ell::LT_BarrierTree Class Reference
#include <LT_BarrierTree.hh>
Inheritance diagram for ell::LT_BarrierTree:
Detailed Description
This class represents a barrier tree of an energy landscape.A barrier tree is a hierachical representation of the minimal energy barriers between minima. Thus leaves represent minima and internal nodes minimal barriers between the children of these nodes.
This implementation stores the minimal barrier state within the internal node.
It is possible that an object of this class represents a FOREST of barrier trees, i.e. it exists at least one pair of minima without a stored barrier between them. Thus not all minima are connected to all other via a barrier.
Furthermore it allows for the aggregation of minima. A minimum M1 is aggregated to another minimum M2 if
- M2 is smaller M1 (according to the State::less order)
- it exists a barrier B between M1-M2 such that E(B)-E(M1) <= maxMergeBarrier (user defined)
In case that holds, the leaf of M1 is merged with the leaf containing M2. Furthermore the barriers of both leaves are merged to maintain the barrier information of both minima. But M1 is NOT removed from the minima list and still accessible via its old index!
When enabling minima merging (maxMergeBarrier >= 0.0) one has to note that the structure of the barrier tree might get depending on the order of the barrier input IF the inserted saddles are only barriers without adjacency information. IF that is the case, the minimum M2 is not ensured to be the NEXT minimum reachable by the barrier given but ANY that is reachable by that barrier.
Definition at line 54 of file LT_BarrierTree.hh.
Public Types | |
typedef std::map< int, size_t > | Int2SizeT_MAP |
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 * | getBarrier (const State *const m1, const State *const m2) const |
virtual const State * | getBarrier (const size_t m1, const size_t m2) const |
virtual double | getDistance (const LandscapeTopology *const lt) 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 |
size_t | getNumOfLeaves (void) const |
size_t | getNumOfTrees (void) const |
bool | isForest (void) const |
virtual bool | isSorted () const |
LT_BarrierTree (const LT_BarrierTree &toCopy) | |
LT_BarrierTree (const double maxMergeBarrier=0.0) | |
virtual LT_BarrierTree & | operator= (const LT_MinimaSet &toCopy) |
virtual LT_BarrierTree & | operator= (const LT_BarrierTree &toCopy) |
virtual std::pair< int, std::string > | read (std::istream &in, const State *const templateState) |
virtual void | sort () |
virtual void | write (std::ostream &out, const bool writeGraph=false) const |
void | write_PStree (std::ostream &out, const size_t maxLeaves2print=UINT_MAX) |
virtual | ~LT_BarrierTree () |
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 <_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 <_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 const std::string | LT_ID |
static double | MISSING_MINIMUM_PENALTY |
Protected Types | |
typedef std::map< const State *, Node * > | Min2Node_MAP |
typedef std::map< const Node *, int > | Node2Int_MAP |
typedef std::map< const Node *, const Node * > | Node2Node_MAP |
typedef std::map< const Node *, size_t > | Node2SizeT_MAP |
typedef std::map< size_t, const Node * > | SizeT2Node_MAP |
Protected Member Functions | |
Node * | checkIfObsolete (Node *n) |
const Node * | getHighestParentLEQ (const Node *child, const double maxEnergy) const |
Node * | getHighestParentLEQ (Node *child, const double maxEnergy) |
const Node * | getLCA (const Node *n1, const Node *n2) const |
Node * | getLCA (Node *n1, Node *n2) |
Node * | mergeSubTrees (Node *t1, Node *t2) |
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 | PS_tree_plot (std::ostream &out, const std::vector< nodeT > &nodes) |
static void | writeConnection (std::ostream &out, const State *const connectionState, const size_t index, const std::vector< size_t > &minConnected, const std::string &connectionKey) |
Protected Attributes | |
double | maxMergeBarrier |
size_t | mfeIndex |
Min2Node_MAP | min2node |
size_t | numOfLeaves |
Node * | root |
bool | sorted |
std::vector< const State * > | vMinima |
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 |
Data Structures | |
class | cmp_saddle |
class | linkT |
class | Node |
class | NodeList |
class | nodeT |
class | StateList |
Member Typedef Documentation
typedef std::map< int, size_t > ell::LandscapeTopology::Int2SizeT_MAP [inherited] |
Definition at line 30 of file LandscapeTopology.hh.
typedef std::map< const State*, Node* > ell::LT_BarrierTree::Min2Node_MAP [protected] |
Definition at line 156 of file LT_BarrierTree.hh.
typedef std::map<const Node*, int > ell::LT_BarrierTree::Node2Int_MAP [protected] |
Definition at line 159 of file LT_BarrierTree.hh.
typedef std::map<const Node*, const Node* > ell::LT_BarrierTree::Node2Node_MAP [protected] |
Definition at line 157 of file LT_BarrierTree.hh.
typedef std::map<const Node*, size_t > ell::LT_BarrierTree::Node2SizeT_MAP [protected] |
Definition at line 158 of file LT_BarrierTree.hh.
typedef std::map< size_t, const Node* > ell::LT_BarrierTree::SizeT2Node_MAP [protected] |
Definition at line 160 of file LT_BarrierTree.hh.
