ell::LandscapeTopology Class Reference

#include <LandscapeTopology.hh>

Inheritance diagram for ell::LandscapeTopology:

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Detailed Description

An abstract representation of the landscapes topology that represents minima and adjacency information like saddle points or barriers between them.

Author:: Hannes Kochniss, Martin Mann

Definition at line 23 of file LandscapeTopology.hh.

Public Types

typedef std::map< int, size_t > Int2SizeT_MAP

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 double getDistance (const LandscapeTopology *const lt) const

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 bool isSorted () const=0

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

virtual void sort ()=0

virtual void write (std::ostream &out, const bool writeGraph=false) const =0

virtual ~LandscapeTopology ()

Static Public Member Functions

static std::pair< int, std::string > parseBarrier (LandscapeTopology &toFill, const std::string &line, const State *const templateState, const Int2SizeT_MAP &idx2min)

static std::pair< int, std::string > parseHeader (const std::string &line, std::string &LT_ID, size_t &minNumber, std::string &StateDescription)

static std::pair< int, std::string > parseMinimum (LandscapeTopology &toFill, const std::string &line, const State *const templateState, Int2SizeT_MAP &idx2min)

static std::pair< int, std::string > parseSaddle (LandscapeTopology &toFill, const std::string &line, const State *const templateState, const Int2SizeT_MAP &idx2min)

static void writeBarrier (std::ostream &out, const State *const barrier, const size_t index, const std::vector< size_t > &minConnected)

static void writeHeader (std::ostream &out, const std::string &LT_ID, const size_t minNumber, const std::string &StateDescription)

static void writeMinimum (std::ostream &out, const std::vector< const State * > &minima, const size_t index)

static void writeMinimum (std::ostream &out, const State *const minimum, const size_t index)

static void writeSaddle (std::ostream &out, const State *const saddle, const size_t index, const std::vector< size_t > &minConnected)

Static Public Attributes

static const double AVOGADRO_CONSTANT_NA

static const double BOLTZMANN_CONSTANT_KB

static double BOLTZMANN_KT

static const double GAS_CONSTANT_R

static const size_t INVALID_INDEX

static double MISSING_MINIMUM_PENALTY

Static Protected Member Functions

static double getSortedMinimaDistance (const std::vector< const State * > &m1, const std::vector< const State * > &m2)

static std::pair< State *,
std::string > parseConnection (const std::string &line, const State *const templateState, const Int2SizeT_MAP &idx2min, const std::string &connectionKey, std::vector< size_t > &connectedMinima)

static void writeConnection (std::ostream &out, const State *const connectionState, const size_t index, const std::vector< size_t > &minConnected, const std::string &connectionKey)

Static Protected Attributes

static const std::string OUTPUT_KEY_BARRIER

static const std::string OUTPUT_KEY_ELL_HEAD

static const std::string OUTPUT_KEY_MINIMUM

static const std::string OUTPUT_KEY_SADDLE

Member Typedef Documentation

typedef std::map< int, size_t > ell::LandscapeTopology::Int2SizeT_MAP

Definition at line 30 of file LandscapeTopology.hh.

Constructor & Destructor Documentation

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

Destruction.

Definition at line 73 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 minimum to add

Returns:: the index of the minimum in the landscape

Implemented in ell::LT_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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

Calculates the relative 'distance' between landscape topologies. On the LandscapeTopology level it is done on the minima only. For each minimum m present in only one of the two LTs a value of MISSING_MINIMUM_PENALTY*(e^(-energy(m)/BOLTZMANN_KT)) is summed. The resulting sum is normalized by the number of (unique) minima in both topologies.

Parameters:

the landscape topology to calculate the distance to

Returns:: the distance

Reimplemented in ell::LT_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet.

Definition at line 88 of file LandscapeTopology.cc.

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_AutoFlood, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

double ell::LandscapeTopology::getSortedMinimaDistance	(	const std::vector< const State * > &	m1,
		const std::vector< const State * > &	m2
	)			`[static, protected]`

Definition at line 121 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_AutoFlood, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

std::pair< int, std::string > ell::LandscapeTopology::parseBarrier	(	LandscapeTopology &	toFill,
		const std::string &	line,
		const State *const	templateState,
		const Int2SizeT_MAP &	idx2min
	)			`[static]`

Parses a barrier string encoding produced by 'writeBarrier' method and adds the encoded BARRIER as a SADDLE to the topology given.

