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libcifpp
Commit cd1e9528 by Maarten L. Hekkelman
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residue::create_new_atom

parent 996f1e42
Showing with 337 additions and 246 deletions
include/cif++/model.hpp
...@@ -350,7 +350,12 @@ class atom ...@@ -350,7 +350,12 @@ class atom
std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); } ///< Return the pdb_ins_code property std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); } ///< Return the pdb_ins_code property
/// Return true if this atom is an alternate /// Return true if this atom is an alternate
bool is_alternate() const { return not get_label_alt_id().empty(); } bool is_alternate() const
{
if (auto alt_id = get_label_alt_id(); alt_id.empty() or alt_id == ".")
return false;
return true;
}
/// Convenience method to return a string that might be ID in PDB space /// Convenience method to return a string that might be ID in PDB space
std::string pdb_id() const std::string pdb_id() const
...@@ -575,6 +580,10 @@ class residue ...@@ -575,6 +580,10 @@ class residue
m_auth_seq_id == rhs.m_auth_seq_id); m_auth_seq_id == rhs.m_auth_seq_id);
} }
/// @brief Create a new atom and add it to the list
/// @return newly created atom
virtual atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation);
protected: protected:
/** @cond */ /** @cond */
residue() {} residue() {}
...@@ -675,6 +684,8 @@ class monomer : public residue ...@@ -675,6 +684,8 @@ class monomer : public residue
return m_polymer == rhs.m_polymer and m_index == rhs.m_index; return m_polymer == rhs.m_polymer and m_index == rhs.m_index;
} }
atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation) override;
private: private:
const polymer *m_polymer; const polymer *m_polymer;
std::size_t m_index; std::size_t m_index;
...@@ -1094,6 +1105,9 @@ class structure ...@@ -1094,6 +1105,9 @@ class structure
/// \brief emplace the moved atom @a atom /// \brief emplace the moved atom @a atom
atom &emplace_atom(atom &&atom); atom &emplace_atom(atom &&atom);
/// \brief Reorder atom_site atoms based on 'natural' ordering
void reorder_atoms();
private: private:
friend polymer; friend polymer;
friend residue; friend residue;
......
src/model.cpp
...@@ -352,9 +352,40 @@ EntityType residue::entity_type() const ...@@ -352,9 +352,40 @@ EntityType residue::entity_type() const
void residue::add_atom(atom &atom) void residue::add_atom(atom &atom)
{ {
// update atom since it is now part of this residue
m_atoms.push_back(atom); m_atoms.push_back(atom);
} }
atom residue::create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation)
{
auto &db = m_structure->get_datablock();
auto &atom_site = db["atom_site"];
auto ai = atom_site.emplace({
{ "group_PDB", "HETATM" },
{ "id", atom_site.get_unique_id("") },
{ "type_symbol", atom_type_traits(inType).symbol() },
{ "label_entity_id", get_entity_id() },
{ "label_atom_id", inAtomID },
{ "label_asym_id", m_asym_id },
{ "label_comp_id", m_compound_id },
{ "label_seq_id", m_seq_id },
{ "auth_asym_id", m_auth_asym_id },
{ "auth_atom_id", inAtomID },
{ "auth_comp_id", m_compound_id },
{ "auth_seq_id", m_auth_seq_id },
{ "pdbx_PDB_model_num", m_structure->get_model_nr() },
});
atom a(db, *ai);
m_atoms.push_back(a);
a.set_location(inLocation);
return a;
}
std::vector<atom> residue::unique_atoms() const std::vector<atom> residue::unique_atoms() const
{ {
std::vector<atom> result; std::vector<atom> result;
...@@ -679,25 +710,26 @@ float monomer::omega() const ...@@ -679,25 +710,26 @@ float monomer::omega() const
} }
const std::map<std::string, std::vector<std::string>> kChiAtomsMap = { const std::map<std::string, std::vector<std::string>> kChiAtomsMap = {
{"ASP", {"CG", "OD1"}}, { "ASP", { "CG", "OD1" } },
{"ASN", {"CG", "OD1"}}, { "ASN", { "CG", "OD1" } },
{"ARG", {"CG", "CD", "NE", "CZ"}}, { "ARG", { "CG", "CD", "NE", "CZ" } },
{"HIS", {"CG", "ND1"}}, { "HIS", { "CG", "ND1" } },
{"GLN", {"CG", "CD", "OE1"}}, { "GLN", { "CG", "CD", "OE1" } },
{"GLU", {"CG", "CD", "OE1"}}, { "GLU", { "CG", "CD", "OE1" } },
{"SER", {"OG"}}, { "SER", { "OG" } },
{"THR", {"OG1"}}, { "THR", { "OG1" } },
{"LYS", {"CG", "CD", "CE", "NZ"}}, { "LYS", { "CG", "CD", "CE", "NZ" } },
{"TYR", {"CG", "CD1"}}, { "TYR", { "CG", "CD1" } },
{"PHE", {"CG", "CD1"}}, { "PHE", { "CG", "CD1" } },
{"LEU", {"CG", "CD1"}}, { "LEU", { "CG", "CD1" } },
{"TRP", {"CG", "CD1"}}, { "TRP", { "CG", "CD1" } },
{"CYS", {"SG"}}, { "CYS", { "SG" } },
{"ILE", {"CG1", "CD1"}}, { "ILE", { "CG1", "CD1" } },
{"MET", {"CG", "SD", "CE"}}, { "MET", { "CG", "SD", "CE" } },
{"MSE", {"CG", "SE", "CE"}}, { "MSE", { "CG", "SE", "CE" } },
{"PRO", {"CG", "CD"}}, { "PRO", { "CG", "CD" } },
{"VAL", {"CG1"}}}; { "VAL", { "CG1" } }
};
