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//
//
// Copyright (C) 2019 Greg Landrum
//
// @@ 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 <string>
#include <GraphMol/RDKitBase.h>
class JSMol {
public:
JSMol() : d_mol(nullptr){};
JSMol(RDKit::RWMol *mol) : d_mol(mol){};
std::string get_smiles() const;
std::string get_cxsmiles() const;
std::string get_molblock() const;
std::string get_v3Kmolblock() const;
std::string get_inchi() const;
std::string get_svg(unsigned int width, unsigned int height) const;
std::string get_svg() const {
return get_svg(d_defaultWidth, d_defaultHeight);
};
std::string get_svg_with_highlights(const std::string &details) const;
std::string get_substruct_match(const JSMol &q) const;
std::string get_substruct_matches(const JSMol &q) const;
std::string get_descriptors() const;
std::string get_morgan_fp(unsigned int radius, unsigned int len) const;
std::string get_morgan_fp() const { return get_morgan_fp(2, 2048); };
std::string condense_abbreviations(double maxCoverage, bool useLinkers);
std::string condense_abbreviations() {
return condense_abbreviations(0.4, false);
};
std::string condense_abbreviations_from_defs(const std::string &definitions,
double maxCoverage,
bool areLinkers);
std::string generate_aligned_coords(const JSMol &templateMol,bool useCoordGen);
std::string generate_aligned_coords(const JSMol &templateMol) { return generate_aligned_coords(templateMol,false);};
bool is_valid() const { return d_mol.get() != nullptr; };
// functionality primarily useful in ketcher
std::string get_stereo_tags() const;
std::string get_aromatic_form() const;
std::string get_kekule_form() const;
std::string get_new_coords(bool useCoordGen) const;
std::string get_new_coords() const { return get_new_coords(false); };
std::string remove_hs() const;
std::string add_hs() const;
std::unique_ptr<RDKit::RWMol> d_mol;
static constexpr unsigned int d_defaultWidth = 250;
static constexpr unsigned int d_defaultHeight = 200;
};
std::string get_inchikey_for_inchi(const std::string &input);
JSMol *get_mol(const std::string &input);
JSMol *get_qmol(const std::string &input);
std::string version();
void prefer_coordgen(bool prefer);
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