Parameters:

	toFill	the landscape topology to add the barrier to
	line	the string that encodes the barrier (encoding follows 'write' method)
	templateState	the State template to create new State objects via its 'fromString' function
	idx2min	the mapping of minima indices in the string to the indices in the given landscape topology 'toFill'

Returns:: an error encoding and an error string : 0 = no error occured, read was successfull -3 = read error (see error string)

Definition at line 458 of file LandscapeTopology.cc.

std::pair< State *, std::string > ell::LandscapeTopology::parseConnection	(	const std::string &	line,
		const State *const	templateState,
		const Int2SizeT_MAP &	idx2min,
		const std::string &	connectionKey,
		std::vector< size_t > &	connectedMinima
	)			`[static, protected]`

Parses a string encoding of a minima connection of a topology produced by 'writeBarrier' method and returns the connection state and the list of minima connected.

Parameters:

	line	the string that encodes the connection (encoding follows 'write' method)
	templateState	the State template to create new State objects via its 'fromString' function
	idx2min	the mapping of minima indices in the string to the indices in the given landscape topology 'toFill'
	connectionKey	the key used to encode the connection
	connectedMinima	OUTPUT parameter where the indices of the connected minima of the parsed connection are stored to

Returns:: a the parsed connection State and an error string if an error occured and the State is NULL

Definition at line 533 of file LandscapeTopology.cc.

std::pair< int, std::string > ell::LandscapeTopology::parseHeader	(	const std::string &	line,
		std::string &	LT_ID,
		size_t &	minNumber,
		std::string &	StateDescription
	)			`[static]`

Parses the descriptive header of a landscape topology produced by 'writeHeader' method.

Parameters:

	line	the string that encodes the header information (encoding follows 'write' method)
	LT_ID	the ID string of the topology in stream
	minNumber	the number of minima the topology in stream holds, if minima are grouped in the topology the number of groups is given.
	StateDescription	a string description of the State model represented by the topology in the stream

Returns:: an error encoding and an error string : 0 = no error occured, read was successfull, the string contains the remaining line content, -3 = read error (see error string)

Definition at line 204 of file LandscapeTopology.cc.

std::pair< int, std::string > ell::LandscapeTopology::parseMinimum	(	LandscapeTopology &	toFill,
		const std::string &	line,
		const State *const	templateState,
		Int2SizeT_MAP &	idx2min
	)			`[static]`

Parses a minimum string encoding produced by 'writeMinimum' method and adds the encoded minimum state to the given topology. Furthermore, it returns the remaining line content that can contain further minima that were merged with the first (already added) 'main' minimum. Thus a further parsing can be done later if necessary.

Parameters:

	toFill	the barrier tree to add the barrier to
	line	the string that encodes the minimum (encoding follows 'write' method)
	templateState	the State template to create new State objects via its 'fromString' function
	idx2min	the mapping of minima indices in the string to the indices in the given landscape topology 'toFill'

Returns:: an error encoding and an error string : 0 = no error occured, read was successfull, the string contains the remaining line content, -3 = read error (see error string)

Definition at line 315 of file LandscapeTopology.cc.

std::pair< int, std::string > ell::LandscapeTopology::parseSaddle	(	LandscapeTopology &	toFill,
		const std::string &	line,
		const State *const	templateState,
		const Int2SizeT_MAP &	idx2min
	)			`[static]`

Parses a saddle string encoding produced by 'writeBarrier' method and adds the encoded direct saddle to the topology given.

Parameters:

	toFill	the landscape topology to add the saddle to
	line	the string that encodes the saddle (encoding follows 'write' method)
	templateState	the State template to create new State objects via its 'fromString' function
	idx2min	the mapping of minima indices in the string to the indices in the given landscape topology 'toFill'

Returns:: an error encoding and an error string : 0 = no error occured, read was successfull -3 = read error (see error string)

Definition at line 494 of file LandscapeTopology.cc.