std::size_t monomer::nr_of_chis() const std::size_t monomer::nr_of_chis() const
{ {
...@@ -719,7 +751,7 @@ float monomer::chi(std::size_t nr) const ...@@ -719,7 +751,7 @@ float monomer::chi(std::size_t nr) const
auto i = kChiAtomsMap.find(m_compound_id); auto i = kChiAtomsMap.find(m_compound_id);
if (i != kChiAtomsMap.end() and nr < i->second.size()) if (i != kChiAtomsMap.end() and nr < i->second.size())
{ {
std::vector<std::string> atoms{"N", "CA", "CB"}; std::vector<std::string> atoms{ "N", "CA", "CB" };
atoms.insert(atoms.end(), i->second.begin(), i->second.end()); atoms.insert(atoms.end(), i->second.begin(), i->second.end());
...@@ -845,7 +877,8 @@ bool monomer::are_bonded(const monomer &a, const monomer &b, float errorMargin) ...@@ -845,7 +877,8 @@ bool monomer::are_bonded(const monomer &a, const monomer &b, float errorMargin)
a.get_atom_by_atom_id("CA").get_location(), a.get_atom_by_atom_id("CA").get_location(),
a.get_atom_by_atom_id("C").get_location(), a.get_atom_by_atom_id("C").get_location(),
b.get_atom_by_atom_id("N").get_location(), b.get_atom_by_atom_id("N").get_location(),
b.get_atom_by_atom_id("CA").get_location()}; b.get_atom_by_atom_id("CA").get_location()
};
auto distanceCACA = distance(atoms[0], atoms[3]); auto distanceCACA = distance(atoms[0], atoms[3]);
double omega = dihedral_angle(atoms[0], atoms[1], atoms[2], atoms[3]); double omega = dihedral_angle(atoms[0], atoms[1], atoms[2], atoms[3]);
...@@ -886,6 +919,15 @@ bool monomer::is_cis(const monomer &a, const monomer &b) ...@@ -886,6 +919,15 @@ bool monomer::is_cis(const monomer &a, const monomer &b)
return std::abs(omega(a, b)) < 30.0f; return std::abs(omega(a, b)) < 30.0f;
} }
atom monomer::create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation)
{
atom a = residue::create_new_atom(inType, inAtomID, inLocation);
a.set_property("group_PDB", "ATOM");
return a;
}
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// polymer // polymer
...@@ -922,7 +964,7 @@ polymer::polymer(structure &s, const std::string &entityID, const std::string &a ...@@ -922,7 +964,7 @@ polymer::polymer(structure &s, const std::string &entityID, const std::string &a
} }
else if (VERBOSE > 0) else if (VERBOSE > 0)
{ {
monomer m{*this, index, seqID, authSeqID, pdbInsCode, compoundID}; monomer m{ *this, index, seqID, authSeqID, pdbInsCode, compoundID };
std::cerr << "Dropping alternate residue " << m << '\n'; std::cerr << "Dropping alternate residue " << m << '\n';
} }
} }
...@@ -990,7 +1032,6 @@ sugar::sugar(sugar &&rhs) ...@@ -990,7 +1032,6 @@ sugar::sugar(sugar &&rhs)
: residue(std::forward<residue>(rhs)) : residue(std::forward<residue>(rhs))
, m_branch(rhs.m_branch) , m_branch(rhs.m_branch)
{ {
} }
sugar &sugar::operator=(sugar &&rhs) sugar &sugar::operator=(sugar &&rhs)
...@@ -1054,19 +1095,19 @@ cif::mm::atom sugar::add_atom(row_initializer atom_info) ...@@ -1054,19 +1095,19 @@ cif::mm::atom sugar::add_atom(row_initializer atom_info)
auto atom_id = atom_site.get_unique_id(""); auto atom_id = atom_site.get_unique_id("");
atom_info.set_value({"group_PDB", "HETATM"}); atom_info.set_value({ "group_PDB", "HETATM" });
atom_info.set_value({"id", atom_id}); atom_info.set_value({ "id", atom_id });
atom_info.set_value({"label_entity_id", m_branch->get_entity_id()}); atom_info.set_value({ "label_entity_id", m_branch->get_entity_id() });
atom_info.set_value({"label_asym_id", m_branch->get_asym_id()}); atom_info.set_value({ "label_asym_id", m_branch->get_asym_id() });
atom_info.set_value({"label_comp_id", m_compound_id}); atom_info.set_value({ "label_comp_id", m_compound_id });
atom_info.set_value({"label_seq_id", "."}); atom_info.set_value({ "label_seq_id", "." });
atom_info.set_value({"label_alt_id", "."}); atom_info.set_value({ "label_alt_id", "." });
atom_info.set_value({"auth_asym_id", m_branch->get_asym_id()}); atom_info.set_value({ "auth_asym_id", m_branch->get_asym_id() });
atom_info.set_value({"auth_comp_id", m_compound_id}); atom_info.set_value({ "auth_comp_id", m_compound_id });
atom_info.set_value({"auth_seq_id", m_auth_seq_id}); atom_info.set_value({ "auth_seq_id", m_auth_seq_id });
atom_info.set_value({"occupancy", 1.0, 2}); atom_info.set_value({ "occupancy", 1.0, 2 });
atom_info.set_value({"B_iso_or_equiv", 30.0, 2}); atom_info.set_value({ "B_iso_or_equiv", 30.0, 2 });
atom_info.set_value({"pdbx_PDB_model_num", 1}); atom_info.set_value({ "pdbx_PDB_model_num", 1 });
auto row = atom_site.emplace(std::move(atom_info)); auto row = atom_site.emplace(std::move(atom_info));
auto result = m_structure->emplace_atom(db, row); auto result = m_structure->emplace_atom(db, row);
...@@ -1139,7 +1180,8 @@ void branch::link_atoms() ...@@ -1139,7 +1180,8 @@ void branch::link_atoms()
sugar &branch::get_sugar_by_num(int nr) sugar &branch::get_sugar_by_num(int nr)
