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libcifpp
Commit af721eb1 by Maarten L. Hekkelman
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Make having no compound less fatal

parent 788e315f
Showing with 144 additions and 161 deletions
src/Structure.cpp
......@@ -148,20 +148,19 @@ int Atom::AtomImpl::charge() const
if (not formalCharge.has_value())
{
auto &compound = comp();
if (compound.atoms().size() == 1)
formalCharge = compound.atoms().front().charge;
// {
// for (auto cAtom : compound.atoms())
// {
// if (cAtom.id != mAtomID)
// continue;
// formalCharge = cAtom.charge;
// break;
// }
// }
try
{
auto &compound = comp();
if (compound.atoms().size() == 1)
formalCharge = compound.atoms().front().charge;
}
catch (const std::exception &ex)
{
if (cif::VERBOSE > 0)
std::cerr << "Error when trying to get charge of atom: " << ex.what() << std::endl;
formalCharge = 0;
}
}
return formalCharge.value_or(0);
......@@ -216,7 +215,7 @@ const std::string Atom::AtomImpl::get_property(const std::string_view name) cons
return ref.as<std::string>();
}
mCachedRefs.emplace_back(name, const_cast<cif::Row&>(mRow)[name]);
mCachedRefs.emplace_back(name, const_cast<cif::Row &>(mRow)[name]);
return std::get<1>(mCachedRefs.back()).as<std::string>();
}
......@@ -357,8 +356,8 @@ bool Atom::operator==(const Atom &rhs) const
{
if (mImpl == rhs.mImpl)
return true;
if (not (mImpl and rhs.mImpl))
if (not(mImpl and rhs.mImpl))
return false;
return &mImpl->mDb == &rhs.mImpl->mDb and mImpl->mID == rhs.mImpl->mID;
......@@ -1190,16 +1189,14 @@ Branch::Branch(Structure &structure, const std::string &asymID)
for (const auto &[entity_id] : struct_asym.find<std::string>("id"_key == asymID, "entity_id"))
{
for (const auto&[comp_id, num] : branch_list.find<std::string,int>(
"entity_id"_key == entity_id, "comp_id", "num"
))
for (const auto &[comp_id, num] : branch_list.find<std::string, int>(
"entity_id"_key == entity_id, "comp_id", "num"))
{
emplace_back(*this, comp_id, asymID, num);
}
for (const auto &[num1, num2, atom1, atom2] : branch_link.find<size_t, size_t, std::string, std::string>(
"entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"
))
"entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
{
if (not cif::iequals(atom1, "c1"))
throw std::runtime_error("invalid pdbx_entity_branch_link");
......@@ -1224,8 +1221,7 @@ void Branch::linkAtoms()
auto entity_id = front().entityID();
for (const auto &[num1, num2, atom1, atom2] : branch_link.find<size_t, size_t, std::string, std::string>(
"entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"
))
"entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
{
if (not cif::iequals(atom1, "c1"))
throw std::runtime_error("invalid pdbx_entity_branch_link");
......@@ -1242,7 +1238,6 @@ std::string Branch::name() const
return empty() ? "" : name(front());
}
std::string Branch::name(const Sugar &s) const
{
using namespace cif::literals;
......@@ -1261,19 +1256,18 @@ std::string Branch::name(const Sugar &s) const
if (not result.empty() and result.back() != ']')
result += '-';
return result + s.name();
}
float Branch::weight() const
{
return std::accumulate(begin(), end(), 0.f, [](float sum, const Sugar &s)
{
{
auto compound = mmcif::CompoundFactory::instance().create(s.compoundID());
if (compound)
sum += compound->formulaWeight();
return sum;
});
return sum; });
}
// --------------------------------------------------------------------
......@@ -1528,7 +1522,7 @@ void Structure::loadData()
{
if (res.asymID() != atom.labelAsymID())
continue;
res.addAtom(atom);
break;
}
......@@ -1614,7 +1608,7 @@ AtomView Structure::waters() const
Atom Structure::getAtomByID(const std::string &id) const
{
assert(mAtoms.size() == mAtomIndex.size());
int L = 0, R = mAtoms.size() - 1;
while (L <= R)
{
......@@ -1711,7 +1705,7 @@ Polymer &Structure::getPolymerByAsymID(const std::string &asymID)
{
if (poly.asymID() != asymID)
continue;
return poly;
}
......@@ -1794,7 +1788,7 @@ Residue &Structure::getResidue(const std::string &asymID, const std::string &com