Constructor & Destructor Documentation
ell::LT_BarrierTree::LT_BarrierTree | ( | const double | maxMergeBarrier = 0.0 |
) |
ell::LT_BarrierTree::LT_BarrierTree | ( | const LT_BarrierTree & | toCopy | ) |
ell::LT_BarrierTree::~LT_BarrierTree | ( | ) | [virtual] |
Member Function Documentation
const size_t ell::LT_BarrierTree::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:
-
m the first minimum to add
- Returns:
- the index of the minimum in the landscape
Reimplemented from ell::LT_MinimaSet.
Definition at line 506 of file LT_BarrierTree.cc.
bool ell::LT_BarrierTree::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
Reimplemented from ell::LT_MinimaSet.
Definition at line 478 of file LT_BarrierTree.cc.
bool ell::LT_BarrierTree::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
Reimplemented from ell::LT_MinimaSet.
Definition at line 222 of file LT_BarrierTree.cc.
LT_BarrierTree::Node * ell::LT_BarrierTree::checkIfObsolete | ( | Node * | n | ) | [protected] |
Checks if an internal node has only one child node and is therefore obsolete in the tree. If so, the node is removed from the tree. NOTE: The node itself is NOT DELETED, only unlinked!
- Parameters:
-
n the node to check
- Returns:
- the final root of this subtree
Definition at line 1449 of file LT_BarrierTree.cc.
void ell::LT_BarrierTree::clear | ( | ) | [virtual] |
Clears the data structure and removes all stored information to be filled again afterwards.
Reimplemented from ell::LT_MinimaSet.
Definition at line 198 of file LT_BarrierTree.cc.
const std::vector< const State * > & ell::LT_MinimaSet::getAllMin | ( | ) | const [virtual, inherited] |
Access to all minima.
- Returns:
- a vector representation of all minima
Definition at line 137 of file LT_MinimaSet.cc.
const State * ell::LT_BarrierTree::getBarrier | ( | const State *const | m1, | |
const State *const | m2 | |||
) | const [virtual] |
Access to the smallest barrier state between two minima. NOTE : the two minima have to be already part of the topology !!!
- Parameters:
-
m1 the first minimum m2 the second minimum
- Returns:
- the smallest barrier state known between two minima or NULL if minima belong to not connected trees of a forest
Definition at line 1432 of file LT_BarrierTree.cc.
const State * ell::LT_BarrierTree::getBarrier | ( | const size_t | m1, | |
const size_t | m2 | |||
) | const [virtual] |
Access to the smallest barrier state between two minima.
- Parameters:
-
m1 the index of the first minimum m2 the index of the second minimum
- Returns:
- the smallest barrier state known between two minima or NULL if minima belong to not connected trees of a forest
Definition at line 1414 of file LT_BarrierTree.cc.
double ell::LT_BarrierTree::getDistance | ( | const LandscapeTopology *const | lt | ) | const [virtual] |
Calculates the relative 'distance' between two barrier trees. It is done on the minima and barriers. 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. For all O(n^2) barriers in the trees the RMSD is calculated and summed to the minima penalty. For each barrier present in one of the trees only, the maximal barrier of both trees (root(mfe_tree)-mfe) is used in the RMSD calculation for the missing barrier. Note: The used 'dummy' barrier height is only the highest barrier if the barrier tree is no forest (only mfe-tree considered) ...
- Parameters:
-
lt the barrier tree to calculate the distance to
- Returns:
- the distance
Reimplemented from ell::LT_MinimaSet.
Definition at line 571 of file LT_BarrierTree.cc.
const LT_BarrierTree::Node * ell::LT_BarrierTree::getHighestParentLEQ | ( | const Node * | child, | |
const double | maxEnergy | |||
) | const [protected] |
Constant Access to the highest (grand) parent node in the tree of a given node that represents an energy below or equal to the given maximum.
