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* Copyright 2024 DeepMind Technologies Limited
*
* AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
* this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
*
* To request access to the AlphaFold 3 model parameters, follow the process set
* out at https://github.com/google-deepmind/alphafold3. You may only use these
* if received directly from Google. Use is subject to terms of use available at
* https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
*/
#ifndef ALPHAFOLD3_SRC_ALPHAFOLD3_STRUCTURE_PYTHON_MMCIF_ALTLOCS_H_
#define ALPHAFOLD3_SRC_ALPHAFOLD3_STRUCTURE_PYTHON_MMCIF_ALTLOCS_H_
#include <cstddef>
#include <cstdint>
#include <string>
#include <vector>
#include "absl/types/span.h"
#include "alphafold3/structure/cpp/mmcif_layout.h"
namespace alphafold3 {
// Returns the list of indices that should be kept after resolving alt-locs.
// 1) Partial Residue. Each cycle of alt-locs are resolved separately with the
// highest occupancy alt-loc. Tie-breaks are resolved alphabetically. See
// tests for examples.
// 2) Whole Residue. These are resolved in two passes.
// a) The residue with the highest occupancy is chosen.
// b) The locations for a given residue are resolved.
// All tie-breaks are resolved alphabetically. See tests for examples.
//
// Preconditions: layout and comp_ids, alt_ids, occupancies are all from same
// mmCIF file and chain_indices are monotonically increasing and less than
// layout.num_chains().
//
// comp_ids from '_atom_site.label_comp_id'.
// alt_ids from '_atom_site.label_alt_id'.
// occupancies from '_atom_site.occupancy'.
std::vector<std::uint64_t> ResolveMmcifAltLocs(
const MmcifLayout& layout, absl::Span<const std::string> comp_ids,
absl::Span<const std::string> atom_ids,
absl::Span<const std::string> alt_ids,
absl::Span<const std::string> occupancies,
absl::Span<const std::size_t> chain_indices);
} // namespace alphafold3
#endif // ALPHAFOLD3_SRC_ALPHAFOLD3_STRUCTURE_PYTHON_MMCIF_ALTLOCS_H_
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