55 #ifndef QSAR_EXCEPTION
67 class MolecularSimilarity;
86 bool isDataCentered()
const;
89 bool isResponseCentered()
const;
95 vector<String>* readPropertyNames(
String sd_file);
100 void readSDFile(
const char* file);
107 void readSDFile(
const char* file, std::multiset<int>& act,
bool useExDesc=1,
bool append=0,
bool translate_class_labels=0);
109 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);
112 void displayMatrix();
116 void centerData(
bool center_Y=0);
119 void scaleAllDescriptors();
122 unsigned int getNoSubstances()
const;
125 unsigned int getNoDescriptors()
const;
134 void readCSVFile(
const char* file,
int no_y,
bool xlabels,
bool ylabels,
const char* sep=
",",
bool appendDescriptors=0,
bool translate_class_labels=0);
137 void manipulateY(std::vector<String> v);
141 void manipulateY(
String v);
145 void discretizeY(std::vector<double> thresholds);
147 void transformX(std::vector<String> v);
150 std::vector<QSARData*> partitionInputData(
int p);
153 void saveToFile(
string filename)
const;
156 void readFromFile(
string filename);
160 std::vector<QSARData*> generateExternalSet(
double fraction)
const;
166 std::vector<QSARData*> evenSplit(
int no_test_splits,
int current_test_split_id,
int response_id=0)
const;
169 std::vector<double>* getSubstance(
int s)
const;
172 std::vector<double>* getActivity(
int s)
const;
175 unsigned int getNoResponseVariables()
const;
177 const std::vector<string>* getSubstanceNames()
const;
180 bool checkforDiscreteY()
const;
184 bool checkforDiscreteY(
const char* file, std::multiset<int>& activity_IDs)
const;
187 void setDataFolder(
const char* folder);
191 void removeHighlyCorrelatedCompounds(
double& compound_cor_threshold,
double& feature_cor_threshold);
198 void getSimilarDescriptors(
int descriptor_ID,
double correlation, std::list<std::pair<uint,String> >& similar_descriptor_IDs)
const;
211 void calculateBALLDescriptors(
Molecule& m);
217 void setDescriptorNames(
const Molecule& m, std::multiset<int>& activity_IDs,
bool useExDesc=1,
bool resize=1);
221 void removeInvalidDescriptors(std::multiset<int>& invalidDescriptors);
223 void removeInvalidSubstances(std::multiset<int>& inv);
226 void readMatrix(VMatrix& mat, std::ifstream& in,
char seperator,
unsigned int lines,
unsigned int col);
230 void checkActivityIDs(std::multiset<int>& act,
int no_properties);
234 void insertSubstance(
const QSARData* source,
int s,
bool backtransformation=0);
237 void printMatrix(
const VMatrix& mat, std::ostream& out)
const;
278 friend class FitModel;
std::map< String, int > class_names_
vector< string > substance_names_
vector< string > column_names_
VMatrix y_transformations_
VMatrix descriptor_transformations_
std::multiset< int > invalidDescriptors_
VMatrix descriptor_matrix_
-*- Mode: C++; tab-width: 2; -*-
std::multiset< int > invalidSubstances_