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https://github.com/rdkit/rdkit.git
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23ffd85f60
- implement get_v2Kmolblock() in MinimalLib - add the possibility to specify the MDL version preference as a get_molblock() forceMDLVersion JSON parameter, which is ignored by get_v3Kmolblock() and get_v2Kmolblock() - changes in response to review Co-authored-by: ptosco <paolo.tosco@novartis.com>
210 lines
11 KiB
C
210 lines
11 KiB
C
//
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// Copyright (C) 2021 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#pragma once
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#include <RDGeneral/export.h>
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#ifdef RDKIT_RDKITCFFI_BUILD
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#define RDKIT_RDKITCFFI_EXPORT RDKIT_EXPORT_API
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#else
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#define RDKIT_RDKITCFFI_EXPORT RDKIT_IMPORT_API
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#endif
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#ifdef __cplusplus
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extern "C" {
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#endif
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// I/O
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RDKIT_RDKITCFFI_EXPORT char *get_mol(const char *input, size_t *mol_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_qmol(const char *input, size_t *mol_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_molblock(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_v3kmolblock(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_v2kmolblock(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_smiles(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_smarts(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_cxsmiles(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_cxsmarts(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_json(const char *pkl, size_t pkl_sz,
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const char *details_json);
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#ifdef RDK_BUILD_INCHI_SUPPORT
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RDKIT_RDKITCFFI_EXPORT char *get_inchi(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_inchi_for_molblock(const char *ctab,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_inchikey_for_inchi(const char *inchi);
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#endif
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RDKIT_RDKITCFFI_EXPORT char *get_rxn(const char *input, size_t *mol_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char **get_mol_frags(const char *pkl, size_t pkl_sz,
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size_t **frags_pkl_sz_array,
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size_t *num_frags,
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const char *details_json,
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char **mappings_json);
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// substructure
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RDKIT_RDKITCFFI_EXPORT char *get_substruct_match(const char *mol_pkl,
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size_t mol_pkl_sz,
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const char *query_pkl,
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size_t query_pkl_sz,
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const char *options_json);
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RDKIT_RDKITCFFI_EXPORT char *get_substruct_matches(const char *mol_pkl,
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size_t mol_pkl_sz,
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const char *query_pkl,
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size_t query_pkl_sz,
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const char *options_json);
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// Drawing
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RDKIT_RDKITCFFI_EXPORT char *get_svg(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_rxn_svg(const char *pkl, size_t pkl_sz,
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const char *details_json);
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// Calculators
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RDKIT_RDKITCFFI_EXPORT char *get_descriptors(const char *pkl, size_t pkl_sz);
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RDKIT_RDKITCFFI_EXPORT char *get_morgan_fp(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_morgan_fp_as_bytes(const char *pkl,
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size_t pkl_sz,
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size_t *nbytes,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_rdkit_fp(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_rdkit_fp_as_bytes(const char *pkl,
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size_t pkl_sz,
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size_t *nbytes,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_pattern_fp(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_pattern_fp_as_bytes(const char *pkl,
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size_t pkl_sz,
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size_t *nbytes,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_topological_torsion_fp(
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const char *pkl, size_t pkl_sz, const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_topological_torsion_fp_as_bytes(
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const char *pkl, size_t pkl_sz, size_t *nbytes, const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_atom_pair_fp(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_atom_pair_fp_as_bytes(
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const char *pkl, size_t pkl_sz, size_t *nbytes, const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_maccs_fp(const char *pkl, size_t pkl_sz);
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RDKIT_RDKITCFFI_EXPORT char *get_maccs_fp_as_bytes(const char *pkl,
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size_t pkl_sz,
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size_t *nbytes);
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#ifdef RDK_BUILD_AVALON_SUPPORT
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RDKIT_RDKITCFFI_EXPORT char *get_avalon_fp(const char *pkl, size_t pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT char *get_avalon_fp_as_bytes(const char *pkl,
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size_t pkl_sz,
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size_t *nbytes,
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const char *details_json);
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#endif