{ {
auto i = find_if(begin(), end(), [nr](const sugar &s) { return s.num() == nr; }); auto i = find_if(begin(), end(), [nr](const sugar &s)
{ return s.num() == nr; });
if (i == end()) if (i == end())
throw std::out_of_range("Sugar with num " + std::to_string(nr) + " not found in branch " + m_asym_id); throw std::out_of_range("Sugar with num " + std::to_string(nr) + " not found in branch " + m_asym_id);
...@@ -1163,32 +1205,29 @@ sugar &branch::construct_sugar(const std::string &compound_id) ...@@ -1163,32 +1205,29 @@ sugar &branch::construct_sugar(const std::string &compound_id)
auto r = chemComp.find(key("id") == compound_id); auto r = chemComp.find(key("id") == compound_id);
if (r.empty()) if (r.empty())
{ {
chemComp.emplace({ chemComp.emplace({ { "id", compound_id },
{"id", compound_id}, { "name", compound->name() },
{"name", compound->name()}, { "formula", compound->formula() },
{"formula", compound->formula()}, { "formula_weight", compound->formula_weight() },
{"formula_weight", compound->formula_weight()}, { "type", compound->type() } });
{"type", compound->type()}});
} }
sugar &result = emplace_back(*this, compound_id, m_asym_id, static_cast<int>(size() + 1)); sugar &result = emplace_back(*this, compound_id, m_asym_id, static_cast<int>(size() + 1));
db["pdbx_branch_scheme"].emplace({ db["pdbx_branch_scheme"].emplace({ { "asym_id", result.get_asym_id() },
{"asym_id", result.get_asym_id()}, { "entity_id", result.get_entity_id() },
{"entity_id", result.get_entity_id()}, { "num", result.num() },
{"num", result.num()}, { "mon_id", result.get_compound_id() },
{"mon_id", result.get_compound_id()},
{"pdb_asym_id", result.get_asym_id()}, { "pdb_asym_id", result.get_asym_id() },
{"pdb_seq_num", result.num()}, { "pdb_seq_num", result.num() },
{"pdb_mon_id", result.get_compound_id()}, { "pdb_mon_id", result.get_compound_id() },
{"auth_asym_id", result.get_auth_asym_id()}, { "auth_asym_id", result.get_auth_asym_id() },
{"auth_mon_id", result.get_compound_id()}, { "auth_mon_id", result.get_compound_id() },
{"auth_seq_num", result.get_auth_seq_id()}, { "auth_seq_num", result.get_auth_seq_id() },
{"hetero", "n"} { "hetero", "n" } });
});
return result; return result;
} }
...@@ -1206,8 +1245,7 @@ sugar &branch::construct_sugar(const std::string &compound_id, const std::string ...@@ -1206,8 +1245,7 @@ sugar &branch::construct_sugar(const std::string &compound_id, const std::string
auto &pdbx_entity_branch_link = db["pdbx_entity_branch_link"]; auto &pdbx_entity_branch_link = db["pdbx_entity_branch_link"];
auto linkID = pdbx_entity_branch_link.get_unique_id(""); auto linkID = pdbx_entity_branch_link.get_unique_id("");
db["pdbx_entity_branch_link"].emplace({ db["pdbx_entity_branch_link"].emplace({ { "link_id", linkID },
{ "link_id", linkID },
{ "entity_id", get_entity_id() }, { "entity_id", get_entity_id() },
{ "entity_branch_list_num_1", result.num() }, { "entity_branch_list_num_1", result.num() },
{ "comp_id_1", compound_id }, { "comp_id_1", compound_id },
...@@ -1217,8 +1255,7 @@ sugar &branch::construct_sugar(const std::string &compound_id, const std::string ...@@ -1217,8 +1255,7 @@ sugar &branch::construct_sugar(const std::string &compound_id, const std::string
{ "comp_id_2", linked.get_compound_id() }, { "comp_id_2", linked.get_compound_id() },
{ "atom_id_2", linked_atom_id }, { "atom_id_2", linked_atom_id },
{ "leaving_atom_id_2", "." }, { "leaving_atom_id_2", "." },
{ "value_order", "sing" } { "value_order", "sing" } });
});
return result; return result;
} }
...@@ -1327,7 +1364,7 @@ void structure::load_data() ...@@ -1327,7 +1364,7 @@ void structure::load_data()
{ {
auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"]; auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"];
for (const auto &[asym_id, auth_asym_id, entityID] : polySeqScheme.rows<std::string,std::string,std::string>("asym_id", "pdb_strand_id", "entity_id")) for (const auto &[asym_id, auth_asym_id, entityID] : polySeqScheme.rows<std::string, std::string, std::string>("asym_id", "pdb_strand_id", "entity_id"))
{ {
if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id or m_polymers.back().get_entity_id() != entityID) if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id or m_polymers.back().get_entity_id() != entityID)
m_polymers.emplace_back(*this, entityID, asym_id, auth_asym_id); m_polymers.emplace_back(*this, entityID, asym_id, auth_asym_id);
...@@ -1335,7 +1372,7 @@ void structure::load_data() ...@@ -1335,7 +1372,7 @@ void structure::load_data()
auto &branchScheme = m_db["pdbx_branch_scheme"]; auto &branchScheme = m_db["pdbx_branch_scheme"];