throw std::out_of_range("Could not find residue " + asymID + '/' + std::to_string(seqID) + '-' + authSeqID);
}
Branch& Structure::getBranchByAsymID(const std::string &asymID)
Branch &Structure::getBranchByAsymID(const std::string &asymID)
{
for (auto &branch : mBranches)
{
......@@ -1856,7 +1850,7 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
// --------------------------------------------------------------------
Atom& Structure::emplace_atom(Atom &&atom)
Atom &Structure::emplace_atom(Atom &&atom)
{
int L = 0, R = mAtomIndex.size() - 1;
while (L <= R)
......@@ -1940,7 +1934,7 @@ void Structure::removeAtom(Atom &a)
R = i - 1;
}
#ifndef NDEBUG
assert(removed);
assert(removed);
#endif
}
......@@ -1964,7 +1958,7 @@ void Structure::swapAtoms(Atom a1, Atom a2)
auto l4 = r2["auth_atom_id"];
l3.swap(l4);
}
catch (const std::exception& ex)
catch (const std::exception &ex)
{
std::throw_with_nested(std::runtime_error("Failed to swap atoms"));
}
......@@ -2092,12 +2086,11 @@ void Structure::removeResidue(Residue &res)
{
case EntityType::Polymer:
{
Monomer &monomer = dynamic_cast<Monomer&>(res);
Monomer &monomer = dynamic_cast<Monomer &>(res);
db["pdbx_poly_seq_scheme"].erase(
"asym_id"_key == res.asymID() and
"seq_id"_key == res.seqID()
);
"seq_id"_key == res.seqID());
for (auto &poly : mPolymers)
poly.erase(std::remove(poly.begin(), poly.end(), monomer), poly.end());
......@@ -2114,7 +2107,7 @@ void Structure::removeResidue(Residue &res)
db["pdbx_nonpoly_scheme"].erase("asym_id"_key == res.asymID());
mNonPolymers.erase(std::remove(mNonPolymers.begin(), mNonPolymers.end(), res), mNonPolymers.end());
break;
case EntityType::Branched:
throw std::runtime_error("Don't remove a sugar using removeResidue...");
......@@ -2172,8 +2165,7 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
{
auto atom_id = atom_site.getUniqueID("");
auto &&[row, inserted] = atom_site.emplace({
{"group_PDB", atom.get_property<std::string>("group_PDB")},
auto &&[row, inserted] = atom_site.emplace({{"group_PDB", atom.get_property<std::string>("group_PDB")},
{"id", atom_id},
{"type_symbol", atom.get_property<std::string>("type_symbol")},
{"label_atom_id", atom.get_property<std::string>("label_atom_id")},
......@@ -2193,8 +2185,7 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
{"auth_comp_id", comp_id},
{"auth_asym_id", asym_id},
{"auth_atom_id", atom.get_property<std::string>("label_atom_id")},
{"pdbx_PDB_model_num", 1}
});
{"pdbx_PDB_model_num", 1}});
auto &newAtom = emplace_atom(std::make_shared<Atom::AtomImpl>(db, atom_id, row));
res.addAtom(newAtom);
......@@ -2203,16 +2194,16 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
int ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1;
pdbx_nonpoly_scheme.emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "mon_id", comp_id },
{ "ndb_seq_num", ndb_nr },
{ "pdb_seq_num", res.authSeqID() },
{ "auth_seq_num", res.authSeqID() },
{ "pdb_mon_id", comp_id },
{ "auth_mon_id", comp_id },
{ "pdb_strand_id", asym_id },
{ "pdb_ins_code", "." },
{"asym_id", asym_id},
{"entity_id", entity_id},
{"mon_id", comp_id},
{"ndb_seq_num", ndb_nr},
{"pdb_seq_num", res.authSeqID()},
{"auth_seq_num", res.authSeqID()},
{"pdb_mon_id", comp_id},
{"auth_mon_id", comp_id},
{"pdb_strand_id", asym_id},
{"pdb_ins_code", "."},
});
return asym_id;
......@@ -2226,8 +2217,7 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
auto &struct_asym = db["struct_asym"];
std::string asym_id = struct_asym.getUniqueID();
struct_asym.emplace({
{"id", asym_id},
struct_asym.emplace({{"id", asym_id},
{"pdbx_blank_PDB_chainid_flag", "N"},
{"pdbx_modified", "N"},
{"entity_id", entity_id},
......@@ -2241,7 +2231,8 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
auto appendUnlessSet = [](std::vector<cif::Item> &ai, cif::Item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci) { return ci.name() == name; }) == ai.end())
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci)