- Parameters:
-
child the child node to start search from maxEnergy the energy maximum that should not be exceeded
- Returns:
- the highest anchester of the node below the energy maximum
Definition at line 1204 of file LT_BarrierTree.cc.
LT_BarrierTree::Node * ell::LT_BarrierTree::getHighestParentLEQ | ( | Node * | child, | |
const double | maxEnergy | |||
) | [protected] |
Access to the highest (grand) parent node in the tree of a given node that represents an energy below or equal to the given maximum.
- Parameters:
-
child the child node to start search from maxEnergy the energy maximum that should not be exceeded
- Returns:
- the highest anchester of the node below the energy maximum
Definition at line 1180 of file LT_BarrierTree.cc.
const LT_BarrierTree::Node * ell::LT_BarrierTree::getLCA | ( | const Node * | n1, | |
const Node * | n2 | |||
) | const [protected] |
Constant access to the lowest common anchester of two nodes in the tree.
- Parameters:
-
n1 the first node of the query n2 the second node of the query
- Returns:
- the LCA of the two nodes in the tree
Definition at line 1333 of file LT_BarrierTree.cc.
LT_BarrierTree::Node * ell::LT_BarrierTree::getLCA | ( | Node * | n1, | |
Node * | n2 | |||
) | [protected] |
Access to the lowest common anchester of two nodes in the tree.
- Parameters:
-
n1 the first node of the query n2 the second node of the query
- Returns:
- the LCA of the two nodes in the tree
Definition at line 1374 of file LT_BarrierTree.cc.
const State *const ell::LT_MinimaSet::getMFEState | ( | ) | const [virtual, inherited] |
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 131 of file LT_MinimaSet.cc.
const State *const ell::LT_MinimaSet::getMin | ( | size_t | i | ) | const [virtual, inherited] |
Access to a minimum.
- Parameters:
-
i index of the minimum to access
- Returns:
- the State with the specified minimum index
Implements ell::LandscapeTopology.
Definition at line 106 of file LT_MinimaSet.cc.
const size_t ell::LT_MinimaSet::getMinCount | ( | ) | const [virtual, inherited] |
Access to the number of stored minima.
- Returns:
- the number of minima
Implements ell::LandscapeTopology.
Definition at line 125 of file LT_MinimaSet.cc.
const size_t ell::LT_MinimaSet::getMinIndex | ( | const State *const | m | ) | const [virtual, inherited] |
Access to the minimum index.
- Parameters:
-
m 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 114 of file LT_MinimaSet.cc.
size_t ell::LT_BarrierTree::getNumOfLeaves | ( | void | ) | const |
Access to the number of leaves the tree holds. The number corresponds to the number of minima cluster / equivalence classes.
- Returns:
- the number of tree leaves
Definition at line 1530 of file LT_BarrierTree.cc.
size_t ell::LT_BarrierTree::getNumOfTrees | ( | void | ) | const |
Access for the number of trees this barrier tree represents.
- Returns:
- if isForest() == true, the number of trees, otherwise 1
Definition at line 1506 of file LT_BarrierTree.cc.
double ell::LandscapeTopology::getSortedMinimaDistance | ( | const std::vector< const State * > & | m1, | |
const std::vector< const State * > & | m2 | |||
) | [static, protected, inherited] |
Definition at line 121 of file LandscapeTopology.cc.
bool ell::LT_BarrierTree::isForest | ( | void | ) | const |
Checks whether or not the barrier tree represents one tree or a forest of at least two unconnected trees.
- Returns:
- true if this tree represents more than one unconnected barrier tree; false otherwise
Definition at line 1495 of file LT_BarrierTree.cc.
bool ell::LT_MinimaSet::isSorted | ( | ) | const [virtual, inherited] |
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 213 of file LT_MinimaSet.cc.
LT_BarrierTree::Node * ell::LT_BarrierTree::mergeSubTrees | ( | Node * | t1, | |
Node * | t2 | |||
) | [protected] |
Merges recursively two subtrees until the tree is valid again. It returns the root node of the resulting merged subtree that has to be checked if it is obsolete afterwards (checkIfObsolete).
Definition at line 1227 of file LT_BarrierTree.cc.
LT_BarrierTree & ell::LT_BarrierTree::operator= | ( | const LT_MinimaSet & | toCopy | ) | [virtual] |
Assignment operator.
- Parameters:
-
toCopy the minima set this object should be a copy of
- Returns:
- access to the changed this object
Reimplemented from ell::LT_MinimaSet.
Definition at line 44 of file LT_BarrierTree.cc.