for (const auto &[asym_id, entity_id] : branchScheme.rows<std::string,std::string>("asym_id", "entity_id")) for (const auto &[asym_id, entity_id] : branchScheme.rows<std::string, std::string>("asym_id", "entity_id"))
{ {
if (m_branches.empty() or m_branches.back().get_asym_id() != asym_id) if (m_branches.empty() or m_branches.back().get_asym_id() != asym_id)
m_branches.emplace_back(*this, asym_id, entity_id); m_branches.emplace_back(*this, asym_id, entity_id);
...@@ -1343,8 +1380,8 @@ void structure::load_data() ...@@ -1343,8 +1380,8 @@ void structure::load_data()
auto &nonPolyScheme = m_db["pdbx_nonpoly_scheme"]; auto &nonPolyScheme = m_db["pdbx_nonpoly_scheme"];
for (const auto&[asym_id, monID, pdbStrandID, pdbSeqNum, pdbInsCode] : for (const auto &[asym_id, monID, pdbStrandID, pdbSeqNum, pdbInsCode] :
nonPolyScheme.rows<std::string,std::string,std::string,std::string,std::string>("asym_id", "mon_id", "pdb_strand_id", "pdb_seq_num", "pdb_ins_code")) nonPolyScheme.rows<std::string, std::string, std::string, std::string, std::string>("asym_id", "mon_id", "pdb_strand_id", "pdb_seq_num", "pdb_ins_code"))
m_non_polymers.emplace_back(*this, monID, asym_id, 0, pdbStrandID, pdbSeqNum, pdbInsCode); m_non_polymers.emplace_back(*this, monID, asym_id, 0, pdbStrandID, pdbSeqNum, pdbInsCode);
// place atoms in residues // place atoms in residues
...@@ -1355,18 +1392,18 @@ void structure::load_data() ...@@ -1355,18 +1392,18 @@ void structure::load_data()
for (auto &poly : m_polymers) for (auto &poly : m_polymers)
{ {
for (auto &res : poly) for (auto &res : poly)
resMap[{res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id()}] = &res; resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id() }] = &res;
} }
for (auto &res : m_non_polymers) for (auto &res : m_non_polymers)
resMap[{res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id()}] = &res; resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id() }] = &res;
std::set<std::string> sugars; std::set<std::string> sugars;
for (auto &branch : m_branches) for (auto &branch : m_branches)
{ {
for (auto &sugar : branch) for (auto &sugar : branch)
{ {
resMap[{sugar.get_asym_id(), sugar.get_seq_id(), sugar.get_auth_seq_id()}] = &sugar; resMap[{ sugar.get_asym_id(), sugar.get_seq_id(), sugar.get_auth_seq_id() }] = &sugar;
sugars.insert(sugar.get_compound_id()); sugars.insert(sugar.get_compound_id());
} }
} }
...@@ -1398,7 +1435,9 @@ void structure::load_data() ...@@ -1398,7 +1435,9 @@ void structure::load_data()
} }
// what the ... // what the ...
m_branches.erase(std::remove_if(m_branches.begin(), m_branches.end(), [](const branch &b) { return b.empty(); }), m_branches.end()); m_branches.erase(std::remove_if(m_branches.begin(), m_branches.end(), [](const branch &b)
{ return b.empty(); }),
m_branches.end());
for (auto &branch : m_branches) for (auto &branch : m_branches)
branch.link_atoms(); branch.link_atoms();
...@@ -1720,12 +1759,11 @@ std::string structure::insert_compound(const std::string &compoundID, bool is_en ...@@ -1720,12 +1759,11 @@ std::string structure::insert_compound(const std::string &compoundID, bool is_en
auto r = chemComp.find(key("id") == compoundID); auto r = chemComp.find(key("id") == compoundID);
if (r.empty()) if (r.empty())
{ {
chemComp.emplace({ chemComp.emplace({ { "id", compoundID },
{"id", compoundID}, { "name", compound->name() },
{"name", compound->name()}, { "formula", compound->formula() },
{"formula", compound->formula()}, { "formula_weight", compound->formula_weight() },
{"formula_weight", compound->formula_weight()}, { "type", compound->type() } });
{"type", compound->type()}});
} }
std::string entity_id; std::string entity_id;
...@@ -1741,16 +1779,14 @@ std::string structure::insert_compound(const std::string &compoundID, bool is_en ...@@ -1741,16 +1779,14 @@ std::string structure::insert_compound(const std::string &compoundID, bool is_en
auto &entity = m_db["entity"]; auto &entity = m_db["entity"];
entity_id = entity.get_unique_id(""); entity_id = entity.get_unique_id("");
entity.emplace({ entity.emplace({ { "id", entity_id },
{"id", entity_id}, { "type", "non-polymer" },
{"type", "non-polymer"}, { "pdbx_description", compound->name() },
{"pdbx_description", compound->name()}, { "formula_weight", compound->formula_weight() } });
{"formula_weight", compound->formula_weight()}});
pdbxEntityNonpoly.emplace({ pdbxEntityNonpoly.emplace({ { "entity_id", entity_id },
{"entity_id", entity_id}, { "name", compound->name() },
{"name", compound->name()}, { "comp_id", compoundID } });
{"comp_id", compoundID}});
} }
} }
...@@ -1835,19 +1871,15 @@ void structure::remove_atom(atom &a, bool removeFromResidue) ...@@ -1835,19 +1871,15 @@ void structure::remove_atom(atom &a, bool removeFromResidue)
for (std::string prefix : { "ptnr1_", "ptnr2_", "pdbx_ptnr3_" }) for (std::string prefix : { "ptnr1_", "ptnr2_", "pdbx_ptnr3_" })