{ return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
......@@ -2249,17 +2240,17 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
{
auto atom_id = atom_site.getUniqueID("");
appendUnlessSet(atom, { "group_PDB", "HETATM"} );
appendUnlessSet(atom, { "id", atom_id} );
appendUnlessSet(atom, { "label_comp_id", comp_id} );
appendUnlessSet(atom, { "label_asym_id", asym_id} );
appendUnlessSet(atom, { "label_seq_id", ""} );
appendUnlessSet(atom, { "label_entity_id", entity_id} );
appendUnlessSet(atom, { "auth_comp_id", comp_id} );
appendUnlessSet(atom, { "auth_asym_id", asym_id} );
appendUnlessSet(atom, { "auth_seq_id", 1} );
appendUnlessSet(atom, { "pdbx_PDB_model_num", 1} );
appendUnlessSet(atom, { "label_alt_id", ""} );
appendUnlessSet(atom, {"group_PDB", "HETATM"});
appendUnlessSet(atom, {"id", atom_id});
appendUnlessSet(atom, {"label_comp_id", comp_id});
appendUnlessSet(atom, {"label_asym_id", asym_id});
appendUnlessSet(atom, {"label_seq_id", ""});
appendUnlessSet(atom, {"label_entity_id", entity_id});
appendUnlessSet(atom, {"auth_comp_id", comp_id});
appendUnlessSet(atom, {"auth_asym_id", asym_id});
appendUnlessSet(atom, {"auth_seq_id", 1});
appendUnlessSet(atom, {"pdbx_PDB_model_num", 1});
appendUnlessSet(atom, {"label_alt_id", ""});
auto &&[row, inserted] = atom_site.emplace(atom.begin(), atom.end());
......@@ -2270,22 +2261,22 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
int ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1;
pdbx_nonpoly_scheme.emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "mon_id", comp_id },
{ "ndb_seq_num", ndb_nr },
{ "pdb_seq_num", res.authSeqID() },
{ "auth_seq_num", res.authSeqID() },
{ "pdb_mon_id", comp_id },
{ "auth_mon_id", comp_id },
{ "pdb_strand_id", asym_id },
{ "pdb_ins_code", "." },
{"asym_id", asym_id},
{"entity_id", entity_id},
{"mon_id", comp_id},
{"ndb_seq_num", ndb_nr},
{"pdb_seq_num", res.authSeqID()},
{"auth_seq_num", res.authSeqID()},
{"pdb_mon_id", comp_id},
{"auth_mon_id", comp_id},
{"pdb_strand_id", asym_id},
{"pdb_ins_code", "."},
});
return asym_id;
}
Branch& Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
Branch &Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
{
// sanity check
for (auto &nag_atom : nag_atoms)
......@@ -2311,7 +2302,8 @@ Branch& Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
auto appendUnlessSet = [](std::vector<cif::Item> &ai, cif::Item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci) { return ci.name() == name; }) == ai.end())
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci)
{ return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
......@@ -2319,17 +2311,17 @@ Branch& Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
{
auto atom_id = atom_site.getUniqueID("");
appendUnlessSet(atom, { "group_PDB", "HETATM"} );
appendUnlessSet(atom, { "id", atom_id} );
appendUnlessSet(atom, { "label_comp_id", "NAG"} );
appendUnlessSet(atom, { "label_asym_id", asym_id} );
appendUnlessSet(atom, { "label_seq_id", "."} );
appendUnlessSet(atom, { "label_entity_id", tmp_entity_id} );
appendUnlessSet(atom, { "auth_comp_id", "NAG"} );
appendUnlessSet(atom, { "auth_asym_id", asym_id} );
appendUnlessSet(atom, { "auth_seq_id", 1} );
appendUnlessSet(atom, { "pdbx_PDB_model_num", 1} );
appendUnlessSet(atom, { "label_alt_id", ""} );
appendUnlessSet(atom, {"group_PDB", "HETATM"});
appendUnlessSet(atom, {"id", atom_id});
appendUnlessSet(atom, {"label_comp_id", "NAG"});
appendUnlessSet(atom, {"label_asym_id", asym_id});
appendUnlessSet(atom, {"label_seq_id", "."});
appendUnlessSet(atom, {"label_entity_id", tmp_entity_id});
appendUnlessSet(atom, {"auth_comp_id", "NAG"});
appendUnlessSet(atom, {"auth_asym_id", asym_id});
appendUnlessSet(atom, {"auth_seq_id", 1});
appendUnlessSet(atom, {"pdbx_PDB_model_num", 1});
appendUnlessSet(atom, {"label_alt_id", ""});
auto &&[row, inserted] = atom_site.emplace(atom.begin(), atom.end());
......@@ -2340,8 +2332,7 @@ Branch& Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
