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acedrg_tables: extract insert_bond_row / insert_angle_row #438

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acedrg_tables: extract insert_bond_row / insert_angle_row #438

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41 changes: 41 additions & 0 deletions include/gemmi/acedrg_tables.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -367,6 +367,47 @@ struct GEMMI_DLL AcedrgTables {
void load_prot_hydr_dists(const std::string& path);
void load_angle_tables(const std::string& dir);

// Insert one parsed bond-table row into the bond index containers,
// using the same compound-key construction as load_bond_tables().
// key_buf and hybr_buf are scratch buffers that the caller can hoist
// out of its loop to avoid per-row allocations.
void insert_bond_row(int ha1, int ha2,
const std::string& hybr_comb,
const std::string& in_ring,
const std::string& a1_nb2,
const std::string& a2_nb2,
const std::string& a1_nb,
const std::string& a2_nb,
const std::string& a1_type_m,
const std::string& a2_type_m,
const std::string& a1_type_f,
const std::string& a2_type_f,
const CodStats& vs,
const CodStats& vs1d,
std::string& key_buf,
std::string& hybr_buf);

// Insert one parsed angle-table row into the angle index containers.
// v/s/c carry the six per-level value/sigma/count columns of the row.
void insert_angle_row(int ha1, int ha2, int ha3,
const std::string& value_key,
const std::string& a1_root,
const std::string& a2_root,
const std::string& a3_root,
const std::string& a1_nb2,
const std::string& a2_nb2,
const std::string& a3_nb2,
const std::string& a1_nb,
const std::string& a2_nb,
const std::string& a3_nb,
const std::string& a1_type,
const std::string& a2_type,
const std::string& a3_type,
const double v[6],
const double s[6],
const int c[6],
std::string& key_buf);

private:
void compute_hash(CodAtomInfo& atom) const;

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142 changes: 100 additions & 42 deletions src/acedrg_tables.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -783,10 +783,53 @@ void AcedrgTables::load_bond_index(const std::string& path) {
}
}

void AcedrgTables::insert_bond_row(int ha1, int ha2,
const std::string& hybr_comb,
const std::string& in_ring,
const std::string& a1_nb2,
const std::string& a2_nb2,
const std::string& a1_nb,
const std::string& a2_nb,
const std::string& a1_type_m,
const std::string& a2_type_m,
const std::string& a1_type_f,
const std::string& a2_type_f,
const CodStats& vs,
const CodStats& vs1d,
std::string& key_buf,
std::string& hybr_buf) {
// Construct compound keys for flat lookup structures
key_buf.clear();
cat_to(key_buf, ha1, '|', ha2, '|', hybr_comb, '|', in_ring);
const size_t key_4_len = key_buf.size();
cat_to(key_buf, '|', a1_nb2, '|', a2_nb2, '|', a1_nb, '|', a2_nb);

// Populate 1D structure (8-component key + 2 inner type levels)
bond_idx_1d_[key_buf][a1_type_m][a2_type_m].push_back(vs1d);

// Store full COD-class stats for exact matches
if (!a1_type_f.empty() && !a2_type_f.empty()) {
cat_to(key_buf, '|', a1_type_m, '|', a2_type_m);
bond_idx_full_[key_buf][a1_type_f][a2_type_f] = vs;
key_buf.resize(key_4_len);
bond_full_4prefix_keys_.insert(key_buf);
} else {
key_buf.resize(key_4_len);
}

// Populate 2D structure (4-component key + 4 inner levels)
bond_idx_2d_[key_buf][a1_nb2][a2_nb2][a1_nb][a2_nb].push_back(vs);

hybr_buf.clear();
cat_to(hybr_buf, ha1, '|', ha2, '|', hybr_comb);
bond_2d_hybr_keys_.insert(hybr_buf);
}

void AcedrgTables::load_bond_tables(const std::string& dir) {
// Load each bond table file referenced in the index
std::set<int> loaded_files;
int n_files = 0, n_lines = 0;
std::string key_buf, hybr_buf;

for (const auto& fi_kv : bond_file_index_) {
{
Expand Down Expand Up @@ -841,23 +884,10 @@ void AcedrgTables::load_bond_tables(const std::string& dir) {
CodStats vs(value, sigma, count);
CodStats vs1d(value2, sigma2, count2);

// Construct compound keys for flat lookup structures
auto key_4 = cat(ha1, '|', ha2, '|', hybr_comb, '|', in_ring);
auto key_8 = cat(key_4, '|', a1_nb2, '|', a2_nb2, '|', a1_nb, '|', a2_nb);

// Populate 1D structure (8-component key + 2 inner type levels)
bond_idx_1d_[key_8][a1_type_m][a2_type_m].push_back(vs1d);

// Store full COD-class stats for exact matches
if (!a1_type_f.empty() && !a2_type_f.empty()) {
auto key_10 = cat(key_8, '|', a1_type_m, '|', a2_type_m);
bond_idx_full_[key_10][a1_type_f][a2_type_f] = vs;
bond_full_4prefix_keys_.insert(key_4);
}

