5#ifndef BALL_QSAR_MODEL_H
6#define BALL_QSAR_MODEL_H
9#ifndef BALL_QSAR_VALIDATION_H
13#ifndef BALL_QSAR_QSARDATA_H
17#ifndef BALL_QSAR_EXCEPTION_H
21#ifndef BALL_MATHS_PARSEDFUNCTION_H
50 EIGEN_MAKE_ALIGNED_OPERATOR_NEW
76 virtual Eigen::VectorXd
predict(
const vector<double>& substance,
bool transform) =0;
174 void addLambda(Eigen::MatrixXd& matrix,
double& lambda);
185 void readMatrix(Eigen::MatrixXd& mat, std::ifstream& in,
unsigned int lines,
unsigned int col);
187 void readVector(Eigen::RowVectorXd& vec, std::ifstream& in,
unsigned int no_cells,
bool column_vector);
BALL_EXPORT Model * createNewModelFromFile(String model_file, const QSARData &q)
virtual void saveToFile(string filename)=0
const vector< string > * getDescriptorNames()
virtual void readDescriptorInformationFromFile(std::ifstream &in, int no_descriptors, bool transformation)
std::multiset< unsigned int > descriptor_IDs_
const Eigen::MatrixXd * getDescriptorMatrix()
void addLambda(Eigen::MatrixXd &matrix, double &lambda)
vector< string > descriptor_names_
void readVector(Eigen::RowVectorXd &vec, std::ifstream &in, unsigned int no_cells, bool column_vector)
virtual void readFromFile(string filename)=0
void getUnnormalizedFeatureValue(int compound, int feature, double &return_value)
const Eigen::MatrixXd getYTransformations()
void setDataSource(const QSARData *q)
virtual vector< double > getParameters() const
virtual double calculateStdErr()
const Eigen::MatrixXd * getY()
virtual bool optimizeParameters(int, int)
void copyData(const Model &m)
virtual void operator=(const Model &m)
void readResponseTransformationFromFile(std::ifstream &in, int no_y)
void deleteDescriptorIDs()
const vector< string > * getSubstanceNames()
std::multiset< unsigned int > * getDescriptorIDs()
Eigen::VectorXd getSubstanceVector(const vector< double > &substance, bool transform)
void setDescriptorIDs(const std::multiset< unsigned int > &sl)
const Eigen::MatrixXd getDescriptorTransformations()
void backTransformPrediction(Eigen::VectorXd &pred)
void getUnnormalizedResponseValue(int compound, int response, double &return_value)
Eigen::MatrixXd y_transformations_
int default_no_opt_steps_
void readModelParametersFromFile(std::ifstream &in)
void saveModelParametersToFile(std::ofstream &out)
virtual void setParameters(vector< double > &)
virtual void saveDescriptorInformationToFile(std::ofstream &out)
Eigen::MatrixXd descriptor_transformations_
bool optimizeParameters(int k)
void readMatrix(Eigen::MatrixXd &mat, std::ifstream &in, unsigned int lines, unsigned int col)
void copyDescriptorIDs(const Model &m)
Eigen::VectorXd getSubstanceVector(const Eigen::VectorXd &substance, bool transform)
virtual Eigen::VectorXd predict(const vector< double > &substance, bool transform)=0
Eigen::MatrixXd descriptor_matrix_
void saveResponseTransformationToFile(std::ofstream &out)
void readDescriptorInformation()
vector< string > substance_names_