// now we can create the entity and get the real ID
auto entity_id = createEntityForBranch(branch);
struct_asym.emplace({
{"id", asym_id},
struct_asym.emplace({{"id", asym_id},
{"pdbx_blank_PDB_chainid_flag", "N"},
{"pdbx_modified", "N"},
{"entity_id", entity_id},
......@@ -2350,28 +2341,26 @@ Branch& Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
for (auto &a : sugar.atoms())
a.set_property("label_entity_id", entity_id);
db["pdbx_branch_scheme"].emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "num", 1 },
{ "mon_id", "NAG" },
db["pdbx_branch_scheme"].emplace({{"asym_id", asym_id},
{"entity_id", entity_id},
{"num", 1},
{"mon_id", "NAG"},
{ "pdb_asym_id", asym_id },
{ "pdb_seq_num", 1 },
{ "pdb_mon_id", "NAG" },
{"pdb_asym_id", asym_id},
{"pdb_seq_num", 1},
{"pdb_mon_id", "NAG"},
// TODO: need fix, collect from nag_atoms?
{ "auth_asym_id", asym_id },
{ "auth_mon_id", "NAG" },
{ "auth_seq_num", 1 },
{"auth_asym_id", asym_id},
{"auth_mon_id", "NAG"},
{"auth_seq_num", 1},
{ "hetero", "n" }
});
{"hetero", "n"}});
return branch;
}
Branch& Structure::extendBranch(const std::string &asym_id, std::vector<std::vector<cif::Item>> &atom_info,
Branch &Structure::extendBranch(const std::string &asym_id, std::vector<std::vector<cif::Item>> &atom_info,
int link_sugar, const std::string &link_atom)
{
// sanity check
......@@ -2383,7 +2372,7 @@ Branch& Structure::extendBranch(const std::string &asym_id, std::vector<std::vec
{
if (info.name() != "label_comp_id")
continue;
if (compoundID.empty())
compoundID = info.value();
else if (info.value() != compoundID)
......@@ -2402,11 +2391,13 @@ Branch& Structure::extendBranch(const std::string &asym_id, std::vector<std::vec
auto appendUnlessSet = [](std::vector<cif::Item> &ai, cif::Item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci) { return ci.name() == name; }) == ai.end())
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci)
{ return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
auto bi = std::find_if(mBranches.begin(), mBranches.end(), [asym_id](Branch &b) { return b.asymID() == asym_id; });
auto bi = std::find_if(mBranches.begin(), mBranches.end(), [asym_id](Branch &b)
{ return b.asymID() == asym_id; });
if (bi == mBranches.end())
throw std::logic_error("Create a branch first!");
......@@ -2420,14 +2411,14 @@ Branch& Structure::extendBranch(const std::string &asym_id, std::vector<std::vec
{
auto atom_id = atom_site.getUniqueID("");
appendUnlessSet(atom, { "group_PDB", "HETATM"} );
appendUnlessSet(atom, { "id", atom_id} );
appendUnlessSet(atom, { "label_comp_id", compoundID} );
appendUnlessSet(atom, { "label_entity_id", tmp_entity_id} );
appendUnlessSet(atom, { "auth_comp_id", compoundID} );
appendUnlessSet(atom, { "auth_asym_id", asym_id} );
appendUnlessSet(atom, { "pdbx_PDB_model_num", 1} );
appendUnlessSet(atom, { "label_alt_id", ""} );
appendUnlessSet(atom, {"group_PDB", "HETATM"});
appendUnlessSet(atom, {"id", atom_id});
appendUnlessSet(atom, {"label_comp_id", compoundID});
appendUnlessSet(atom, {"label_entity_id", tmp_entity_id});
appendUnlessSet(atom, {"auth_comp_id", compoundID});
appendUnlessSet(atom, {"auth_asym_id", asym_id});
appendUnlessSet(atom, {"pdbx_PDB_model_num", 1});
appendUnlessSet(atom, {"label_alt_id", ""});
auto &&[row, inserted] = atom_site.emplace(atom.begin(), atom.end());
......@@ -2450,25 +2441,23 @@ Branch& Structure::extendBranch(const std::string &asym_id, std::vector<std::vec
for (auto &sugar : branch)
{
pdbx_branch_scheme.emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "num", sugar.num() },
{ "mon_id", sugar.compoundID() },
pdbx_branch_scheme.emplace({{"asym_id", asym_id},
{"entity_id", entity_id},
{"num", sugar.num()},
{"mon_id", sugar.compoundID()},
{ "pdb_asym_id", asym_id },
{ "pdb_seq_num", sugar.num() },
{ "pdb_mon_id", sugar.compoundID() },
{"pdb_asym_id", asym_id},
{"pdb_seq_num", sugar.num()},
{"pdb_mon_id", sugar.compoundID()},
// TODO: need fix, collect from nag_atoms?