{ {
if (a.get_label_seq_id() == 0) if (a.get_label_seq_id() == 0)
cond = std::move(cond) or ( cond = std::move(cond) or (cif::key(prefix + "label_asym_id") == a.get_label_asym_id() and
cif::key(prefix + "label_asym_id") == a.get_label_asym_id() and
cif::key(prefix + "label_seq_id") == null and cif::key(prefix + "label_seq_id") == null and
cif::key(prefix + "auth_seq_id") == a.get_auth_seq_id() and cif::key(prefix + "auth_seq_id") == a.get_auth_seq_id() and
cif::key(prefix + "label_atom_id") == a.get_label_atom_id() cif::key(prefix + "label_atom_id") == a.get_label_atom_id());
);
else else
cond = std::move(cond) or ( cond = std::move(cond) or (cif::key(prefix + "label_asym_id") == a.get_label_asym_id() and
cif::key(prefix + "label_asym_id") == a.get_label_asym_id() and
cif::key(prefix + "label_seq_id") == a.get_label_seq_id() and cif::key(prefix + "label_seq_id") == a.get_label_seq_id() and
cif::key(prefix + "auth_seq_id") == a.get_auth_seq_id() and cif::key(prefix + "auth_seq_id") == a.get_auth_seq_id() and
cif::key(prefix + "label_atom_id") == a.get_label_atom_id() cif::key(prefix + "label_atom_id") == a.get_label_atom_id());
);
} }
if (cond) if (cond)
...@@ -1953,15 +1985,15 @@ void structure::change_residue(residue &res, const std::string &newCompound, ...@@ -1953,15 +1985,15 @@ void structure::change_residue(residue &res, const std::string &newCompound,
if (entityID.empty()) if (entityID.empty())
{ {
entityID = entity.get_unique_id(""); entityID = entity.get_unique_id("");
entity.emplace({{"id", entityID}, entity.emplace({ { "id", entityID },
{"type", "non-polymer"}, { "type", "non-polymer" },
{"pdbx_description", compound->name()}, { "pdbx_description", compound->name() },
{"formula_weight", compound->formula_weight()}}); { "formula_weight", compound->formula_weight() } });
auto &pdbxEntityNonpoly = m_db["pdbx_entity_nonpoly"]; auto &pdbxEntityNonpoly = m_db["pdbx_entity_nonpoly"];
pdbxEntityNonpoly.emplace({{"entity_id", entityID}, pdbxEntityNonpoly.emplace({ { "entity_id", entityID },
{"name", compound->name()}, { "name", compound->name() },
{"comp_id", newCompound}}); { "comp_id", newCompound } });
} }
auto &pdbxNonPolyScheme = m_db["pdbx_nonpoly_scheme"]; auto &pdbxNonPolyScheme = m_db["pdbx_nonpoly_scheme"];
...@@ -1977,11 +2009,11 @@ void structure::change_residue(residue &res, const std::string &newCompound, ...@@ -1977,11 +2009,11 @@ void structure::change_residue(residue &res, const std::string &newCompound,
auto &chemComp = m_db["chem_comp"]; auto &chemComp = m_db["chem_comp"];
if (not chemComp.contains(key("id") == newCompound)) if (not chemComp.contains(key("id") == newCompound))
{ {
chemComp.emplace({{"id", newCompound}, chemComp.emplace({ { "id", newCompound },
{"name", compound->name()}, { "name", compound->name() },
{"formula", compound->formula()}, { "formula", compound->formula() },
{"formula_weight", compound->formula_weight()}, { "formula_weight", compound->formula_weight() },
{"type", compound->type()}}); { "type", compound->type() } });
} }
// update the struct_asym for the new entity // update the struct_asym for the new entity
...@@ -2111,7 +2143,7 @@ void structure::remove_residue(residue &res) ...@@ -2111,7 +2143,7 @@ void structure::remove_residue(residue &res)
case EntityType::Branched: case EntityType::Branched:
{ {
auto &s = dynamic_cast<sugar&>(res); auto &s = dynamic_cast<sugar &>(res);
remove_sugar(s); remove_sugar(s);
...@@ -2167,7 +2199,9 @@ void structure::remove_sugar(sugar &s) ...@@ -2167,7 +2199,9 @@ void structure::remove_sugar(sugar &s)
remove_atom(atom, false); remove_atom(atom, false);
} }
branch.erase(remove_if(branch.begin(), branch.end(), [dix](const sugar &s) { return dix.count(s.num()); }), branch.end()); branch.erase(remove_if(branch.begin(), branch.end(), [dix](const sugar &s)
{ return dix.count(s.num()); }),
branch.end());
auto entity_id = create_entity_for_branch(branch); auto entity_id = create_entity_for_branch(branch);
...@@ -2187,23 +2221,21 @@ void structure::remove_sugar(sugar &s) ...@@ -2187,23 +2221,21 @@ void structure::remove_sugar(sugar &s)
for (auto &sugar : branch) for (auto &sugar : branch)
{ {
pdbx_branch_scheme.emplace({ pdbx_branch_scheme.emplace({ { "asym_id", asym_id },
{"asym_id", asym_id}, { "entity_id", entity_id },
{"entity_id", entity_id}, { "num", sugar.num() },
{"num", sugar.num()}, { "mon_id", sugar.get_compound_id() },
{"mon_id", sugar.get_compound_id()},
{"pdb_asym_id", asym_id}, { "pdb_asym_id", asym_id },
{"pdb_seq_num", sugar.num()}, { "pdb_seq_num", sugar.num() },
{"pdb_mon_id", sugar.get_compound_id()}, { "pdb_mon_id", sugar.get_compound_id() },
// TODO: need fix, collect from nag_atoms? // TODO: need fix, collect from nag_atoms?