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

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_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

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_AutoFlood, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

virtual void ell::LandscapeTopology::write	(	std::ostream &	out,
		const bool	writeGraph = `false`
	)			const `[pure virtual]`

Writes the current landscape topology to stream.

Parameters:

	out	the output stream to write to.
	writeGraph	whether or not the output should contain a graph representation of the topology in graphviz DOT format

Implemented in ell::LT_AutoFlood, ell::LT_BarrierTree, ell::LT_MinimaSet, and ell::LT_SaddleNet_AM.

void ell::LandscapeTopology::writeBarrier	(	std::ostream &	out,
		const State *const	barrier,
		const size_t	index,
		const std::vector< size_t > &	minConnected
	)			`[static]`

Writes a barrier of a landscape topology to stream.

Parameters:

	out	the output stream to write to.
	barrier	the barrier to add
	index	the index of the barrier
	minConnected	the minima connected by the barrier

Definition at line 398 of file LandscapeTopology.cc.

void ell::LandscapeTopology::writeConnection	(	std::ostream &	out,
		const State *const	connectionState,
		const size_t	index,
		const std::vector< size_t > &	minConnected,
		const std::string &	connectionKey
	)			`[static, protected]`

Writes a minima connection of a landscape topology to stream.

Parameters:

	out	the output stream to write to.
	connectionState	the State representing the connection
	index	the index of the connection
	minConnected	the minima connected
	connectionKey	the key used to encode the connection

Definition at line 430 of file LandscapeTopology.cc.

void ell::LandscapeTopology::writeHeader	(	std::ostream &	out,
		const std::string &	LT_ID,
		const size_t	minNumber,
		const std::string &	StateDescription
	)			`[static]`

Writes the descriptive header of a landscape topology to stream.

Parameters:

	out	the output stream to write to.
	LT_ID	the ID string of the topology to write
	minNumber	the number of minima the topology holds, if minima are grouped in the topology the number of groups has to be given.
	StateDescription	a string description of the State model represented by the topology

Definition at line 188 of file LandscapeTopology.cc.

void ell::LandscapeTopology::writeMinimum	(	std::ostream &	out,
		const std::vector< const State * > &	minima,
		const size_t	index
	)			`[static]`

Writes a group of minima of a landscape topology to stream. NOTE: The FIRST minimum is the only one read by the read function and thus the representative for the whole group!

Parameters:

	out	the output stream to write to.
	minima	the minima to add
	index	the index of the minimum

Definition at line 296 of file LandscapeTopology.cc.

void ell::LandscapeTopology::writeMinimum	(	std::ostream &	out,
		const State *const	minimum,
		const size_t	index
	)			`[static]`

Writes a minimum of a landscape topology to stream.

Parameters:

	out	the output stream to write to.
	minimum	the minimum to add
	index	the index of the minimum

Definition at line 280 of file LandscapeTopology.cc.

void ell::LandscapeTopology::writeSaddle	(	std::ostream &	out,
		const State *const	saddle,
		const size_t	index,
		const std::vector< size_t > &	minConnected
	)			`[static]`

Writes a saddle of a landscape topology to stream.

Parameters:

	out	the output stream to write to.
	saddle	the saddle to write
	index	the index of the saddle
	minConnected	the minima connected by the saddle

Definition at line 414 of file LandscapeTopology.cc.

Field Documentation

const double ell::LandscapeTopology::AVOGADRO_CONSTANT_NA [static]

Avogadro constant N_A = 6.02214179 * 10^(23) unit : 1/mol

Definition at line 41 of file LandscapeTopology.hh.

const double ell::LandscapeTopology::BOLTZMANN_CONSTANT_KB [static]

Boltzmann constant K_b = R / N_A = 1.3806504 * 10^(-23) unit : Joule / Kelvin

Definition at line 47 of file LandscapeTopology.hh.

double ell::LandscapeTopology::BOLTZMANN_KT [static]

The kT value used to calculate the Boltzmann weight e^(-E/kT) of a state in the landscape with an energy of E. NOTE: Has to be set according to the used energy function !!!

