MTK++ Latest version: 0.2.0

Public Member Functions | Protected Member Functions | Protected Attributes
MTKpp::pharmacophore Class Reference

Determines the Maximum Common Pharmacophore (MCP) between two molecules. More...

#include <mtkpp/src/Molecule/pharmacophore.h>

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List of all members.

Public Member Functions

 pharmacophore (molecule *parent, double distMax=0.5)
 pharmacophore Constructor
virtual ~pharmacophore ()
 pharmacophore Destructor
int run (molecule *mol, std::vector< std::vector< unsigned int > > &mcp, std::vector< vector3d > &mcpCoords)
 Determines the Maximum Common Pharmacophore (MCP) between two molecules.
int getCliques (molecule *mol, std::vector< clique * > &cliqueList)
 Determines all possible Pharmacophores between two molecules.

Protected Member Functions

int generateCorrMatrix (unsigned int nFeaturesA, unsigned int nFeaturesB, std::vector< std::string > featureLabelsA, std::vector< std::string > featureLabelsB, int crpdeMatrix[])
 Generate the correspondence matrix between molecule A and B.
int getCGood (double &cGood, unsigned int nFeaturesA, unsigned int nFeaturesB, std::vector< std::string > featureLabelsA, double *featureDistMatrixA, double *featureDistMatrixB, int crpdeMatrix[])
 Get the c good value.
int getClique (unsigned int iA, unsigned int jB, unsigned int nFeaturesA, unsigned int nFeaturesB, std::vector< std::string > featureLabelsA, double *featureDistMatrixA, double *featureDistMatrixB, int crpdeMatrix[], double cGood, std::vector< std::vector< unsigned int > > &clique, double &score, double &score2, double &dMax)
 Get clique.

Protected Attributes

moleculepParent
 molecule pointer
atompAtom
 atom pointer
double deltaDistMax
 ddMax

Detailed Description

Determines the Maximum Common Pharmacophore (MCP) between two molecules.


Constructor & Destructor Documentation

MTKpp::pharmacophore::pharmacophore ( molecule parent,
double  distMax = 0.5 
)

pharmacophore Constructor

Parameters:
parentmolecule pointer
distMaxFeature distance parameter

References deltaDistMax, and pParent.

MTKpp::pharmacophore::~pharmacophore ( ) [virtual]

pharmacophore Destructor


Member Function Documentation

int MTKpp::pharmacophore::run ( molecule mol,
std::vector< std::vector< unsigned int > > &  mcp,
std::vector< vector3d > &  mcpCoords 
)

Determines the Maximum Common Pharmacophore (MCP) between two molecules.

Parameters:
molmolecule pointer
mcpMaximum Common Pharmacophore
mcpCoordsmcp coordinates
Returns:
success

References generateCorrMatrix(), getCGood(), getClique(), MTKpp::molecule::getFeatureCoordinates(), MTKpp::molecule::getFeatureDistMatrix(), MTKpp::molecule::getFeatureLabels(), and pParent.

Referenced by MTKpp::molecule::findPharmacophore().

int MTKpp::pharmacophore::getCliques ( molecule mol,
std::vector< clique * > &  cliqueList 
)

Determines all possible Pharmacophores between two molecules.

Parameters:
molmolecule pointer
cliqueListall possible pharmacophores
Returns:
success

References MTKpp::clique::coords, generateCorrMatrix(), getCGood(), getClique(), MTKpp::molecule::getFeatureCoordinates(), MTKpp::molecule::getFeatureDistMatrix(), MTKpp::molecule::getFeatureLabels(), MTKpp::clique::indicesA, MTKpp::clique::indicesB, pParent, MTKpp::clique::score, and MTKpp::clique::score2.

Referenced by MTKpp::molecule::findPharmacophore().

int MTKpp::pharmacophore::generateCorrMatrix ( unsigned int  nFeaturesA,
unsigned int  nFeaturesB,
std::vector< std::string >  featureLabelsA,
std::vector< std::string >  featureLabelsB,
int  crpdeMatrix[] 
) [protected]

Generate the correspondence matrix between molecule A and B.

Parameters:
nFeaturesANumber of feature in mol A
nFeaturesBNumber of feature in mol B
featureLabelsAFeature labels in mol A
featureLabelsBFeature labels in mol B
crpdeMatrixCorrespondence matrix
Todo:
determine the doxygen error here
Returns:
success

Referenced by getCliques(), and run().

int MTKpp::pharmacophore::getCGood ( double &  cGood,
unsigned int  nFeaturesA,
unsigned int  nFeaturesB,
std::vector< std::string >  featureLabelsA,
double *  featureDistMatrixA,
double *  featureDistMatrixB,
int  crpdeMatrix[] 
) [protected]

Get the c good value.

Parameters:
cGoodc good value
nFeaturesANumber of feature in mol A
nFeaturesBNumber of feature in mol B
featureLabelsAFeature labels in mol A
featureDistMatrixA
featureDistMatrixB
crpdeMatrixCorrespondence matrix
Returns:
success

References deltaDistMax.

Referenced by getCliques(), and run().

int MTKpp::pharmacophore::getClique ( unsigned int  iA,
unsigned int  jB,
unsigned int  nFeaturesA,
unsigned int  nFeaturesB,
std::vector< std::string >  featureLabelsA,
double *  featureDistMatrixA,
double *  featureDistMatrixB,
int  crpdeMatrix[],
double  cGood,
std::vector< std::vector< unsigned int > > &  clique,
double &  score,
double &  score2,
double &  dMax 
) [protected]

Get clique.

Parameters:
iA?
jB?
nFeaturesANumber of feature in mol A
nFeaturesBNumber of feature in mol B
featureLabelsAFeature labels in mol A
featureDistMatrixA
featureDistMatrixB
crpdeMatrixCorrespondence matrix
cGood?
clique?
score?
score2?
dMax?
Returns:
success

References deltaDistMax.

Referenced by getCliques(), and run().


Member Data Documentation

molecule pointer

Referenced by getCliques(), pharmacophore(), and run().

atom pointer

ddMax

Referenced by getCGood(), getClique(), and pharmacophore().


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

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