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//
//
// Copyright (C) 2019-2021 Greg Landrum and other RDKit contributors
//
// @@ 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>
#include <GraphMol/SubstructLibrary/SubstructLibrary.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.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_smarts() const;
std::string get_cxsmarts() const;
std::string get_molblock() const;
std::string get_v3Kmolblock() const;
std::string get_pickle() const;
std::string get_inchi() const;
std::string get_json() const;
std::string get_svg(int width, 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(const std::string &details) const;
std::string get_morgan_fp() const { return get_morgan_fp("{}"); }
std::string get_morgan_fp_as_binary_text(const std::string &details) const;
std::string get_morgan_fp_as_binary_text() const {
return get_morgan_fp_as_binary_text("{}");
}
std::string get_pattern_fp(const std::string &details) const;
std::string get_pattern_fp() const { return get_pattern_fp("{}"); }
std::string get_pattern_fp_as_binary_text(const std::string &details) const;
std::string get_pattern_fp_as_binary_text() const {
return get_pattern_fp_as_binary_text("{}");
}
std::string get_topological_torsion_fp(const std::string &details) const;
std::string get_topological_torsion_fp() const {
return get_topological_torsion_fp("{}");
};
std::string get_topological_torsion_fp_as_binary_text(
const std::string &details) const;
std::string get_topological_torsion_fp_as_binary_text() const {
return get_topological_torsion_fp_as_binary_text("{}");
}
std::string get_rdkit_fp(const std::string &details) const;
std::string get_rdkit_fp() const { return get_rdkit_fp("{}"); }
std::string get_rdkit_fp_as_binary_text(const std::string &details) const;
std::string get_rdkit_fp_as_binary_text() const {
return get_rdkit_fp_as_binary_text("{}");
}
std::string get_atom_pair_fp(const std::string &details) const;
std::string get_atom_pair_fp() const { return get_atom_pair_fp("{}"); }
std::string get_atom_pair_fp_as_binary_text(const std::string &details) const;
std::string get_atom_pair_fp_as_binary_text() const {
return get_atom_pair_fp_as_binary_text("{}");
}
#ifdef RDK_BUILD_AVALON_SUPPORT
std::string get_avalon_fp(const std::string &details) const;
std::string get_avalon_fp() const { return get_avalon_fp("{}"); }
std::string get_avalon_fp_as_binary_text(const std::string &details) const;
std::string get_avalon_fp_as_binary_text() const {
return get_avalon_fp_as_binary_text("{}");
}
#endif
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,
const std::string &details);
std::string generate_aligned_coords(const JSMol &templateMol) {
return generate_aligned_coords(templateMol, "{}");
}
bool is_valid() const { return d_mol.get() != nullptr; }
bool has_coords() const {
return d_mol.get() != nullptr && d_mol->getNumConformers() != 0;
}
std::string get_stereo_tags() const;
std::string get_aromatic_form() const;
std::string get_kekule_form() const;
bool set_new_coords(bool useCoordGen);
bool set_new_coords() { return set_new_coords(false); }
std::string get_new_coords(bool useCoordGen) const;
std::string get_new_coords() const { return get_new_coords(false); }
bool has_prop(const std::string &key) const;
std::vector<std::string> get_prop_list(bool includePrivate,
bool includeComputed) const;
std::vector<std::string> get_prop_list(bool includePrivate) const {
return get_prop_list(includePrivate, true);
}
std::vector<std::string> get_prop_list() const {
return get_prop_list(true, true);
}
bool set_prop(const std::string &key, const std::string &val, bool computed);
bool set_prop(const std::string &key, const std::string &val) {
return set_prop(key, val, false);
}
std::string get_prop(const std::string &key) const;
std::string remove_hs() const;
std::string add_hs() const;
double normalize_depiction(int canonicalize, double scaleFactor);
double normalize_depiction(int canonicalize) {
return normalize_depiction(canonicalize, -1.);
}
double normalize_depiction() { return normalize_depiction(1, -1.); }
void straighten_depiction(bool minimizeRotation);
void straighten_depiction() { straighten_depiction(false); }
std::unique_ptr<RDKit::RWMol> d_mol;
static constexpr int d_defaultWidth = 250;
static constexpr int d_defaultHeight = 200;
};
class JSReaction {
public:
JSReaction() : d_rxn(nullptr) {}
JSReaction(RDKit::ChemicalReaction *rxn) : d_rxn(rxn) {}
bool is_valid() const { return d_rxn.get() != nullptr; }
std::string get_svg(int width, 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::unique_ptr<RDKit::ChemicalReaction> d_rxn;
static constexpr int d_defaultWidth = 800;
static constexpr int d_defaultHeight = 200;
};
class JSSubstructLibrary {
public:
JSSubstructLibrary(unsigned int num_bits);
JSSubstructLibrary() : JSSubstructLibrary(d_defaultNumBits) {}
int add_mol(const JSMol &m);
int add_smiles(const std::string &smi);
int add_trusted_smiles(const std::string &smi);
JSMol *get_mol(unsigned int i);
std::string get_matches(const JSMol &q, bool useChirality, int numThreads,
int maxResults) const;
std::string get_matches(const JSMol &q, int maxResults) const {
return get_matches(q, d_defaultUseChirality, d_defaultNumThreads,
maxResults);
}
std::string get_matches(const JSMol &q) const {
return get_matches(q, d_defaultUseChirality, d_defaultNumThreads,
d_defaultMaxResults);
}
unsigned int count_matches(const JSMol &q, bool useChirality,
int numThreads) const;
unsigned int count_matches(const JSMol &q) const {
return count_matches(q, d_defaultUseChirality, d_defaultNumThreads);
}
std::unique_ptr<RDKit::SubstructLibrary> d_sslib;
RDKit::CachedTrustedSmilesMolHolder *d_molHolder;
RDKit::PatternHolder *d_fpHolder;
unsigned int d_num_bits;
static constexpr unsigned int d_defaultNumBits = 2048;
static constexpr bool d_defaultUseChirality = true;
static constexpr int d_defaultNumThreads = -1;
static constexpr int d_defaultMaxResults = 1000;
private:
inline int add_mol_helper(const RDKit::ROMol &mol);
};
std::string get_inchikey_for_inchi(const std::string &input);
JSMol *get_mol(const std::string &input, const std::string &details_json);
JSMol *get_mol_from_pickle(const std::string &pkl);
JSMol *get_mol_copy(const JSMol &other);
JSMol *get_qmol(const std::string &input);
JSReaction *get_rxn(const std::string &input, const std::string &details_json);
std::string version();
void prefer_coordgen(bool prefer);
void use_legacy_stereo_perception(bool value);
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