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// modification
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RDKIT_RDKITCFFI_EXPORT short add_hs(char **pkl, size_t *pkl_sz);
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RDKIT_RDKITCFFI_EXPORT short remove_all_hs(char **pkl, size_t *pkl_sz);
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RDKIT_RDKITCFFI_EXPORT short remove_hs(char **pkl, size_t *pkl_sz,
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const char *details_json);
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// standardization
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RDKIT_RDKITCFFI_EXPORT short cleanup(char **pkl, size_t *pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short normalize(char **pkl, size_t *pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short neutralize(char **pkl, size_t *pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short reionize(char **pkl, size_t *pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short canonical_tautomer(char **pkl, size_t *pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short charge_parent(char **pkl, size_t *pkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short fragment_parent(char **pkl, size_t *pkl_sz,
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const char *details_json);
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// coordinates
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RDKIT_RDKITCFFI_EXPORT void prefer_coordgen(short val);
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RDKIT_RDKITCFFI_EXPORT short has_coords(const char *mol_pkl, size_t mol_pkl_sz);
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RDKIT_RDKITCFFI_EXPORT short set_2d_coords(char **pkl, size_t *pkl_sz);
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RDKIT_RDKITCFFI_EXPORT short set_3d_coords(char **pkl, size_t *pkl_sz,
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const char *params_json);
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RDKIT_RDKITCFFI_EXPORT short set_2d_coords_aligned(char **pkl, size_t *pkl_sz,
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const char *template_pkl,
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size_t template_sz,
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const char *details_json,
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char **match_json);
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// housekeeping
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RDKIT_RDKITCFFI_EXPORT void free_ptr(char *ptr);
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RDKIT_RDKITCFFI_EXPORT char *version();
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RDKIT_RDKITCFFI_EXPORT short enable_logging();
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RDKIT_RDKITCFFI_EXPORT short enable_logger(const char *log_name);
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RDKIT_RDKITCFFI_EXPORT short disable_logging();
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RDKIT_RDKITCFFI_EXPORT short disable_logger(const char *log_name);
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// chirality
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RDKIT_RDKITCFFI_EXPORT short use_legacy_stereo_perception(short value);
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RDKIT_RDKITCFFI_EXPORT short allow_non_tetrahedral_chirality(short value);
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// PNG metadata
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RDKIT_RDKITCFFI_EXPORT short add_mol_to_png_blob(char **png_blob,
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size_t *png_blob_sz,
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const char *mpkl,
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size_t mpkl_size,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short get_mol_from_png_blob(const char *png_blob,
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size_t png_blob_sz,
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char **mpkl, size_t *mpkl_sz,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT short get_mols_from_png_blob(const char *png_blob,
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size_t png_blob_sz,
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char ***mpkl_array,
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size_t **mpkl_sz_array,
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const char *details_json);
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RDKIT_RDKITCFFI_EXPORT void free_mol_array(char ***pkl_array,
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size_t **pkl_sz_array);
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// logging
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RDKIT_RDKITCFFI_EXPORT void *set_log_tee(const char *log_name);
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RDKIT_RDKITCFFI_EXPORT void *set_log_capture(const char *log_name);
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RDKIT_RDKITCFFI_EXPORT short destroy_log_handle(void **log_handle);
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RDKIT_RDKITCFFI_EXPORT char *get_log_buffer(void *log_handle);
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RDKIT_RDKITCFFI_EXPORT short clear_log_buffer(void *log_handle);
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// props
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RDKIT_RDKITCFFI_EXPORT short has_prop(const char *mol_pkl, size_t mol_pkl_sz,
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const char *key);
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RDKIT_RDKITCFFI_EXPORT char **get_prop_list(const char *mol_pkl,
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size_t mol_pkl_sz,
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short includePrivate,
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short includeComputed);
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RDKIT_RDKITCFFI_EXPORT void set_prop(char **mol_pkl, size_t *mol_pkl_sz,
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const char *key, const char *val,
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short computed);
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RDKIT_RDKITCFFI_EXPORT char *get_prop(const char *mol_pkl, size_t mol_pkl_sz,
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const char *key);
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RDKIT_RDKITCFFI_EXPORT short clear_prop(char **mol_pkl, size_t *mol_pkl_sz,
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const char *key);
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RDKIT_RDKITCFFI_EXPORT void keep_props(char **mol_pkl, size_t *mol_pkl_sz,
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const char *details_json);
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#ifdef __cplusplus
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}
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#endif
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