ell::LandscapeTopology Class Reference

#include <LandscapeTopology.hh>

Inheritance diagram for ell::LandscapeTopology:

Detailed Description

An abstract representation of the landscapes topology that stores minima and allows for saddle point storage.

Author:: Hannes Kochniß, Martin Mann

Definition at line 16 of file LandscapeTopology.hh.

Public Member Functions

virtual const size_t addMin (const State *const m)=0

virtual bool addSaddle (const State *const m_i, const State *const m_j, const State *const s)=0

virtual bool addSaddle (const size_t i, const size_t j, const State *const s)=0

virtual void clear ()=0

virtual const State *const getMFEState () const=0

virtual const State *const getMin (size_t i) const =0

virtual const size_t getMinCount () const=0

virtual const size_t getMinIndex (const State *const m) const=0

virtual double getRMSD (const LandscapeTopology *const lt) const=0

virtual bool isSorted () const=0

virtual std::pair< int, std::string > read (std::istream &in, const State *const templateState, const std::string &StateDescription)=0

virtual void sort ()=0

virtual void write (std::ostream &out, const std::string &StateDescription) const=0

virtual ~LandscapeTopology ()

Static Public Attributes

static const size_t INVALID_INDEX

Static Protected Member Functions

static bool isSmaller_E_S (const State *a, const State *b)

Constructor & Destructor Documentation

ell::LandscapeTopology::~LandscapeTopology ( ) [virtual]

Destruction.

Definition at line 16 of file LandscapeTopology.cc.

Member Function Documentation

virtual const size_t ell::LandscapeTopology::addMin ( const State *const m ) [pure virtual]

Adds an UNKNOWN minimum to the topology. NOTE : this operation should NOT change the indices of already existing minima in the topology ! FURTHER : the minimum is not checked if it is already known

Parameters:

the first minimum to add

Returns:: the index of the minimum in the landscape

Implemented in ell::LT_MinimaSet.

virtual bool ell::LandscapeTopology::addSaddle	(	const State *const	m_i,
		const State *const	m_j,
		const State *const	s
	)			`[pure virtual]`

Sets a saddle point that connects two minima

Parameters:

	m_i	the first minimum to connect
	m_j	the second minimum to connect
	s	the State representating the saddle point

Returns:: whether or not the data structure has been changed

Implemented in ell::LT_MinimaSet.

virtual bool ell::LandscapeTopology::addSaddle	(	const size_t	i,
		const size_t	j,
		const State *const	s
	)			`[pure virtual]`

Sets a saddle point that connects two minima

Parameters:

	i	index of the first minimum to connect
	j	index of the second minimum to connect
	s	the State representating the saddle point

Returns:: whether or not the data structure has been changed

Implemented in ell::LT_MinimaSet.

virtual void ell::LandscapeTopology::clear ( ) [pure virtual]

Clears the data structure and removes all stored information to be filled again afterwards.

Implemented in ell::LT_MinimaSet.

virtual const State* const ell::LandscapeTopology::getMFEState ( ) const [pure virtual]

Access to the global minimum of the landscape with minimal free energy (mfe).

Returns:: the minimum with smallest energy (and smallest string representation for tiebreaking)

Implemented in ell::LT_MinimaSet.

virtual const State* const ell::LandscapeTopology::getMin ( size_t i ) const [pure virtual]

Access to a minimum.

Parameters:

index of the minimum to access

Returns:: the State with the specified minimum index

Implemented in ell::LT_MinimaSet.

virtual const size_t ell::LandscapeTopology::getMinCount ( ) const [pure virtual]

Access to the number of stored minima.

Returns:: the number of minima

Implemented in ell::LT_MinimaSet.

virtual const size_t ell::LandscapeTopology::getMinIndex ( const State *const m ) const [pure virtual]

Access to the minimum index.

Parameters:

the minimum of that the index should be accessed

Returns:: the index of the minimum, or INVALID_INDEX if 'm' is no known minimum

Implemented in ell::LT_MinimaSet.

virtual double ell::LandscapeTopology::getRMSD ( const LandscapeTopology *const lt ) const [pure virtual]

Calculates the root mean square deviation between landscape topologies.

Parameters:

the landscape topology to calculate the RMSD

Returns:: the RMSD

Implemented in ell::LT_MinimaSet.

bool ell::LandscapeTopology::isSmaller_E_S	(	const State *	a,
		const State *	b
	)			`[static, protected]`

Comparison function that compares on energy and string representation

Returns:: true if energy of a smaller than b or if equal if the string represenation of a is lexicographically smaller than b

Definition at line 10 of file LandscapeTopology.cc.

virtual bool ell::LandscapeTopology::isSorted ( ) const [pure virtual]

Check if the minima of the landscape are sorted ascendingly by their energy (mfe minimum gets index 0). If energy is equal they are sorted by their string representation.

Implemented in ell::LT_MinimaSet.

virtual std::pair<int,std::string> ell::LandscapeTopology::read	(	std::istream &	in,
		const State *const	templateState,
		const std::string &	StateDescription
	)			`[pure virtual]`

Fills the landscape topology from stream.

Parameters:

	in	the input stream to read from.
	templateState	the State template to create new State objects via its 'fromString' function
	StateDescription	a string that describes the type of states that should be read and that is compared to the LT information header in the stream

Returns:: an error encoding and an error string : 0 = no error occured, read was successfull -1 = landscape topology type not supported -2 = state description differs from the given one -3 = other read errors

Implemented in ell::LT_MinimaSet.

virtual void ell::LandscapeTopology::sort ( ) [pure virtual]

Sorts the minima ascending by their energy (mfe minimum gets index 0). If energy is equal they are sorted by their string representation.

Implemented in ell::LT_MinimaSet.

virtual void ell::LandscapeTopology::write	(	std::ostream &	out,
		const std::string &	StateDescription
	)			const `[pure virtual]`

Writes the current landscape topology to stream.

Parameters:

	out	the output stream to write to.
	StateDescription	a string that describes the type of states written to the stream (will be part of the LT information header)

Implemented in ell::LT_MinimaSet.

Field Documentation

const size_t ell::LandscapeTopology::INVALID_INDEX [static]

Index value that is used to propagate the information about invalid indexing.

Definition at line 32 of file LandscapeTopology.hh.

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

src/ell/LandscapeTopology.hh
src/ell/LandscapeTopology.cc


Public Member Functions
virtual const size_t	addMin (const State *const m)=0
virtual bool	addSaddle (const State const m_i, const State const m_j, const State *const s)=0
virtual bool	addSaddle (const size_t i, const size_t j, const State *const s)=0
virtual void	clear ()=0
virtual const State *const	getMFEState () const=0
virtual const State *const	getMin (size_t i) const =0
virtual const size_t	getMinCount () const=0
virtual const size_t	getMinIndex (const State *const m) const=0
virtual double	getRMSD (const LandscapeTopology *const lt) const=0
virtual bool	isSorted () const=0
virtual std::pair< int, std::string >	read (std::istream &in, const State *const templateState, const std::string &StateDescription)=0
virtual void	sort ()=0
virtual void	write (std::ostream &out, const std::string &StateDescription) const=0
virtual	~LandscapeTopology ()
Static Public Attributes
static const size_t	INVALID_INDEX
Static Protected Member Functions
static bool	isSmaller_E_S (const State a, const State b)