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95 lines
2.8 KiB
C++
95 lines
2.8 KiB
C++
/*******************************************************************************
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options.h - Shape-it
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Copyright 2012 by Silicos-it, a division of Imacosi BVBA
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This file is part of Shape-it.
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Shape-it is free software: you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as published
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by the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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Shape-it is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with Shape-it. If not, see <http://www.gnu.org/licenses/>.
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Shape-it is linked against OpenBabel version 2.
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OpenBabel is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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***********************************************************************/
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#ifndef __SILICOSIT_SHAPEIT_OPTIONS_H__
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#define __SILICOSIT_SHAPEIT_OPTIONS_H__
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// General
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#include <string>
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#include <iostream>
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#include <fstream>
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// OpenBabel
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// RDKit
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/MolWriters.h>
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// Shape-it
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const std::string tanimoto = "Tanimoto";
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const std::string tversky_ref = "Tversky_Ref";
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const std::string tversky_db = "Tversky_Db";
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class Options
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{
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public:
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std::string refInpFile; // -r --reference
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std::ifstream* refInpStream;
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RDKit::SDMolSupplier* refInpReader;
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std::string dbInpFile; // -d --dbase
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std::ifstream* dbInpStream;
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RDKit::SDMolSupplier* dbInpReader;
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std::string molOutFile; // -o --out
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std::ofstream* molOutStream;
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RDKit::SDWriter* molOutWriter;
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std::string scoreOutFile; // -s --score
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std::ofstream* scoreOutStream;
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unsigned int bestHits; // --best
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double cutOff; // --cutOff
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double maxIter; // --maxIterations
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std::string whichScore; // --rankBy
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bool scoreOnly; // --scoreOnly
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bool showRef; // --noRef
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bool version; // -v --version
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bool help; // -h --help
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Options(void);
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~Options(void);
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std::string print(void) const;
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};
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#endif
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