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fix validation
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@mhekkel
mhekkel committed Feb 21, 2024
1 parent f99371d commit 458470f
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Showing 3 changed files with 32 additions and 24 deletions.
48 changes: 27 additions & 21 deletions src/alphafill.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -143,7 +143,7 @@ std::tuple<UniqueType, std::string> isUniqueLigand(const cif::mm::structure &str
result = { UniqueType::MoreAtoms, np.get_asym_id() };
else
result = { UniqueType::Seen, np.get_asym_id() };

break;
}
}
Expand All @@ -158,7 +158,8 @@ std::tuple<UniqueType, std::string> isUniqueLigand(const cif::mm::structure &str

for (auto &a : lig.atoms())
atoms_a.emplace_back(a.get_label_atom_id(), a.get_location());
sort(atoms_a.begin(), atoms_a.end(), [](auto &a, auto &b) { return std::get<0>(a) < std::get<0>(b); });
sort(atoms_a.begin(), atoms_a.end(), [](auto &a, auto &b)
{ return std::get<0>(a) < std::get<0>(b); });

for (auto &np : structure.non_polymers())
{
Expand All @@ -169,7 +170,8 @@ std::tuple<UniqueType, std::string> isUniqueLigand(const cif::mm::structure &str

for (auto &a : np.atoms())
atoms_b.emplace_back(a.get_label_atom_id(), a.get_location());
sort(atoms_b.begin(), atoms_b.end(), [](auto &a, auto &b) { return std::get<0>(a) < std::get<0>(b); });
sort(atoms_b.begin(), atoms_b.end(), [](auto &a, auto &b)
{ return std::get<0>(a) < std::get<0>(b); });

std::vector<point> pa, pb;

Expand Down Expand Up @@ -425,7 +427,7 @@ int create_index(int argc, char *const argv[])
fs::path file = fiter->path();

std::string name = file.filename().string();
if (not (cif::ends_with(name, "_final.cif") or cif::ends_with(name, "_final.cif.gz")))
if (not(cif::ends_with(name, "_final.cif") or cif::ends_with(name, "_final.cif.gz")))
continue;

q1.push(file);
Expand Down Expand Up @@ -573,7 +575,7 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
auto j = seq.find(')', i + 1);
if (j == std::string::npos or j > i + 2)
throw std::runtime_error("Invalid sequence");

seq.erase(i, j - i + 1);
i = seq.find('(', i + 1);
}
Expand Down Expand Up @@ -810,14 +812,10 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
json r_hsp{
{ "pdb_id", pdb_id },
{ "pdb_asym_id", pdb_res.front()->get_asym_id() },
{
"alignment", {
{ "af_start", hsp.mQueryStart },
{ "identity", hsp.identity() },
{ "length", hsp.length() },
{ "pdb_start", hsp.mTargetStart }
}
},
{ "alignment", { { "af_start", hsp.mQueryStart },
{ "identity", hsp.identity() },
{ "length", hsp.length() },
{ "pdb_start", hsp.mTargetStart } } },
{ "global_rmsd", rmsd }
};

Expand Down Expand Up @@ -876,29 +874,28 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
auto &rep_res = af_structure.get_residue(replace_id);
if (cif::VERBOSE > 0)
std::cerr << "Residue " << res << " has more atoms than the first transplant " << rep_res << '\n';

try
{
af_structure.remove_residue(rep_res);

for (auto &hit : hits)
{
auto ti = std::find_if(hit["transplants"].begin(), hit["transplants"].end(), [id=replace_id](json &e) {
return e["asym_id"] == id;
});
auto ti = std::find_if(hit["transplants"].begin(), hit["transplants"].end(), [id = replace_id](json &e)
{ return e["asym_id"] == id; });
if (ti != hit["transplants"].end())
{
hit["transplants"].erase(ti);
break;
}
}
}
catch(const std::exception& e)
catch (const std::exception &e)
{
if (cif::VERBOSE > 0)
std::cerr << "Failed to remove residue with asym ID " << replace_id << ": " << e.what() << '\n';
}

break;
}

Expand Down Expand Up @@ -1076,8 +1073,17 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>

// validation info?
if (hsp.identity() == 1)
hsp_t["validation"] = calculateValidationScores(db, pdb_res, af_ix_trimmed, pdb_ix_trimmed,
af_structure.get_residue(asym_id), res, config.get<float>("max-ligand-to-polymer-atom-distance"), ligand);
{
try
{
hsp_t["validation"] = calculateValidationScores(db, af_asym_id, pdb_res, af_ix_trimmed, pdb_ix_trimmed,
af_structure.get_residue(asym_id), res, config.get<float>("max-ligand-to-polymer-atom-distance"), ligand);
}
catch (const std::exception &e)
{
std::cerr << e.what() << '\n';
}
}

if (cif::VERBOSE > 0)
std::cerr << "Created asym " << asym_id << " for " << res << '\n';
Expand Down
5 changes: 3 additions & 2 deletions src/validate.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -521,13 +521,14 @@ zeep::json::element calculatePAEScore(const std::vector<cif::mm::residue *> &af_
// --------------------------------------------------------------------

zeep::json::element calculateValidationScores(
cif::datablock af_db, const std::vector<cif::mm::residue *> &pdb_res,
cif::datablock af_db, const std::string &asym_id,
const std::vector<cif::mm::residue *> &pdb_res,
const std::vector<size_t> &af_ix, const std::vector<size_t> &pdb_ix,
const cif::mm::residue &af_ligand, const cif::mm::residue &pdb_ligand,
float maxDistance, const Ligand &ligand)
{
cif::mm::structure af_structure(af_db);
auto &poly = af_structure.get_polymer_by_asym_id(pdb_res.front()->get_asym_id());
auto &poly = af_structure.get_polymer_by_asym_id(asym_id);

std::vector<cif::mm::monomer *> af_res_selected, pdb_res_selected;

Expand Down
3 changes: 2 additions & 1 deletion src/validate.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,8 @@ float ClashScore(cif::datablock &db, float maxDistance = 4);
// --------------------------------------------------------------------

zeep::json::element calculateValidationScores(
cif::datablock af_db, const std::vector<cif::mm::residue *> &pdb_res,
cif::datablock af_db, const std::string &asym_id,
const std::vector<cif::mm::residue *> &pdb_res,
const std::vector<size_t> &af_ix, const std::vector<size_t> &pdb_ix,
const cif::mm::residue &af_ligand, const cif::mm::residue &pdb_ligand,
float maxDistance, const Ligand &ligand);
Expand Down

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