{"auth_asym_id", asym_id}, { "auth_asym_id", asym_id },
{"auth_mon_id", sugar.get_compound_id()}, { "auth_mon_id", sugar.get_compound_id() },
{"auth_seq_num", sugar.get_auth_seq_id()}, { "auth_seq_num", sugar.get_auth_seq_id() },
{"hetero", "n"} { "hetero", "n" } });
});
} }
} }
} }
...@@ -2238,13 +2270,11 @@ std::string structure::create_non_poly(const std::string &entity_id, const std:: ...@@ -2238,13 +2270,11 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
auto &struct_asym = m_db["struct_asym"]; auto &struct_asym = m_db["struct_asym"];
std::string asym_id = struct_asym.get_unique_id(); std::string asym_id = struct_asym.get_unique_id();
struct_asym.emplace({ struct_asym.emplace({ { "id", asym_id },
{"id", asym_id}, { "pdbx_blank_PDB_chainid_flag", "N" },
{"pdbx_blank_PDB_chainid_flag", "N"}, { "pdbx_modified", "N" },
{"pdbx_modified", "N"}, { "entity_id", entity_id },
{"entity_id", entity_id}, { "details", "?" } });
{"details", "?"}
});
std::string comp_id = m_db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id"); std::string comp_id = m_db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
...@@ -2256,29 +2286,27 @@ std::string structure::create_non_poly(const std::string &entity_id, const std:: ...@@ -2256,29 +2286,27 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
{ {
auto atom_id = atom_site.get_unique_id(""); auto atom_id = atom_site.get_unique_id("");
auto row = atom_site.emplace({ auto row = atom_site.emplace({ { "group_PDB", atom.get_property("group_PDB") },
{"group_PDB", atom.get_property("group_PDB")}, { "id", atom_id },
{"id", atom_id}, { "type_symbol", atom.get_property("type_symbol") },
{"type_symbol", atom.get_property("type_symbol")}, { "label_atom_id", atom.get_property("label_atom_id") },
{"label_atom_id", atom.get_property("label_atom_id")}, { "label_alt_id", atom.get_property("label_alt_id") },
{"label_alt_id", atom.get_property("label_alt_id")}, { "label_comp_id", comp_id },
{"label_comp_id", comp_id}, { "label_asym_id", asym_id },
{"label_asym_id", asym_id}, { "label_entity_id", entity_id },
{"label_entity_id", entity_id}, { "label_seq_id", "." },
{"label_seq_id", "."}, { "pdbx_PDB_ins_code", "" },
{"pdbx_PDB_ins_code", ""}, { "Cartn_x", atom.get_property("Cartn_x") },
{"Cartn_x", atom.get_property("Cartn_x")}, { "Cartn_y", atom.get_property("Cartn_y") },
{"Cartn_y", atom.get_property("Cartn_y")}, { "Cartn_z", atom.get_property("Cartn_z") },
{"Cartn_z", atom.get_property("Cartn_z")}, { "occupancy", atom.get_property("occupancy") },
{"occupancy", atom.get_property("occupancy")}, { "B_iso_or_equiv", atom.get_property("B_iso_or_equiv") },
{"B_iso_or_equiv", atom.get_property("B_iso_or_equiv")}, { "pdbx_formal_charge", atom.get_property("pdbx_formal_charge") },
{"pdbx_formal_charge", atom.get_property("pdbx_formal_charge")}, { "auth_seq_id", 1 },
{"auth_seq_id", 1}, { "auth_comp_id", comp_id },
{"auth_comp_id", comp_id}, { "auth_asym_id", asym_id },
{"auth_asym_id", asym_id}, { "auth_atom_id", atom.get_property("label_atom_id") },
{"auth_atom_id", atom.get_property("label_atom_id")}, { "pdbx_PDB_model_num", 1 } });
{"pdbx_PDB_model_num", 1}
});
auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id)); auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
res.add_atom(newAtom); res.add_atom(newAtom);
...@@ -2287,16 +2315,16 @@ std::string structure::create_non_poly(const std::string &entity_id, const std:: ...@@ -2287,16 +2315,16 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"]; auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"];
std::size_t ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1; std::size_t ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1;
pdbx_nonpoly_scheme.emplace({ pdbx_nonpoly_scheme.emplace({
{"asym_id", asym_id}, { "asym_id", asym_id },
{"entity_id", entity_id}, { "entity_id", entity_id },
{"mon_id", comp_id}, { "mon_id", comp_id },
{"ndb_seq_num", ndb_nr}, { "ndb_seq_num", ndb_nr },
{"pdb_seq_num", res.get_auth_seq_id()}, { "pdb_seq_num", res.get_auth_seq_id() },
{"auth_seq_num", res.get_auth_seq_id()}, { "auth_seq_num", res.get_auth_seq_id() },
{"pdb_mon_id", comp_id}, { "pdb_mon_id", comp_id },
{"auth_mon_id", comp_id}, { "auth_mon_id", comp_id },
{"pdb_strand_id", asym_id}, { "pdb_strand_id", asym_id },
{"pdb_ins_code", "."}, { "pdb_ins_code", "." },
}); });
return asym_id; return asym_id;
...@@ -2309,13 +2337,11 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector ...@@ -2309,13 +2337,11 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
auto &struct_asym = m_db["struct_asym"]; auto &struct_asym = m_db["struct_asym"];
std::string asym_id = struct_asym.get_unique_id(); std::string asym_id = struct_asym.get_unique_id();
struct_asym.emplace({ struct_asym.emplace({ { "id", asym_id },
{"id", asym_id}, { "pdbx_blank_PDB_chainid_flag", "N" },
{"pdbx_blank_PDB_chainid_flag", "N"}, { "pdbx_modified", "N" },
{"pdbx_modified", "N"}, { "entity_id", entity_id },
{"entity_id", entity_id}, { "details", "?" } });
{"details", "?"}
});
std::string comp_id = m_db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id"); std::string comp_id = m_db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