Definition at line 54 of file LandscapeTopology.hh.

const double ell::LandscapeTopology::GAS_CONSTANT_R [static]

Gas constant R = 8.314472 unit : Joule / (Kelvin * mol)

Definition at line 44 of file LandscapeTopology.hh.

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

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

Definition at line 37 of file LandscapeTopology.hh.

double ell::LandscapeTopology::MISSING_MINIMUM_PENALTY [static]

The penalty used to score a missing minimum when comparing two landscape topologies using the 'getDistance' method. NOTE: Has to be set according to the used energy function and the weighting of missing minima in the distance score. If missing minima are of no relevance set this value to 0.0!

Definition at line 61 of file LandscapeTopology.hh.

const std::string ell::LandscapeTopology::OUTPUT_KEY_BARRIER [static, protected]

keyword used by the read and write method to identify information on a barrier

Definition at line 347 of file LandscapeTopology.hh.

const std::string ell::LandscapeTopology::OUTPUT_KEY_ELL_HEAD [static, protected]

keyword used by the read and write method to identify information on the landscape topology type etc.

Definition at line 341 of file LandscapeTopology.hh.

const std::string ell::LandscapeTopology::OUTPUT_KEY_MINIMUM [static, protected]

keyword used by the read and write method to identify information on a minimum

Definition at line 344 of file LandscapeTopology.hh.

const std::string ell::LandscapeTopology::OUTPUT_KEY_SADDLE [static, protected]

keyword used by the read and write method to identify information on a saddle point

Definition at line 350 of file LandscapeTopology.hh.

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

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


Public Types
typedef std::map< int, size_t >	Int2SizeT_MAP
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 double	getDistance (const LandscapeTopology *const lt) const
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 bool	isSorted () const=0
virtual std::pair< int, std::string >	read (std::istream &in, const State *const templateState)=0
virtual void	sort ()=0
virtual void	write (std::ostream &out, const bool writeGraph=false) const =0
virtual	~LandscapeTopology ()
Static Public Member Functions
static std::pair< int, std::string >	parseBarrier (LandscapeTopology &toFill, const std::string &line, const State *const templateState, const Int2SizeT_MAP &idx2min)
static std::pair< int, std::string >	parseHeader (const std::string &line, std::string &LT_ID, size_t &minNumber, std::string &StateDescription)
static std::pair< int, std::string >	parseMinimum (LandscapeTopology &toFill, const std::string &line, const State *const templateState, Int2SizeT_MAP &idx2min)
static std::pair< int, std::string >	parseSaddle (LandscapeTopology &toFill, const std::string &line, const State *const templateState, const Int2SizeT_MAP &idx2min)
static void	writeBarrier (std::ostream &out, const State *const barrier, const size_t index, const std::vector< size_t > &minConnected)
static void	writeHeader (std::ostream &out, const std::string &LT_ID, const size_t minNumber, const std::string &StateDescription)
static void	writeMinimum (std::ostream &out, const std::vector< const State * > &minima, const size_t index)
static void	writeMinimum (std::ostream &out, const State *const minimum, const size_t index)
static void	writeSaddle (std::ostream &out, const State *const saddle, const size_t index, const std::vector< size_t > &minConnected)
Static Public Attributes
static const double	AVOGADRO_CONSTANT_NA
static const double	BOLTZMANN_CONSTANT_KB
static double	BOLTZMANN_KT
static const double	GAS_CONSTANT_R
static const size_t	INVALID_INDEX
static double	MISSING_MINIMUM_PENALTY
Static Protected Member Functions
static double	getSortedMinimaDistance (const std::vector< const State * > &m1, const std::vector< const State * > &m2)
static std::pair< State *, std::string >	parseConnection (const std::string &line, const State *const templateState, const Int2SizeT_MAP &idx2min, const std::string &connectionKey, std::vector< size_t > &connectedMinima)
static void	writeConnection (std::ostream &out, const State *const connectionState, const size_t index, const std::vector< size_t > &minConnected, const std::string &connectionKey)
Static Protected Attributes
static const std::string	OUTPUT_KEY_BARRIER
static const std::string	OUTPUT_KEY_ELL_HEAD
static const std::string	OUTPUT_KEY_MINIMUM
static const std::string	OUTPUT_KEY_SADDLE