ggl::chem::AP_NSPDK_Model Class Reference

NSPDK aromaticity model. More...

#include <AP_NSPDK_Model.hh>

Inheritance diagram for ggl::chem::AP_NSPDK_Model:

Public Member Functions
	AP_NSPDK_Model ()
	construction More...
	~AP_NSPDK_Model ()
	destruction More...

Static Public Member Functions
static const std::set < std::string > &	getAvailableModels (void)
static const AP_NSPDK_Model *const	getInstance (const std::string &modelID)

Data Fields
std::string	description
	a description of the model, e.g. its sources etc. More...
size_t	maxRingSize
	the maximal ring size considered when the model was created More...
std::string	modelID
	the ID of the model More...
size_t	nspdk_featureBitSize
size_t	nspdk_maxDistance
	the NSPDK distance parameter used to generate the model More...
size_t	nspdk_maxRadius
	the NSPDK radius parameter used to generate the model More...
size_t	nspdk_maxRingDistance
bool	ringCentered
	whether or not the NSPDK features are ring centered or not More...
std::string	ringEdgeLabel
std::string	ringNodeLabelPrefix
std::string	ringViewLabelPrefix

Protected Types
typedef boost::shared_ptr < AP_NSPDK_Model >	AP_NSPDK_Model_Pointer

Static Protected Attributes
static std::set< std::string >	availableModelIDs
	list of all available IDs of predefined models More...
static std::map< std::string, AP_NSPDK_Model_Pointer >	availableModels
	container of all available predefined models More...
static sgd::SVector::Pair	Marvin_general_2013_wdata []
	the feature weight entries of the model "Marvin:general:2013" More...
static int	Marvin_general_2013_wdatasize
	the number of entries covered by the model "Marvin:general:2013" More...
static sgd::SVector::Pair	OpenBabel_2013_wdata []
	the feature weight entries of the model "OpenBabel:2013" More...
static int	OpenBabel_2013_wdatasize
	the number of entries covered by the model "OpenBabel:2013" More...

Detailed Description

   A linear SVM model derived using the NSPDK kernel that defines an
   aromaticity classifier used by ggl::chem::AP_NSPDK to identify
   aromatic rings.

Author

Martin Mann (c) 2011 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 59 of file AP_NSPDK_Model.hh.

Member Typedef Documentation

typedef boost::shared_ptr<AP_NSPDK_Model> ggl::chem::AP_NSPDK_Model::AP_NSPDK_Model_Pointer

protected

Definition at line 122 of file AP_NSPDK_Model.hh.

Constructor & Destructor Documentation

ggl::chem::AP_NSPDK_Model::AP_NSPDK_Model

(

)

ggl::chem::AP_NSPDK_Model::~AP_NSPDK_Model

(

)

Member Function Documentation

static const std::set< std::string >& ggl::chem::AP_NSPDK_Model::getAvailableModels ( void  )

static

Enables the access to all registered predefined model IDs that are handled via getInstance(modelID).

Returns

the set of all available model IDs

static const AP_NSPDK_Model* const ggl::chem::AP_NSPDK_Model::getInstance ( const std::string &  modelID )

static

Access to the predefined instances via their identifier.

Parameters

modelID

the identifier of the model of interest

Returns

the model or NULL if no model is available for the given identifier

Field Documentation

std::set< std::string > ggl::chem::AP_NSPDK_Model::availableModelIDs

staticprotected

Definition at line 126 of file AP_NSPDK_Model.hh.

std::map< std::string, AP_NSPDK_Model_Pointer > ggl::chem::AP_NSPDK_Model::availableModels

staticprotected

Definition at line 124 of file AP_NSPDK_Model.hh.

std::string ggl::chem::AP_NSPDK_Model::description

Definition at line 71 of file AP_NSPDK_Model.hh.

sgd::SVector::Pair ggl::chem::AP_NSPDK_Model::Marvin_general_2013_wdata[]

staticprotected

Definition at line 160 of file AP_NSPDK_Model.hh.

int ggl::chem::AP_NSPDK_Model::Marvin_general_2013_wdatasize

staticprotected

Definition at line 158 of file AP_NSPDK_Model.hh.

size_t ggl::chem::AP_NSPDK_Model::maxRingSize

Definition at line 94 of file AP_NSPDK_Model.hh.

std::string ggl::chem::AP_NSPDK_Model::modelID

Definition at line 68 of file AP_NSPDK_Model.hh.

size_t ggl::chem::AP_NSPDK_Model::nspdk_featureBitSize

the NSPDK parameter that defines the number of bits that define the feature space size used to generate the model

Definition at line 91 of file AP_NSPDK_Model.hh.

size_t ggl::chem::AP_NSPDK_Model::nspdk_maxDistance

Definition at line 84 of file AP_NSPDK_Model.hh.

size_t ggl::chem::AP_NSPDK_Model::nspdk_maxRadius

Definition at line 87 of file AP_NSPDK_Model.hh.

size_t ggl::chem::AP_NSPDK_Model::nspdk_maxRingDistance

If ringCentered == true, this parameter defines up to what distance of ring nodes nodes are viewPoints, ie. a value of 0 restricts the viewpoints to the ring only.

Definition at line 81 of file AP_NSPDK_Model.hh.

sgd::SVector::Pair ggl::chem::AP_NSPDK_Model::OpenBabel_2013_wdata[]

staticprotected

Definition at line 155 of file AP_NSPDK_Model.hh.

int ggl::chem::AP_NSPDK_Model::OpenBabel_2013_wdatasize

staticprotected

Definition at line 153 of file AP_NSPDK_Model.hh.

bool ggl::chem::AP_NSPDK_Model::ringCentered

Definition at line 74 of file AP_NSPDK_Model.hh.

std::string ggl::chem::AP_NSPDK_Model::ringEdgeLabel

the edge label used within all rings, used to minimize the uncertain information for prediction

Definition at line 103 of file AP_NSPDK_Model.hh.

std::string ggl::chem::AP_NSPDK_Model::ringNodeLabelPrefix

the prefix added to all node label within all rings, used to minimize the uncertain information for prediction NOTE: the node label has to be set non-aromatic as well!

Definition at line 99 of file AP_NSPDK_Model.hh.

std::string ggl::chem::AP_NSPDK_Model::ringViewLabelPrefix

the label prefix that is added in front of each node and edge label participating in the ring currently under consideration

Definition at line 107 of file AP_NSPDK_Model.hh.

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

• src/ggl/chem/AP_NSPDK_Model.hh