...@@ -2332,14 +2358,14 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector ...@@ -2332,14 +2358,14 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
atom.set_value("auth_asym_id", asym_id); atom.set_value("auth_asym_id", asym_id);
atom.set_value("label_entity_id", entity_id); atom.set_value("label_entity_id", entity_id);
atom.set_value_if_empty({"group_PDB", "HETATM"}); atom.set_value_if_empty({ "group_PDB", "HETATM" });
atom.set_value_if_empty({"label_comp_id", comp_id}); atom.set_value_if_empty({ "label_comp_id", comp_id });
atom.set_value_if_empty({"label_seq_id", "."}); atom.set_value_if_empty({ "label_seq_id", "." });
atom.set_value_if_empty({"auth_comp_id", comp_id}); atom.set_value_if_empty({ "auth_comp_id", comp_id });
atom.set_value_if_empty({"auth_seq_id", 1}); atom.set_value_if_empty({ "auth_seq_id", 1 });
atom.set_value_if_empty({"pdbx_PDB_model_num", 1}); atom.set_value_if_empty({ "pdbx_PDB_model_num", 1 });
atom.set_value_if_empty({"label_alt_id", ""}); atom.set_value_if_empty({ "label_alt_id", "" });
atom.set_value_if_empty({"occupancy", 1.0, 2}); atom.set_value_if_empty({ "occupancy", 1.0, 2 });
auto row = atom_site.emplace(atom.begin(), atom.end()); auto row = atom_site.emplace(atom.begin(), atom.end());
...@@ -2350,16 +2376,16 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector ...@@ -2350,16 +2376,16 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"]; auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"];
std::size_t ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1; std::size_t ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1;
pdbx_nonpoly_scheme.emplace({ pdbx_nonpoly_scheme.emplace({
{"asym_id", asym_id}, { "asym_id", asym_id },
{"entity_id", entity_id}, { "entity_id", entity_id },
{"mon_id", comp_id}, { "mon_id", comp_id },
{"ndb_seq_num", ndb_nr}, { "ndb_seq_num", ndb_nr },
{"pdb_seq_num", res.get_auth_seq_id()}, { "pdb_seq_num", res.get_auth_seq_id() },
{"auth_seq_num", res.get_auth_seq_id()}, { "auth_seq_num", res.get_auth_seq_id() },
{"pdb_mon_id", comp_id}, { "pdb_mon_id", comp_id },
{"auth_mon_id", comp_id}, { "auth_mon_id", comp_id },
{"pdb_strand_id", asym_id}, { "pdb_strand_id", asym_id },
{"pdb_ins_code", "."}, { "pdb_ins_code", "." },
}); });
return asym_id; return asym_id;
...@@ -2381,13 +2407,11 @@ void structure::create_water(row_initializer atom) ...@@ -2381,13 +2407,11 @@ void structure::create_water(row_initializer atom)
{ {
asym_id = struct_asym.get_unique_id(); asym_id = struct_asym.get_unique_id();
struct_asym.emplace({ struct_asym.emplace({ { "id", asym_id },
{"id", asym_id}, { "pdbx_blank_PDB_chainid_flag", "N" },
{"pdbx_blank_PDB_chainid_flag", "N"}, { "pdbx_modified", "N" },
{"pdbx_modified", "N"}, { "entity_id", entity_id },
{"entity_id", entity_id}, { "details", "?" } });
{"details", "?"}
});
} }
auto &atom_site = m_db["atom_site"]; auto &atom_site = m_db["atom_site"];
...@@ -2403,13 +2427,13 @@ void structure::create_water(row_initializer atom) ...@@ -2403,13 +2427,13 @@ void structure::create_water(row_initializer atom)
atom.set_value("label_entity_id", entity_id); atom.set_value("label_entity_id", entity_id);
atom.set_value("auth_seq_id", std::to_string(auth_seq_id)); atom.set_value("auth_seq_id", std::to_string(auth_seq_id));
atom.set_value_if_empty({"group_PDB", "HETATM"}); atom.set_value_if_empty({ "group_PDB", "HETATM" });
atom.set_value_if_empty({"label_comp_id", "HOH"}); atom.set_value_if_empty({ "label_comp_id", "HOH" });
atom.set_value_if_empty({"label_seq_id", "."}); atom.set_value_if_empty({ "label_seq_id", "." });
atom.set_value_if_empty({"auth_comp_id", "HOH"}); atom.set_value_if_empty({ "auth_comp_id", "HOH" });
atom.set_value_if_empty({"pdbx_PDB_model_num", 1}); atom.set_value_if_empty({ "pdbx_PDB_model_num", 1 });
atom.set_value_if_empty({"label_alt_id", ""}); atom.set_value_if_empty({ "label_alt_id", "" });
atom.set_value_if_empty({"occupancy", 1.0, 2}); atom.set_value_if_empty({ "occupancy", 1.0, 2 });
auto row = atom_site.emplace(atom.begin(), atom.end()); auto row = atom_site.emplace(atom.begin(), atom.end());
...@@ -2418,16 +2442,16 @@ void structure::create_water(row_initializer atom) ...@@ -2418,16 +2442,16 @@ void structure::create_water(row_initializer atom)
auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"]; auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"];
int ndb_nr = pdbx_nonpoly_scheme.find_max<int>("ndb_seq_num") + 1; int ndb_nr = pdbx_nonpoly_scheme.find_max<int>("ndb_seq_num") + 1;
pdbx_nonpoly_scheme.emplace({ pdbx_nonpoly_scheme.emplace({
{"asym_id", asym_id}, { "asym_id", asym_id },
{"entity_id", entity_id}, { "entity_id", entity_id },
{"mon_id", "HOH"}, { "mon_id", "HOH" },
{"ndb_seq_num", ndb_nr}, { "ndb_seq_num", ndb_nr },
{"pdb_seq_num", auth_seq_id}, { "pdb_seq_num", auth_seq_id },
{"auth_seq_num", auth_seq_id}, { "auth_seq_num", auth_seq_id },
{"pdb_mon_id", "HOH"}, { "pdb_mon_id", "HOH" },
{"auth_mon_id", "HOH"}, { "auth_mon_id", "HOH" },
{"pdb_strand_id", asym_id}, { "pdb_strand_id", asym_id },
{"pdb_ins_code", "."}, { "pdb_ins_code", "." },
}); });
} }
...@@ -2439,18 +2463,14 @@ branch &structure::create_branch() ...@@ -2439,18 +2463,14 @@ branch &structure::create_branch()
auto entity_id = entity.get_unique_id(""); auto entity_id = entity.get_unique_id("");
