited from bio::chemical::LinearStructureInterface
 LinearStructureInterface ()
 
virtual ~LinearStructureInterface ()
 
template<typename T >
Emission ForEach (ExcitationBase *excitation)
 
template<typename T >
T GetById (StandardDimension id)
 
template<typename T >
const T GetById (StandardDimension id) const
 
template<typename T >
T GetByName (Name name)
 
template<typename T >
const T GetByName (Name name) const
 
template<typename T >
T GetOrCreateById (StandardDimension id)
 
template<typename T >
T GetOrCreateByName (Name name)
 
template<typename T >
Code Insert (T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 

Additional Inherited Members

- Static Public Member Functions inherited from bio::physical::Wave
static Properties GetResonanceBetween (const Wave *wave, const Properties &properties)
 
static Properties GetResonanceBetween (const Wave *wave1, const Wave *wave2)
 
static Properties GetResonanceBetween (ConstWaves waves)
 
- Protected Member Functions inherited from bio::chemical::Atom
virtual bool BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)
 
virtual bool FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)
 
- Protected Attributes inherited from bio::chemical::Atom
Bonds m_bonds
 
- Protected Attributes inherited from bio::physical::Class< Atom >
Atom * m_object
 
- Protected Attributes inherited from bio::physical::Wave
Wave * m_signal
 
Symmetry * m_symmetry
 

Detailed Description

Chemical structures can have Motifs. Here, we implement all the necessary interfaces for adding Motifs to your classes.

This class should be virtually inherited.

Motifs should be inherited (but can be added through Bonding). The reason that we break the "has a motif" idea and instead go for "is a motif" inheritance style is that chemical compositions define the identity of chemical structures. So if a chemical substance would change its identity by containing different motifs, it makes sense that the motifs define the class structure of the substance.

Definition at line 38 of file Structure.h.

Constructor & Destructor Documentation

◆ Structure()

bio::chemical::Structure::Structure ( )

Definition at line 27 of file Structure.cpp.

28{
29}

◆ ~Structure()

bio::chemical::Structure::~Structure ( )
virtual

Definition at line 31 of file Structure.cpp.

32{
33}
The documentation for this class was generated from the following files: