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// $Id$
//
// Created by Greg Landrum, July 2008
//
#ifndef __AVALONTOOLS_H__
#define __AVALONTOOLS_H__
#include <string>
#include <GraphMol/RDKitBase.h>
#include <DataStructs/ExplicitBitVect.h>
#include <vector>
#include <boost/cstdint.hpp>
namespace AvalonTools {
static int avalonSSSBits=0x007FFF;
static int avalonSimilarityBits=0xF07FFF;
std::string getCanonSmiles(RDKit::ROMol &mol,int flags=-1);
void getAvalonFP(const RDKit::ROMol &mol,ExplicitBitVect &res,
unsigned int nBits=512,
bool isQuery=false,
bool resetVect=true,
unsigned int bitFlags=avalonSSSBits);
void getAvalonFP(const RDKit::ROMol &mol,std::vector<boost::uint32_t> &res,
unsigned int nBits=512,
bool isQuery=false,
bool resetVect=true,
unsigned int bitFlags=avalonSSSBits);
unsigned int set2DCoords(RDKit::ROMol &mol,bool clearConfs=true);
std::string getCanonSmiles(const std::string &data,bool isSmiles,int flags=-1);
void getAvalonFP(const std::string &data,bool isSmiles,ExplicitBitVect &res,
unsigned int nBits=512,
bool isQuery=false,
bool resetVect=true,
unsigned int bitFlags=avalonSSSBits);
void getAvalonFP(const std::string &data,bool isSmiles,std::vector<boost::uint32_t> &res,
unsigned int nBits=512,
bool isQuery=false,
bool resetVect=true,
unsigned int bitFlags=avalonSSSBits);
std::string set2DCoords(const std::string &data,bool isSmiles);
int initCheckMol(const std::string &optString);
RDKit::ROMOL_SPTR checkMol(int &errors, RDKit::ROMol& inMol);
RDKit::ROMOL_SPTR checkMol(int &errors, const std::string &data, bool isSmiles);
std::pair<std::string,int> checkMolString(const std::string &data, bool isSmiles);
void closeCheckMolFiles();
}
#endif
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