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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_FRAG_CAT_PARAMS_H_
#define _RD_FRAG_CAT_PARAMS_H_
#include <Catalogs/CatalogParams.h>
#include <string>
#include <vector>
#include <boost/shared_ptr.hpp>
namespace RDKit {
class ROMol;
typedef std::vector<boost::shared_ptr<ROMol> > MOL_SPTR_VECT;
//! container for user parameters used to create a fragment catalog
class RDKIT_FRAGCATALOG_EXPORT FragCatParams : public RDCatalog::CatalogParams {
// FIX: this container is still missing all the CASE-type functional groups
// stuff
public:
FragCatParams() {
d_typeStr = "Fragment Catalog Parameters";
d_lowerFragLen = 0;
d_upperFragLen = 0;
d_tolerance = 1e-8;
d_funcGroups.clear();
}
//! construct from a function-group file
/*!
\param lLen the lower limit on fragment size
\param uLen the upper limit on fragment size
\param fgroupFile the name of the function-group file
\param tol (optional) the eigenvalue tolerance to be used
when comparing fragments
*/
FragCatParams(unsigned int lLen, unsigned int uLen,
const std::string &fgroupFile, double tol = 1e-08);
//! copy constructor
FragCatParams(const FragCatParams &other);
//! construct from a pickle string (serialized representation)
FragCatParams(const std::string &pickle);
~FragCatParams();
//! returns our lower fragment length
unsigned int getLowerFragLength() const { return d_lowerFragLen; }
//! sets our lower fragment length
void setLowerFragLength(unsigned int lFrLen) { d_lowerFragLen = lFrLen; }
//! returns our upper fragment length
unsigned int getUpperFragLength() const { return d_upperFragLen; }
//! sets our upper fragment length
void setUpperFragLength(unsigned int uFrLen) { d_upperFragLen = uFrLen; }
//! returns our fragment-comparison tolerance
double getTolerance() const { return d_tolerance; }
//! sets our fragment-comparison tolerance
void setTolerance(double val) { d_tolerance = val; }
//! returns our number of functional groups
unsigned int getNumFuncGroups() const { return static_cast<unsigned int>(d_funcGroups.size()); }
//! returns our std::vector of functional groups
const MOL_SPTR_VECT &getFuncGroups() const;
//! returns a pointer to a specific functional group
const ROMol *getFuncGroup(unsigned int fid) const;
void toStream(std::ostream &) const;
std::string Serialize() const;
void initFromStream(std::istream &ss);
void initFromString(const std::string &text);
private:
unsigned int d_lowerFragLen;
unsigned int d_upperFragLen;
double d_tolerance; //!< tolerance value used when comparing subgraph
// discriminators
MOL_SPTR_VECT d_funcGroups;
};
}
#endif
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