LT_BarrierTree & ell::LT_BarrierTree::operator= | ( | const LT_BarrierTree & | toCopy | ) | [virtual] |
Assignment operator.
- Parameters:
-
toCopy the barrier tree this object should be a copy of
- Returns:
- access to the changed this object
Definition at line 80 of file LT_BarrierTree.cc.
std::pair< int, std::string > ell::LandscapeTopology::parseBarrier | ( | LandscapeTopology & | toFill, | |
const std::string & | line, | |||
const State *const | templateState, | |||
const Int2SizeT_MAP & | idx2min | |||
) | [static, inherited] |
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, inherited] |
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
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, inherited] |
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, inherited] |
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, inherited] |
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.
void ell::LT_BarrierTree::PS_tree_plot | ( | std::ostream & | out, | |
const std::vector< nodeT > & | nodes | |||
) | [static, protected] |
Prints a barrier tree encoded in nodeT structures to stream.
The original source code was derived from the 'barriers' program by the TBI group of Vienna University.
- Parameters:
-
out the stream to write to nodes the list of leaf nodes to print
Definition at line 1629 of file LT_BarrierTree.cc.
std::pair< int, std::string > ell::LT_BarrierTree::read | ( | std::istream & | in, | |
const State *const | templateState | |||
) | [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 (see error string)
parse whole input
if graphViz data starts.. end the reading
Reimplemented from ell::LT_MinimaSet.
Definition at line 843 of file LT_BarrierTree.cc.
void ell::LT_MinimaSet::sort | ( | ) | [virtual, inherited] |
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 200 of file LT_MinimaSet.cc.
void ell::LT_BarrierTree::write | ( | std::ostream & | out, | |
const bool | writeGraph = false | |||
) | const [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
step 1: save the datastructure for later reconstruction as comments in graphviz file
step 1: print minima and barriers
step 2: write the graph in DOT language
Reimplemented from ell::LT_MinimaSet.
Definition at line 1044 of file LT_BarrierTree.cc.
void ell::LT_BarrierTree::write_PStree | ( | std::ostream & | out, | |
const size_t | maxLeaves2print = UINT_MAX | |||
) |
Writes the barrier tree in postscript format to stream for a viewable tree representation.
NOTE: Currently NO FORESTS are supported and no output will be generated in case this object represents a forest.
The original source code was derived from the 'barriers' program by the TBI group of Vienna University.
NOTE: The barrier tree will be sorted to enable the printing!!! This might cause additional runtime and a changed minima indexing!
- Parameters:
-
out the stream to write to maxLeaves2print maximal number of leaves to print
Definition at line 1542 of file LT_BarrierTree.cc.
void ell::LandscapeTopology::writeBarrier | ( | std::ostream & | out, | |
const State *const | barrier, | |||
const size_t | index, | |||
const std::vector< size_t > & | minConnected | |||
) | [static, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
Index value that is used to propagate the information about invalid indexing.
Definition at line 37 of file LandscapeTopology.hh.
const std::string ell::LT_BarrierTree::LT_ID [static] |
the landscape topology id string used in the output header to identify a minima set
Reimplemented from ell::LT_MinimaSet.
Definition at line 60 of file LT_BarrierTree.hh.
double ell::LT_BarrierTree::maxMergeBarrier [protected] |
the energy threshold used to merge minima to equivalence classes
Definition at line 173 of file LT_BarrierTree.hh.
size_t ell::LT_MinimaSet::mfeIndex [protected, inherited] |
index of the global minimum (with minimal free energy)
Definition at line 26 of file LT_MinimaSet.hh.
Min2Node_MAP ell::LT_BarrierTree::min2node [protected] |
double ell::LandscapeTopology::MISSING_MINIMUM_PENALTY [static, inherited] |
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.
size_t ell::LT_BarrierTree::numOfLeaves [protected] |
const std::string ell::LandscapeTopology::OUTPUT_KEY_BARRIER [static, protected, inherited] |
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, inherited] |
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, inherited] |
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, inherited] |
keyword used by the read and write method to identify information on a saddle point
Definition at line 350 of file LandscapeTopology.hh.
Node* ell::LT_BarrierTree::root [protected] |
bool ell::LT_MinimaSet::sorted [protected, inherited] |
internal flag that stores if vMinima is sorted or not
Definition at line 28 of file LT_MinimaSet.hh.
std::vector<const State*> ell::LT_MinimaSet::vMinima [mutable, protected, inherited] |
The documentation for this class was generated from the following files:
- src/ell/LT_BarrierTree.hh
- src/ell/LT_BarrierTree.cc