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