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//
// 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
#include "alphafold3/structure/cpp/mmcif_altlocs.h"
#include <cstddef>
#include <cstdint>
#include <functional>
#include <iterator>
#include <limits>
#include <string>
#include <utility>
#include <vector>
#include "absl/algorithm/container.h"
#include "absl/log/log.h"
#include "absl/strings/numbers.h"
#include "absl/strings/string_view.h"
#include "absl/types/span.h"
#include "alphafold3/structure/cpp/mmcif_layout.h"
namespace alphafold3 {
namespace {
float OccupancyToFloat(absl::string_view occupancy) {
float result = 0.0f;
LOG_IF(ERROR, !absl::SimpleAtof(occupancy, &result))
<< "Invalid Occupancy: " << occupancy;
return result;
}
// Deuterium is the same atom as Hydrogen so keep equivalent for grouping.
bool AtomEquiv(absl::string_view lhs, absl::string_view rhs) {
if (lhs == rhs) return true;
if (lhs.empty() != rhs.empty()) return false;
// Both lhs and rhs are guaranteed to be non-empty after this.
char first_lhs = lhs.front();
char second_rhs = rhs.front();
if ((first_lhs == 'H' && second_rhs == 'D') ||
(first_lhs == 'D' && second_rhs == 'H')) {
lhs.remove_prefix(1);
rhs.remove_prefix(1);
return lhs == rhs;
}
return false;
}
// Calls group_callback with that start index and count for each group of
// equivalent values in `values`, starting at `start` and ending at `count`.
// Example:
// GroupBy({"B", "B", "B", "C", "C"}, 0, 5, [](size_t start, size_t count) {
// absl::Printf("start=%d, count=%d\n", start, count);
// });
// Would print:
// start=0, count=3
// start=3, count=2
template <typename GroupCallback,
typename IsEqual = std::equal_to<absl::string_view>>
void GroupBy(absl::Span<const std::string> values, std::size_t start,
std::size_t count, GroupCallback&& group_callback,
IsEqual&& is_equal = std::equal_to<absl::string_view>{}) {
std::size_t span_start = start;
if (count > 0) {
for (std::size_t i = start + 1; i < start + count; ++i) {
if (!is_equal(values[i], values[span_start])) {
group_callback(span_start, i - span_start);
span_start = i;
}
}
group_callback(span_start, start + count - span_start);
}
}
void ProcessAltLocGroupsWhole(std::size_t alt_loc_start,
std::size_t alt_loc_count,
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,
std::vector<std::uint64_t>& in_out_keep_indices) {
std::pair<std::size_t, std::size_t> best_split = {alt_loc_start,
alt_loc_count};
std::vector<char> alt_loc_groups;
float best_occupancy = -std::numeric_limits<float>::infinity();
char best_group = alt_ids[alt_loc_start].front();
std::vector<std::pair<std::size_t, float>> occupancy_stats;
// Group by residue type.
GroupBy(comp_ids, alt_loc_start, alt_loc_count,
[&](std::size_t start, std::size_t count) {
// This callback selects the best residue group and the best
// Alt-loc char within that group.
alt_loc_groups.clear();
occupancy_stats.clear();
// Calculate total occupancy for residue type.
for (std::size_t i = 0; i < count; ++i) {
char alt_loc_id = alt_ids[start + i].front();
float occupancy = OccupancyToFloat(occupancies[start + i]);
if (auto loc = absl::c_find(alt_loc_groups, alt_loc_id);
loc == alt_loc_groups.end()) {
occupancy_stats.emplace_back(1, occupancy);
alt_loc_groups.push_back(alt_loc_id);
} else {
auto& stat =
occupancy_stats[std::distance(alt_loc_groups.begin(), loc)];
++stat.first;
stat.second += occupancy;
}
}
float total_occupancy = 0.0;
for (auto& stat : occupancy_stats) {
total_occupancy += stat.second / stat.first;
}
char group = *absl::c_min_element(alt_loc_groups);
// Compares occupancy of residue to best seen so far.
