BALL::QSAR::QSARData Class Reference

#include <BALL/QSAR/QSARData.h>

Public Member Functions
	QSARData ()
	~QSARData ()
Predicates

bool	isDataCentered () const
bool	isResponseCentered () const
Protected Attributes
Attributes

VMatrix	descriptor_matrix_
VMatrix	Y_
VMatrix	descriptor_transformations_
VMatrix	y_transformations_
vector< string >	column_names_
vector< string >	substance_names_
std::multiset< int >	invalidDescriptors_
std::multiset< int >	invalidSubstances_
String	data_folder_
std::map< String, int >	class_names_
Friends
class	ClassificationValidation
class	RegressionValidation
class	Validation
class	Model
class	FitModel
class	FeatureSelection
Accessors

vector< String > *	readPropertyNames (String sd_file)
void	readSDFile (const char *file)
void	readSDFile (const char *file, std::multiset< int > &act, bool useExDesc=1, bool append=0, bool translate_class_labels=0)
void	calculateBALLDescriptors (Molecule &m)
void	displayMatrix ()
void	centerData (bool center_Y=0)
void	scaleAllDescriptors ()
unsigned int	getNoSubstances () const
unsigned int	getNoDescriptors () const
void	readCSVFile (const char file, int no_y, bool xlabels, bool ylabels, const char sep=",", bool appendDescriptors=0, bool translate_class_labels=0)
void	manipulateY (vector< String > v)
void	manipulateY (String v)
void	discretizeY (vector< double > thresholds)
void	transformX (vector< String > v)
vector< QSARData * >	partitionInputData (int p)
void	saveToFile (string filename) const
void	readFromFile (string filename)
vector< QSARData * >	generateExternalSet (double fraction) const
vector< QSARData * >	evenSplit (int no_test_splits, int current_test_split_id, int response_id=0) const
vector< double > *	getSubstance (int s) const
vector< double > *	getActivity (int s) const
unsigned int	getNoResponseVariables () const
const vector< string > *	getSubstanceNames () const
bool	checkforDiscreteY () const
bool	checkforDiscreteY (const char *file, std::multiset< int > &activity_IDs) const
void	setDataFolder (const char *folder)
void	removeHighlyCorrelatedCompounds (double &compound_cor_threshold, double &feature_cor_threshold)
void	getSimilarDescriptors (int descriptor_ID, double correlation, std::list< std::pair< uint, String > > &similar_descriptor_IDs) const
void	setDescriptorNames (const Molecule &m, std::multiset< int > &activity_IDs, bool useExDesc=1)
void	removeInvalidDescriptors (std::multiset< int > &invalidDescriptors)
void	removeInvalidSubstances (std::multiset< int > &inv)
void	readMatrix (VMatrix &mat, std::ifstream &in, char seperator, unsigned int lines, unsigned int col)
void	checkActivityIDs (std::multiset< int > &act, int no_properties)
void	insertSubstance (const QSARData *source, int s, bool backtransformation=0)
void	printMatrix (const VMatrix &mat, std::ostream &out) const

Detailed Description

QSAR

Definition at line 76 of file QSARData.h.

Constructor & Destructor Documentation

BALL::QSAR::QSARData::QSARData ( )

BALL::QSAR::QSARData::~QSARData ( )

Member Function Documentation

void BALL::QSAR::QSARData::calculateBALLDescriptors ( Molecule & m )

Calculates descriptors for one molecule and saves them into one new line of descriptor_matrix

void BALL::QSAR::QSARData::centerData ( bool center_Y = 0 )

centers each descriptor to mean of 0 and stddev of 1

Parameters:

center_Y

if ==1, activity values are also centered. Obviously this should NOT be used for classification experiments!

void BALL::QSAR::QSARData::checkActivityIDs	(	std::multiset< int > &	act,
		int	no_properties
	)			`[protected]`

checks whether the given list of activity IDs contains any values <0 or values that are larger than the number of properties in the current input file.
If such values are found, an Exception of type InvalidActivityID is thrown.

bool BALL::QSAR::QSARData::checkforDiscreteY	(	const char *	file,
		std::multiset< int > &	activity_IDs
	)			const

checks whether the response variables of a specified file contain only discrete values.

bool BALL::QSAR::QSARData::checkforDiscreteY ( ) const

checks whether the response variables contain only discrete values. This can be used to check whether the current input data set is suitable for a ClassificationModel

void BALL::QSAR::QSARData::discretizeY ( vector< double > thresholds )

Discretize the response values. If the response variable(s) of this data object have been normalized, the given thresolds will be automatically normalized accordingly.

Parameters:

thresolds

d thresholds for d+1 classes, that are to be created

void BALL::QSAR::QSARData::displayMatrix ( )

show descriptor_matrix on stdout

vector<QSARData*> BALL::QSAR::QSARData::evenSplit	(	int	no_test_splits,
		int	current_test_split_id,
		int	response_id = `0`
	)			const

Split this data set into a training set and a test set. In contrast to generateExternalSet(), compounds for the test set are *not* randomly selected. Instead, this data set is first sorted according to response values (in order to ensure equal response value ranges) and then split regularly into training and test set.