auto asym_id = struct_asym.get_unique_id(); auto asym_id = struct_asym.get_unique_id();
entity.emplace({ entity.emplace({ { "id", entity_id },
{"id", entity_id}, { "type", "branched" } });
{"type", "branched"}
});
struct_asym.emplace({ struct_asym.emplace({ { "id", asym_id },
{"id", asym_id}, { "pdbx_blank_PDB_chainid_flag", "N" },
{"pdbx_blank_PDB_chainid_flag", "N"}, { "pdbx_modified", "N" },
{"pdbx_modified", "N"}, { "entity_id", entity_id },
{"entity_id", entity_id}, { "details", "?" } });
{"details", "?"}
});
return m_branches.emplace_back(*this, asym_id, entity_id); return m_branches.emplace_back(*this, asym_id, entity_id);
} }
...@@ -2647,22 +2667,19 @@ std::string structure::create_entity_for_branch(branch &branch) ...@@ -2647,22 +2667,19 @@ std::string structure::create_entity_for_branch(branch &branch)
if (VERBOSE) if (VERBOSE)
std::cout << "Creating new entity " << entityID << " for branched sugar " << entityName << '\n'; std::cout << "Creating new entity " << entityID << " for branched sugar " << entityName << '\n';
entity.emplace({ entity.emplace({ { "id", entityID },
{"id", entityID}, { "type", "branched" },
{"type", "branched"}, { "src_method", "man" },
{"src_method", "man"}, { "pdbx_description", entityName },
{"pdbx_description", entityName}, { "formula_weight", branch.weight() } });
{"formula_weight", branch.weight()}});
auto &pdbx_entity_branch_list = m_db["pdbx_entity_branch_list"]; auto &pdbx_entity_branch_list = m_db["pdbx_entity_branch_list"];
for (auto &sugar : branch) for (auto &sugar : branch)
{ {
pdbx_entity_branch_list.emplace({ pdbx_entity_branch_list.emplace({ { "entity_id", entityID },
{"entity_id", entityID}, { "comp_id", sugar.get_compound_id() },
{"comp_id", sugar.get_compound_id()}, { "num", sugar.num() },
{"num", sugar.num()}, { "hetero", "n" } });
{"hetero", "n"}
});
} }
auto &pdbx_entity_branch_link = m_db["pdbx_entity_branch_link"]; auto &pdbx_entity_branch_link = m_db["pdbx_entity_branch_link"];
...@@ -2676,19 +2693,17 @@ std::string structure::create_entity_for_branch(branch &branch) ...@@ -2676,19 +2693,17 @@ std::string structure::create_entity_for_branch(branch &branch)
auto &s2 = branch.at(stoi(l2.get_auth_seq_id()) - 1); auto &s2 = branch.at(stoi(l2.get_auth_seq_id()) - 1);
auto l1 = s2.get_atom_by_atom_id("C1"); auto l1 = s2.get_atom_by_atom_id("C1");
pdbx_entity_branch_link.emplace({ pdbx_entity_branch_link.emplace({ { "link_id", pdbx_entity_branch_link.get_unique_id("") },
{"link_id", pdbx_entity_branch_link.get_unique_id("")}, { "entity_id", entityID },
{"entity_id", entityID}, { "entity_branch_list_num_1", s1.get_auth_seq_id() },
{"entity_branch_list_num_1", s1.get_auth_seq_id()}, { "comp_id_1", s1.get_compound_id() },
{"comp_id_1", s1.get_compound_id()}, { "atom_id_1", l1.get_label_atom_id() },
{"atom_id_1", l1.get_label_atom_id()}, { "leaving_atom_id_1", "O1" },
{"leaving_atom_id_1", "O1"}, { "entity_branch_list_num_2", s2.get_auth_seq_id() },
{"entity_branch_list_num_2", s2.get_auth_seq_id()}, { "comp_id_2", s2.get_compound_id() },
{"comp_id_2", s2.get_compound_id()}, { "atom_id_2", l2.get_label_atom_id() },
{"atom_id_2", l2.get_label_atom_id()}, { "leaving_atom_id_2", "H" + l2.get_label_atom_id() },
{"leaving_atom_id_2", "H" + l2.get_label_atom_id()}, { "value_order", "sing" } });
{"value_order", "sing"}
});
} }
} }
...@@ -2750,7 +2765,7 @@ void structure::cleanup_empty_categories() ...@@ -2750,7 +2765,7 @@ void structure::cleanup_empty_categories()
// the rest? // the rest?
for (const char *cat : {"pdbx_entity_nonpoly"}) for (const char *cat : { "pdbx_entity_nonpoly" })
{ {
auto &category = m_db[cat]; auto &category = m_db[cat];
...@@ -2856,4 +2871,66 @@ void structure::validate_atoms() const ...@@ -2856,4 +2871,66 @@ void structure::validate_atoms() const
assert(atoms.empty()); assert(atoms.empty());
} }
} // namespace pdbx static int compare_numbers(std::string_view a, std::string_view b)
{
int result = 0;
double da, db;
using namespace cif;
using namespace std;
std::from_chars_result ra, rb;
ra = selected_charconv<double>::from_chars(a.data(), a.data() + a.length(), da);
rb = selected_charconv<double>::from_chars(b.data(), b.data() + b.length(), db);
if (not (bool)ra.ec and not (bool)rb.ec)
{
auto d = da - db;
if (std::abs(d) > std::numeric_limits<double>::epsilon())
{
if (d > 0)
result = 1;
else if (d < 0)
result = -1;
}
}
else if ((bool)ra.ec)
result = 1;
else
result = -1;
return result;
}
void structure::reorder_atoms()
{
auto &atom_site = m_db["atom_site"];
atom_site.sort([](row_handle a, row_handle b)
{
int d;
// First by model number
d = a.get<int>("pdbx_PDB_model_num") - b.get<int>("pdbx_PDB_model_num");
if (d == 0)
d = a.get<std::string>("label_asym_id").compare(b.get<std::string>("label_asym_id"));
if (d == 0)
d = a.get<int>("label_seq_id") - b.get<int>("label_seq_id");
if (d == 0)
d = a.get<std::string>("label_alt_id").compare(b.get<std::string>("label_alt_id"));
if (d == 0)
d = compare_numbers(a.get<std::string>("id"), b.get<std::string>("id"));
return d;
});
// atom_site.set_validator(nullptr, m_db);
// for (int nr = 1; auto r : atom_site)
// r["id"] = nr++;
// atom_site.set_validator(m_db.get_validator(), m_db);
}
} // namespace cif::mm
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