{ "auth_asym_id", asym_id },
{ "auth_mon_id", sugar.compoundID() },
{ "auth_seq_num", sugar.num() },
{"auth_asym_id", asym_id},
{"auth_mon_id", sugar.compoundID()},
{"auth_seq_num", sugar.num()},
{ "hetero", "n" }
});
{"hetero", "n"}});
}
return branch;
}
......@@ -2484,20 +2473,18 @@ std::string Structure::createEntityForBranch(Branch &branch)
{
entityID = entity.find1<std::string>("type"_key == "branched" and "pdbx_description"_key == entityName, "id");
}
catch(const std::exception& e)
catch (const std::exception &e)
{
entityID = entity.getUniqueID("");
if (cif::VERBOSE)
std::cout << "Creating new entity " << entityID << " for branched sugar " << entityName << std::endl;
entity.emplace({
{ "id", entityID },
{ "type", "branched" },
{ "src_method", "man" },
{ "pdbx_description", entityName },
{ "formula_weight", branch.weight() }
});
entity.emplace({{"id", entityID},
{"type", "branched"},
{"src_method", "man"},
{"pdbx_description", entityName},
{"formula_weight", branch.weight()}});
}
auto &pdbx_entity_branch_list = mDb["pdbx_entity_branch_list"];
......@@ -2505,12 +2492,10 @@ std::string Structure::createEntityForBranch(Branch &branch)
for (auto &sugar : branch)
{
pdbx_entity_branch_list.emplace({
{ "entity_id", entityID },
{ "comp_id", sugar.compoundID() },
{ "num", sugar.num() },
{ "hetero", "n" }
});
pdbx_entity_branch_list.emplace({{"entity_id", entityID},
{"comp_id", sugar.compoundID()},
{"num", sugar.num()},
{"hetero", "n"}});
}
auto &pdbx_entity_branch_link = mDb["pdbx_entity_branch_link"];
......@@ -2522,23 +2507,21 @@ std::string Structure::createEntityForBranch(Branch &branch)
if (not l2)
continue;
auto &s2 = branch.at(std::stoi(l2.authSeqID()) - 1);
auto l1 = s2.atomByID("C1");
pdbx_entity_branch_link.emplace({
{ "link_id", pdbx_entity_branch_link.getUniqueID("") },
{ "entity_id", entityID },
{ "entity_branch_list_num_1", s1.authSeqID() },
{ "comp_id_1", s1.compoundID() },
{ "atom_id_1", l1.labelAtomID() },
{ "leaving_atom_id_1", "O1" },
{ "entity_branch_list_num_2", s2.authSeqID() },
{ "comp_id_2", s2.compoundID() },
{ "atom_id_2", l2.labelAtomID() },
{ "leaving_atom_id_2", "H" + l2.labelAtomID() },
{ "value_order", "sing" }
});
pdbx_entity_branch_link.emplace({{"link_id", pdbx_entity_branch_link.getUniqueID("")},
{"entity_id", entityID},
{"entity_branch_list_num_1", s1.authSeqID()},
{"comp_id_1", s1.compoundID()},
{"atom_id_1", l1.labelAtomID()},
{"leaving_atom_id_1", "O1"},
{"entity_branch_list_num_2", s2.authSeqID()},
{"comp_id_2", s2.compoundID()},
{"atom_id_2", l2.labelAtomID()},
{"leaving_atom_id_2", "H" + l2.labelAtomID()},
{"value_order", "sing"}});
}
return entityID;
......@@ -2665,7 +2648,7 @@ void Structure::validateAtoms() const
assert(i != atoms.end());
atoms.erase(i);
};
for (auto &poly : mPolymers)
{
for (auto &monomer : poly)
......
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