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reconstruct better when entity ID's are missing

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This commit is contained in:
Maarten L. Hekkelman
2025-09-22 12:59:16 +02:00
parent 1596db8499
commit dbf59ce622
1 changed files with 58 additions and 14 deletions
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72
src/pdb/reconstruct.cpp
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@@ -28,6 +28,8 @@
#include "cif++/compound.hpp"
#include "cif++/row.hpp"
#include <string>
// --------------------------------------------------------------------
namespace cif::pdb
@@ -198,6 +200,7 @@ void createEntityIDs(datablock &db)
// that should cover it
auto &atom_site = db["atom_site"];
auto &entity = db["entity"];
auto &cf = compound_factory::instance();
std::vector<std::vector<row_handle>> entities;
@@ -206,16 +209,26 @@ void createEntityIDs(datablock &db)
int lastSeqID = -1;
std::vector<row_handle> waters;
for (auto rh : atom_site)
int nextEntityID;
try
{
nextEntityID = entity.find_max<int>("id") + 1;
}
catch (...)
{
nextEntityID = 1;
}
for (auto rh : atom_site.find(cif::key("label_entity_id") == cif::null))
{
residue_key_type k = rh.get<std::optional<std::string>,
std::optional<int>,
std::optional<std::string>,
std::optional<std::string>,
std::optional<int>,
std::optional<std::string>>(
"auth_asym_id", "auth_seq_id", "auth_comp_id",
"label_asym_id", "label_seq_id", "label_comp_id");
std::optional<int>,
std::optional<std::string>,
std::optional<std::string>,
std::optional<int>,
std::optional<std::string>>(
"auth_asym_id", "auth_seq_id", "auth_comp_id",
"label_asym_id", "label_seq_id", "label_comp_id");
std::string comp_id = get_comp_id(k);
@@ -230,8 +243,8 @@ void createEntityIDs(datablock &db)
bool is_monomer = cf.is_monomer(comp_id);
if (lastAsymID == asym_id and lastSeqID == seq_id and not is_monomer)
continue;
// if (lastAsymID == asym_id and lastSeqID == seq_id and not is_monomer)
// continue;
if (asym_id != lastAsymID or (not is_monomer and lastSeqID != seq_id))
entities.push_back({});
@@ -243,6 +256,7 @@ void createEntityIDs(datablock &db)
}
std::map<std::size_t, std::string> entity_ids;
std::map<std::string, std::string> newEntitiesForCompound;
atom_site.add_item("label_entity_id");
@@ -251,7 +265,37 @@ void createEntityIDs(datablock &db)
if (entity_ids.contains(i))
continue;
auto entity_id = std::to_string(i + 1);
residue_key_type k = entities[i].front().get<std::optional<std::string>, std::optional<int>, std::optional<std::string>, std::optional<std::string>, std::optional<int>, std::optional<std::string>>(
"auth_asym_id", "auth_seq_id", "auth_comp_id",
"label_asym_id", "label_seq_id", "label_comp_id");
std::string comp_id = get_comp_id(k);
std::string entity_id;
if (auto v = db["pdbx_entity_nonpoly"].find_first(cif::key("comp_id") == comp_id); v)
entity_id = v.get<std::string>("entity_id");
else if (auto i = newEntitiesForCompound.find(comp_id); i != newEntitiesForCompound.end())
entity_id = i->second;
else
{
entity_id = std::to_string(nextEntityID++);
if (cf.is_monomer(comp_id))
entity.emplace({ //
{ "id", entity_id },
{ "type", "polymer" } });
else if (cf.is_water(comp_id))
entity.emplace({ //
{ "id", entity_id },
{ "type", "water" } });
else
entity.emplace({ //
{ "id", entity_id },
{ "type", "non-polymer" } });
newEntitiesForCompound[comp_id] = entity_id;
}
entity_ids[i] = entity_id;
for (std::size_t j = i + 1; j < entities.size(); ++j)
@@ -439,7 +483,7 @@ void checkAtomRecords(datablock &db)
// And negative seq_id values
if (atom_site.contains(key("label_seq_id") < 0))
fixNegativeSeqID(atom_site);
std::set<std::string> polymer_entities;
if (db["entity"].empty())
{
@@ -576,7 +620,7 @@ void checkAtomRecords(datablock &db)
row["label_atom_id"] = row["auth_atom_id"].text();
else if (row["auth_atom_id"].empty())
row["auth_atom_id"] = row["label_atom_id"].text();
// Rewrite the coordinates and other items that look better in a fixed format
// Be careful not to nuke invalidly formatted data here
for (auto [item_name, prec] : std::vector<std::tuple<std::string_view, int>>{
@@ -1425,7 +1469,7 @@ bool reconstruct_pdbx(file &file, const validator &validator)
checkChemCompRecords(db);
// If the data is really horrible, it might not contain entities
if (not db["atom_site"].find_first(key("label_entity_id") != null))
if (db["atom_site"].find_first(key("label_entity_id") == null))
createEntityIDs(db);
// Now see if atom records make sense at all