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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/QSAR/registry.h>
#include <BALL/QSAR/configIO.h>
#include <fstream>
#include "version.h"
using namespace BALL::QSAR;
using namespace BALL;
using namespace std;
void startInputReading(InputConfiguration& conf, String data_path, QSARData* q, String* data_filename);
void startInputReading(ifstream& in, String data_path, QSARData* q, String* data_filename)
{
InputConfiguration conf = ConfigIO::readInputConfiguration(&in);
if(conf.done) return; // stop processing this section
startInputReading(conf, data_path, q, data_filename);
}
void startInputReading(InputConfiguration& conf, String data_path, QSARData* q, String* data_filename)
{
bool created_data_object=0;
if(q==NULL || data_filename==NULL || conf.output!=*data_filename)
{
if(q==NULL)
{
q = new QSARData;
created_data_object=1;
}
if(data_filename) *data_filename = conf.output;
}
if(data_path!="")
{
q->setDataFolder(data_path.c_str());
}
if(conf.sd_file!="") // read sd-file (and csv-table)
{
if(!conf.separate_activity_file)
{
#ifndef EXT_MAIN
if(conf.activity_names.size()==0)
{
q->readSDFile(conf.sd_file.c_str(),conf.activities,conf.read_sd_descriptors,0,0);
}
else
#endif
{
q->readSDFile(conf.sd_file.c_str(),conf.activity_names,conf.read_sd_descriptors,0,0,1,1);
}
}
else
{
q->readSDFile(conf.sd_file.c_str());
}
uint no_csv = conf.csv_file.size();
for(uint i=0; i<no_csv; i++)
{
q->readCSVFile(conf.csv_file[i].c_str(),0,conf.csv_desc_labels[i],conf.csv_compound_labels[i],conf.csv_separator[i].c_str(),1,conf.nonnumeric_class_names);
}
}
else // read csv-table only
{
if(conf.csv_file.size()==0 || conf.csv_file[0]=="")
{
Log.error()<<"Error: sd-file and/or csv-table must be specified within config-file!"<<endl;
return;
}
q->readCSVFile(conf.csv_file[0].c_str(),conf.csv_no_response[0],conf.csv_desc_labels[0],conf.csv_compound_labels[0],conf.csv_separator[0].c_str(),0,conf.nonnumeric_class_names);
}
if(conf.center_data)
{
q->centerData(conf.center_y);
}
q->saveToFile(conf.output);
if(created_data_object) delete q;
}
#ifndef EXT_MAIN
int main(int argc, char* argv[])
{
CommandlineParser par("InputReader","generate QSAR data set ", VERSION, String(__DATE__), "QuEasy (QSAR)");
par.registerMandatoryInputFile("i", "input sd-file");
par.registerMandatoryOutputFile("o", "output dat-file");
par.registerOptionalStringParameter("act","sd-property containing response values");
par.registerFlag("sdp","use sd-properties as additional descriptors");
par.registerFlag("no_cd","do not center descriptors");
par.registerFlag("no_cr","do not center response values");
par.registerOptionalInputFile("csv","input csv-file w/ additional descriptors");
par.registerOptionalIntegerParameter("csv_nr","no. of response variables in csv-file");
par.registerFlag("csv_cl","csv-file has compound (row) labels");
par.registerFlag("csv_dl","csv-file has descriptor (column) labels");
par.registerOptionalIntegerParameter("csv_sep","separator symbol in csv-file");
String man = "This tool reads input from sd-files and generate features for QSAR analysis.\nActivity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.\nThe following number of features will be automatically created for each molecule in your sd-file:\n\n\
* 40 atom and bond count descriptors\n\
* 2 connectivity indices (Balaban and Zagreb index)\n\
* 4 partial charge descriptors\n\
* 14 surface descriptors\n\
* 133 topological descriptors (functional group counts)\n\nIf desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.\nOutput of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).";
par.setToolManual(man);
par.setSupportedFormats("i","sdf");
par.setSupportedFormats("csv","csv");
par.setSupportedFormats("o","dat");
par.parse(argc,argv);
InputConfiguration conf;
conf.sd_file = par.get("i");
conf.output = par.get("o");
if(par.get("act")!=CommandlineParser::NOT_FOUND)
{
list<String> alist = par.getList("act");
for(list<String>::iterator it=alist.begin(); it!=alist.end(); it++)
{
conf.activity_names.insert(*it);
}
}
conf.read_sd_descriptors = 0;
String s = par.get("sdp");
if(s!=CommandlineParser::NOT_FOUND) conf.read_sd_descriptors = s.toBool();
conf.center_data = 1;
s = par.get("no_cd");
if(s!=CommandlineParser::NOT_FOUND) conf.center_data = false;
conf.center_y = 1;
s = par.get("no_cr");
if(s!=CommandlineParser::NOT_FOUND) conf.center_y = false;
// support for reading one csv-file:
int csv_no_response = 0;
s = par.get("csv_nr");
if(s!=CommandlineParser::NOT_FOUND) csv_no_response = s.toInt();
bool csv_desc_labels = 0;
s = par.get("csv_dl");
if(s!=CommandlineParser::NOT_FOUND) csv_desc_labels = s.toInt();
bool csv_compound_labels = 0;
s = par.get("csv_cl");
if(s!=CommandlineParser::NOT_FOUND) csv_compound_labels = s.toInt();
String csv_separator = "\t";
s = par.get("csv_sep");
if(s!=CommandlineParser::NOT_FOUND) csv_separator = s;
s = par.get("csv");
if(s!=CommandlineParser::NOT_FOUND)
{
conf.csv_file.push_back(s);
conf.csv_no_response.push_back(csv_no_response);
conf.csv_desc_labels.push_back(csv_desc_labels);
conf.csv_compound_labels.push_back(csv_compound_labels);
conf.csv_separator.push_back(csv_separator);
}
startInputReading(conf,"",0,0);
}
#endif
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