// Tie breaks alphabetic.
if (total_occupancy > best_occupancy ||
(total_occupancy == best_occupancy && group < best_group)) {
// Selects the best sub group.
best_group = alt_loc_groups.front();
float best_amount = occupancy_stats.front().second /
occupancy_stats.front().first;
for (std::size_t i = 1; i < occupancy_stats.size(); ++i) {
float amount =
occupancy_stats[i].second / occupancy_stats[i].first;
char group = alt_loc_groups[i];
if (amount > best_amount ||
(amount == best_amount && group < best_group)) {
best_amount = amount;
best_group = group;
}
}
best_occupancy = total_occupancy;
best_split = {start, count};
}
});
// Now that the best residue type has been selected and the best alt-loc
// within that has been selected add indices of indices to keep to the keep
// list.
auto [split_start, split_count] = best_split;
GroupBy(
atom_ids, split_start, split_count,
[&in_out_keep_indices, &alt_ids, best_group](std::size_t start,
std::size_t count) {
// This makes sure we select an atom for each atom id even if it does
// not have our selected alt-loc char.
std::size_t best_index = start;
for (std::size_t i = 1; i < count; ++i) {
if (alt_ids[start + i].front() == best_group) {
best_index = start + i;
break;
}
}
in_out_keep_indices.push_back(best_index);
},
AtomEquiv);
}
// Finds the alt-loc group with the highest score and pushes the indices on to
// the back of in_out_keep_indices.
void ProcessAltLocGroupPartial(
std::size_t alt_loc_start, std::size_t alt_loc_count,
absl::Span<const std::string> atom_ids,
absl::Span<const std::string> alt_ids,
absl::Span<const std::string> occupancies,
std::vector<std::uint64_t>& in_out_keep_indices) {
GroupBy(
atom_ids, alt_loc_start, alt_loc_count,
[&](std::size_t start, std::size_t count) {
if (count == 1) {
in_out_keep_indices.push_back(start);
} else {
float best_occ = OccupancyToFloat(occupancies[start]);
std::size_t best_index = start;
char best_group = alt_ids[start].front();
for (std::size_t i = 0; i < count; ++i) {
float occ = OccupancyToFloat(occupancies[start + i]);
char group = alt_ids[start + i].front();
if (occ > best_occ || (occ == best_occ && group < best_group)) {
best_group = group;
best_index = start + i;
best_occ = occ;
}
}
in_out_keep_indices.push_back(best_index);
}
},
AtomEquiv);
}
} // namespace
// Resolves alt-locs returning the atom indices that will be left.
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) {
std::vector<std::uint64_t> keep_indices;
keep_indices.reserve(layout.num_atoms());
std::size_t alt_loc_start = 0;
for (std::size_t chain_index : chain_indices) {
auto [residues_start, residues_end] = layout.residue_range(chain_index);
for (std::size_t residue = residues_start; residue < residues_end;
++residue) {
std::size_t alt_loc_count = 0;
auto [atom_start, atom_end] = layout.atom_range(residue);
for (std::size_t i = atom_start; i < atom_end; ++i) {
char alt_loc_id = alt_ids[i].front();
if (alt_loc_id == '.' || alt_loc_id == '?') {
if (alt_loc_count > 0) {
ProcessAltLocGroupPartial(alt_loc_start, alt_loc_count, atom_ids,
alt_ids, occupancies, keep_indices);
alt_loc_count = 0;
}
keep_indices.push_back(i);
} else {
if (alt_loc_count == 0) {
alt_loc_start = i;
}
++alt_loc_count;
}
}
if (alt_loc_count > 0) {
if (atom_end - atom_start == alt_loc_count) {
ProcessAltLocGroupsWhole(alt_loc_start, alt_loc_count, comp_ids,
atom_ids, alt_ids, occupancies,
keep_indices);
} else {
ProcessAltLocGroupPartial(alt_loc_start, alt_loc_count, atom_ids,
alt_ids, occupancies, keep_indices);
}
}
}
}
return keep_indices;
}
} // namespace alphafold3
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