// Populate 2D structure (4-component key + 4 inner levels)
bond_idx_2d_[key_4][a1_nb2][a2_nb2][a1_nb][a2_nb].push_back(vs);
bond_2d_hybr_keys_.insert(cat(ha1, '|', ha2, '|', hybr_comb));
insert_bond_row(ha1, ha2, hybr_comb, in_ring,
a1_nb2, a2_nb2, a1_nb, a2_nb,
a1_type_m, a2_type_m, a1_type_f, a2_type_f,
vs, vs1d, key_buf, hybr_buf);

// Levels 9-11 are populated from allOrgBondsHRS.table in load_bond_hrs().
}
Expand All @@ -867,10 +897,59 @@ void AcedrgTables::load_bond_tables(const std::string& dir) {
std::fprintf(stderr, " bond tables: %d files, %d lines\n", n_files, n_lines);
}

void AcedrgTables::insert_angle_row(int ha1, int ha2, int ha3,
const std::string& value_key,
const std::string& a1_root,
const std::string& a2_root,
const std::string& a3_root,
const std::string& a1_nb2,
const std::string& a2_nb2,
const std::string& a3_nb2,
const std::string& a1_nb,
const std::string& a2_nb,
const std::string& a3_nb,
const std::string& a1_type,
const std::string& a2_type,
const std::string& a3_type,
const double v[6],
const double s[6],
const int c[6],
std::string& key_buf) {
// Populate structures at each level with corresponding pre-computed values.
// AceDRG keeps only the first entry for each key (no aggregation).
auto insert_first = [](AngleIdx1D& m, const std::string& k,
double vv, double ss, int cc) {
auto& vec = m[k];
if (vec.empty())
vec.push_back(CodStats(vv, ss, cc));
};

// Levels 1D-4D: flat string keys with decreasing specificity.
key_buf.clear();
cat_to(key_buf, ha1, '|', ha2, '|', ha3, '|', value_key, '|',
a1_root, '|', a2_root, '|', a3_root);
insert_first(angle_idx_4d_, key_buf, v[4], s[4], c[4]);

cat_to(key_buf, '|', a1_nb2, '|', a2_nb2, '|', a3_nb2);
insert_first(angle_idx_3d_, key_buf, v[3], s[3], c[3]);

cat_to(key_buf, '|', a1_nb, '|', a2_nb, '|', a3_nb);
insert_first(angle_idx_2d_, key_buf, v[2], s[2], c[2]);

cat_to(key_buf, '|', a1_type, '|', a2_type, '|', a3_type);
insert_first(angle_idx_1d_, key_buf, v[1], s[1], c[1]);

// Level 5D: nested int-keyed map (different structure)
auto& vec5 = angle_idx_5d_[ha1][ha2][ha3][value_key];
if (vec5.empty())
vec5.push_back(CodStats(v[5], s[5], c[5]));
}

void AcedrgTables::load_angle_tables(const std::string& dir) {
// Load all numbered angle table files from allOrgAngleTables.
// We intentionally ignore angle_idx.table and read full angle statistics.
int n_files = 0, n_lines = 0;
std::string key_buf;

for (int file_num : list_numeric_table_ids(dir)) {
std::string path = cat(dir, '/', file_num, ".table");
Expand Down Expand Up @@ -934,31 +1013,10 @@ void AcedrgTables::load_angle_tables(const std::string& dir) {
std::string a2_type = q2 ? prefix_before(*q2, '{') : std::string();
std::string a3_type = q3 ? prefix_before(*q3, '{') : std::string();

// Populate structures at each level with corresponding pre-computed values.
// AceDRG keeps only the first entry for each key (no aggregation).
// Levels 1D-4D: flat string keys with decreasing specificity.
std::string base_key = cat(ha1, '|', ha2, '|', ha3, '|', value_key, '|',
a1_root, '|', a2_root, '|', a3_root);
std::string keys[4] = {
cat(base_key, '|', a1_nb2, '|', a2_nb2, '|', a3_nb2, '|',
a1_nb, '|', a2_nb, '|', a3_nb, '|',
a1_type, '|', a2_type, '|', a3_type),
cat(base_key, '|', a1_nb2, '|', a2_nb2, '|', a3_nb2, '|',
a1_nb, '|', a2_nb, '|', a3_nb),
cat(base_key, '|', a1_nb2, '|', a2_nb2, '|', a3_nb2),
base_key,
};
AngleIdx1D* maps[4] = {&angle_idx_1d_, &angle_idx_2d_,
&angle_idx_3d_, &angle_idx_4d_};
for (int lvl = 0; lvl < 4; ++lvl) {
auto& vec = (*maps[lvl])[keys[lvl]];
if (vec.empty())
vec.push_back(CodStats(values[lvl + 1], sigmas[lvl + 1], counts[lvl + 1]));
}
// Level 5D: nested int-keyed map (different structure)
auto& angle_5d_vec = angle_idx_5d_[ha1][ha2][ha3][value_key];
if (angle_5d_vec.empty())
angle_5d_vec.push_back(CodStats(values[5], sigmas[5], counts[5]));
insert_angle_row(ha1, ha2, ha3, value_key, a1_root, a2_root, a3_root,
a1_nb2, a2_nb2, a3_nb2, a1_nb, a2_nb, a3_nb,
a1_type, a2_type, a3_type,
values, sigmas, counts, key_buf);

// Level 6D: hash only (leave empty for 34-column data)
}
Expand Down