Parameters:

	no_test_splits	the total number of splits you want to create by successive calls of this function
	current_test_split_id	the split to be produced, with 0<=current_test_split_id<no_test_splits

vector<QSARData*> BALL::QSAR::QSARData::generateExternalSet ( double fraction ) const

generates a training and an external validation set from the current QSARData object

Parameters:

fraction

the fraction of this current coumpounds that should be used as external validation set (by random drawing)

vector<double>* BALL::QSAR::QSARData::getActivity ( int s ) const

returns a pointer to a new vector containing the UNcentered response values for the s'th substance of the current data set

unsigned int BALL::QSAR::QSARData::getNoDescriptors ( ) const

returns the number of descriptors

unsigned int BALL::QSAR::QSARData::getNoResponseVariables ( ) const

returns the number of response variables

unsigned int BALL::QSAR::QSARData::getNoSubstances ( ) const

returns the number of substances

void BALL::QSAR::QSARData::getSimilarDescriptors	(	int	descriptor_ID,
		double	correlation,
		std::list< std::pair< uint, String > > &	similar_descriptor_IDs
	)			const

Find all descriptors of the current data set that have a correlation of at least 'similarity' to the specified feature

Parameters:

	descriptor_ID	the ID of the descriptor for which similar features should be searched
	similarity	the desired minimal correlation
	similar_descriptor_IDs	list to which the IDs of the found descriptors will be saved as pairs of descriptor ID and descriptor name

vector<double>* BALL::QSAR::QSARData::getSubstance ( int s ) const

returns a pointer to a new vector containing the UNcentered descriptor values for the s'th substance of the current data set

const vector<string>* BALL::QSAR::QSARData::getSubstanceNames ( ) const

void BALL::QSAR::QSARData::insertSubstance	(	const QSARData *	source,
		int	s,
		bool	backtransformation = `0`
	)			`[protected]`

appends compound no <s> taken from the given source to the data of this object.

Parameters:

backtransformation

if set to true, all features of the compound are back-transformed after adding them to this object.

bool BALL::QSAR::QSARData::isDataCentered ( ) const

tells whether the features have been centered

bool BALL::QSAR::QSARData::isResponseCentered ( ) const

tells whether the response variables have been centered

void BALL::QSAR::QSARData::manipulateY ( String v )

for testing purposes only: change Y-matrix according to the given equation

Parameters:

v

string containing the equation, e.g."x1+x3*5+x10^2"

void BALL::QSAR::QSARData::manipulateY ( vector< String > v )

for testing purposes only: change Y-matrix according to the given equations

vector<QSARData*> BALL::QSAR::QSARData::partitionInputData ( int p )

partitions the input data into p QSARData object of (approx.) equal size.

void BALL::QSAR::QSARData::printMatrix	(	const VMatrix &	mat,
		std::ostream &	out
	)			const `[protected]`

prints a vector-based matrix to a file

void BALL::QSAR::QSARData::readCSVFile	(	const char *	file,
		int	no_y,
		bool	xlabels,
		bool	ylabels,
		const char *	sep = `","`,
		bool	appendDescriptors = `0`,
		bool	translate_class_labels = `0`
	)

Read input from a csv file.
This file should contain all descriptor values in the first columns and the activity values in the last no_y columns.

Parameters:

	no_y	the number of activities, i.e. the number of columns containing activity values
	xlabels	if ==1, names of descriptors are read from the first line of the table
	ylabel	if ==1, names of substances are read from the first column of the table
	sep	the character used to seperate the cells of the table
	appendDescriptors	if set to 1, descriptors will be read from the file and appended as new columns to the current descriptor_matrix

void BALL::QSAR::QSARData::readFromFile ( string filename )

reconstructs a QSARData object from a text file

void BALL::QSAR::QSARData::readMatrix	(	VMatrix &	mat,
		std::ifstream &	in,
		char	seperator,
		unsigned int	lines,
		unsigned int	col
	)			`[protected]`

reconstructs a vector based matrix from a file

vector<String>* BALL::QSAR::QSARData::readPropertyNames ( String sd_file )

reads the names of the properties from the first molecule in the given sd-file

void BALL::QSAR::QSARData::readSDFile	(	const char *	file,
		std::multiset< int > &	act,
		bool	useExDesc = `1`,
		bool	append = `0`,
		bool	translate_class_labels = `0`
	)

Fetches input from one sd-file containing all structures. The activity value for each molecule is taken from its property in the sd-file.

Parameters:

	a	contains the numbers of the properties that are activity-values
	file	the sd-file containing the input
	useExDesc	if set to 1, descriptors read from the sd-file will be used in addition to those calculated by BALL internally
	append	if set to 1, the substances read from the sd-file will be appended as new lines to the current descriptor_matrix

void BALL::QSAR::QSARData::readSDFile ( const char * file )

Fetches input from one sd-file containing all structures and from one file containing the activities of all structures sorted in ascending order.
The latter file is assumed to have the same name as the first one, with only the extension changed to ".txt"

Parameters:

file

the sd-file containing the input

void BALL::QSAR::QSARData::removeHighlyCorrelatedCompounds	(	double &	compound_cor_threshold,
		double &	feature_cor_threshold
	)

removes compounds whose absolute correlation coefficient to another compound is larger than cor_threshold

Parameters:

feature_cor_threshold

Only features that do not have a correlation larger than this value to another feature are used to calculate the similarity of compounds (=instances).

void BALL::QSAR::QSARData::removeInvalidDescriptors ( std::multiset< int > & invalidDescriptors ) [protected]

removes columns of invalid descriptor from descriptor_matrix

Parameters:

invalidDescriptors

list containing the IDs of the columns to be deleted

void BALL::QSAR::QSARData::removeInvalidSubstances ( std::multiset< int > & inv ) [protected]

void BALL::QSAR::QSARData::saveToFile ( string filename ) const

saves the current QSARData object to a text file

void BALL::QSAR::QSARData::scaleAllDescriptors ( )

scales each descriptor to stddev of 1

void BALL::QSAR::QSARData::setDataFolder ( const char * folder )

allows to set the data-folder neccessary for computation of descriptors without using BALL_DATA_PATH enviroment variable, which is useful for standalone applications