#include <BALL/QSAR/QSARData.h>

Inheritance diagram for BALL::QSAR::QSARData:

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	readSDFile (const char *file, std::set< String > &activity_names, bool useExDesc=1, bool append=0, bool translate_class_labels=0, bool calc_phychem_properties=1, bool calc_topological_properties=1)

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 (std::vector< String > v)

void	manipulateY (String v)

void	discretizeY (std::vector< double > thresholds)

void	transformX (std::vector< String > v)

std::vector< QSARData * >	partitionInputData (int p)

void	saveToFile (string filename) const

void	readFromFile (string filename)

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

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

std::vector< double > *	getSubstance (int s) const

std::vector< double > *	getActivity (int s) const

unsigned int	getNoResponseVariables () const

const std::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	calculateBALLDescriptors (Molecule &m)

void	calculateTopologicalDescriptors (Molecule &mol, MolecularSimilarity &molsim, const std::map< String, int > &descriptor_map)

void	setDescriptorNames (const Molecule &m, std::multiset< int > &activity_IDs, bool useExDesc=1, bool resize=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 55 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 )

protected

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

void BALL::QSAR::QSARData::calculateTopologicalDescriptors	(	Molecule &	mol,
		MolecularSimilarity &	molsim,
		const std::map< String, int > &	descriptor_map
	)

protected

Calculates topological descriptors based on functional groups counts done by SMARTS matching

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

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

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.

void BALL::QSAR::QSARData::discretizeY ( std::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

std::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

std::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)

std::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

std::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 std::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 ( std::vector< String > v )

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

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"

std::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 )

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::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,
		std::set< String > &	activity_names,
		bool	useExDesc = `1`,
		bool	append = `0`,
		bool	translate_class_labels = `0`,
		bool	calc_phychem_properties = `1`,
		bool	calc_topological_properties = `1`
	)

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

void BALL::QSAR::QSARData::setDescriptorNames	(	const Molecule &	m,
		std::multiset< int > &	activity_IDs,
		bool	useExDesc = `1`,
		bool	resize = `1`
	)

protected

writes the names of all external descriptors into column_names

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

Friends And Related Function Documentation

friend class ClassificationValidation

friend

Definition at line 254 of file QSARData.h.

friend class FeatureSelection

friend

Definition at line 259 of file QSARData.h.

friend class FitModel

friend

Definition at line 258 of file QSARData.h.

friend class Model

friend

Definition at line 257 of file QSARData.h.

friend class RegressionValidation

friend

Definition at line 255 of file QSARData.h.

friend class Validation

friend

Definition at line 256 of file QSARData.h.

Member Data Documentation

std::map<String,int> BALL::QSAR::QSARData::class_names_

protected

in case of classification data sets with non-numeric class labels, this member maps the names of the individual classes to their assigned id.

Definition at line 249 of file QSARData.h.

vector<string> BALL::QSAR::QSARData::column_names_

protected

names of all descriptors

Definition at line 236 of file QSARData.h.

String BALL::QSAR::QSARData::data_folder_

protected

Definition at line 246 of file QSARData.h.

VMatrix BALL::QSAR::QSARData::descriptor_matrix_

protected

matrix containing the values of each descriptor for each substance

Definition at line 224 of file QSARData.h.

VMatrix BALL::QSAR::QSARData::descriptor_transformations_

protected

2xm dimensional matrix (m=no of descriptors) containing mean and stddev of each transformed descriptor

Definition at line 230 of file QSARData.h.

std::multiset<int> BALL::QSAR::QSARData::invalidDescriptors_

protected

contains the numbers of external descriptors for which invalid values (e.g. strings instead numerical values) were encountered in some molecules

Definition at line 242 of file QSARData.h.

std::multiset<int> BALL::QSAR::QSARData::invalidSubstances_

protected

Definition at line 244 of file QSARData.h.

vector<string> BALL::QSAR::QSARData::substance_names_

protected

names of all substances

Definition at line 239 of file QSARData.h.

VMatrix BALL::QSAR::QSARData::Y_

protected

matrix containing the experimentally determined results (active/non-active) for each substance. Different activities are saved column-wise.

Definition at line 227 of file QSARData.h.

VMatrix BALL::QSAR::QSARData::y_transformations_

protected

2xc dimensional matrix (c=no of activities) containing mean and stddev of each transformed activity

Definition at line 233 of file QSARData.h.

Public Member Functions

Protected Attributes

Friends

Accessors

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation