ell::LT_MinimaSet Class Reference

#include <LT_MinimaSet.hh>

Inheritance diagram for ell::LT_MinimaSet:

Detailed Description

Definition at line 14 of file LT_MinimaSet.hh.

Public Member Functions

virtual const size_t addMin (const State *const m)

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

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

virtual void clear ()

virtual const std::vector<
const State * > & getAllMin () const

virtual const State *const getMFEState () const

virtual const State *const getMin (size_t i) const

virtual const size_t getMinCount () const

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

virtual double getRMSD (const LandscapeTopology *const lt) const

virtual bool isSorted () const

LT_MinimaSet ()

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

virtual void sort ()

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

virtual ~LT_MinimaSet ()

Static Public Attributes

static const size_t INVALID_INDEX

static const std::string LT_ID

Static Protected Member Functions

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

Protected Attributes

size_t mfeIndex

bool sorted

std::vector< const State * > vMinima

Constructor & Destructor Documentation

ell::LT_MinimaSet::LT_MinimaSet ( )

Constructs an empty minima set.

Definition at line 16 of file LT_MinimaSet.cc.

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

Destruction.

Definition at line 29 of file LT_MinimaSet.cc.

Member Function Documentation

const size_t ell::LT_MinimaSet::addMin ( const State *const m ) [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

Implements ell::LandscapeTopology.

Definition at line 46 of file LT_MinimaSet.cc.

bool ell::LT_MinimaSet::addSaddle	(	const State *const	m_i,
		const State *const	m_j,
		const State *const	s
	)			`[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

Implements ell::LandscapeTopology.

Definition at line 40 of file LT_MinimaSet.cc.

bool ell::LT_MinimaSet::addSaddle	(	const size_t	i,
		const size_t	j,
		const State *const	s
	)			`[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

Implements ell::LandscapeTopology.

Definition at line 34 of file LT_MinimaSet.cc.

void ell::LT_MinimaSet::clear ( ) [virtual]

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

Implements ell::LandscapeTopology.

Definition at line 21 of file LT_MinimaSet.cc.

const std::vector< const State * > & ell::LT_MinimaSet::getAllMin ( ) const [virtual]

Access to all minima.

Returns:: a vector representation of all minima

Definition at line 105 of file LT_MinimaSet.cc.

const State *const ell::LT_MinimaSet::getMFEState ( ) const [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)

Implements ell::LandscapeTopology.

Definition at line 99 of file LT_MinimaSet.cc.

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

Access to a minimum.

Parameters:

index of the minimum to access

Returns:: the State with the specified minimum index

Implements ell::LandscapeTopology.

Definition at line 74 of file LT_MinimaSet.cc.

const size_t ell::LT_MinimaSet::getMinCount ( ) const [virtual]

Access to the number of stored minima.

Returns:: the number of minima

Implements ell::LandscapeTopology.

Definition at line 93 of file LT_MinimaSet.cc.

const size_t ell::LT_MinimaSet::getMinIndex ( const State *const m ) const [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

Implements ell::LandscapeTopology.

Definition at line 82 of file LT_MinimaSet.cc.

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

Calculates the root mean square deviation between landscape topologies.

Parameters:

the landscape topology to calculate the RMSD

Returns:: the RMSD

Implements ell::LandscapeTopology.

Definition at line 112 of file LT_MinimaSet.cc.

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

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.

bool ell::LT_MinimaSet::isSorted ( ) const [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.

Implements ell::LandscapeTopology.

Definition at line 157 of file LT_MinimaSet.cc.

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

first step: get the type information for the saddle net( invisible for graphviz as comments //)

second step: get all the minima and saddles (graphviz comments with // )

if graphViz data starts.. end the reading

Implements ell::LandscapeTopology.

Definition at line 162 of file LT_MinimaSet.cc.

void ell::LT_MinimaSet::sort ( ) [virtual]

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

Implements ell::LandscapeTopology.

Definition at line 144 of file LT_MinimaSet.cc.

void ell::LT_MinimaSet::write	(	std::ostream &	out,
		const std::string &	StateDescription
	)			const `[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)

step 1: save the datastructure for later reconstruction as comments in graphviz file

step2: put all minima in with.. MINIMUM= index toString()-format

step 2: write the graph in DOT language

Implements ell::LandscapeTopology.

Definition at line 274 of file LT_MinimaSet.cc.

Field Documentation

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

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

Definition at line 32 of file LandscapeTopology.hh.

const std::string ell::LT_MinimaSet::LT_ID [static]

the landscape topology id string used in the output header to identify a minima set

Definition at line 28 of file LT_MinimaSet.hh.

size_t ell::LT_MinimaSet::mfeIndex [protected]

index of the global minimum (with minimal free energy)

Definition at line 20 of file LT_MinimaSet.hh.

bool ell::LT_MinimaSet::sorted [protected]

internal flag that stores if vMinima is sorted or not

Definition at line 22 of file LT_MinimaSet.hh.

std::vector<const State*> ell::LT_MinimaSet::vMinima [protected]

the vector of all known minima

Definition at line 18 of file LT_MinimaSet.hh.

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

src/ell/LT_MinimaSet.hh
src/ell/LT_MinimaSet.cc


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