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libcifpp
Commit 4de981a3 by Maarten L. Hekkelman
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better handling of missing residues in pdb2cif

parent 15db026e
Showing with 65 additions and 80 deletions
include/cif++/model.hpp
......@@ -321,13 +321,6 @@ class atom
friend std::ostream &operator<<(std::ostream &os, const atom &atom);
// /// \brief Synchronize data with underlying cif data
// void sync()
// {
// if (m_impl)
// m_impl->prefetch();
// }
private:
friend class structure;
......@@ -341,25 +334,6 @@ class atom
std::shared_ptr<atom_impl> m_impl;
};
// template <>
// inline std::string atom::get_property<std::string>(const std::string_view name) const
// {
// return get_property(name);
// }
// template <>
// inline int atom::get_property<int>(const std::string_view name) const
// {
// auto v = impl().get_property(name);
// return v.empty() ? 0 : stoi(v);
// }
// template <>
// inline float atom::get_property<float>(const std::string_view name) const
// {
// return stof(impl().get_property(name));
// }
inline void swap(atom &a, atom &b)
{
a.swap(b);
......
src/model.cpp
......@@ -618,20 +618,20 @@ float monomer::phi() const
{
float result = 360;
try
if (m_index > 0)
{
if (m_index > 0)
auto &prev = m_polymer->operator[](m_index - 1);
if (prev.m_seq_id + 1 == m_seq_id)
{
auto &prev = m_polymer->operator[](m_index - 1);
if (prev.m_seq_id + 1 == m_seq_id)
result = static_cast<float>(dihedral_angle(prev.C().get_location(), N().get_location(), CAlpha().get_location(), C().get_location()));
auto a1 = prev.C();
auto a2 = N();
auto a3 = CAlpha();
auto a4 = C();
if (a1 and a2 and a3 and a4)
result = dihedral_angle(a1.get_location(), a2.get_location(), a3.get_location(), a4.get_location());
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
return result;
}
......@@ -640,20 +640,20 @@ float monomer::psi() const
{
float result = 360;
try
if (m_index + 1 < m_polymer->size())
{
if (m_index + 1 < m_polymer->size())
auto &next = m_polymer->operator[](m_index + 1);
if (m_seq_id + 1 == next.m_seq_id)
{
auto &next = m_polymer->operator[](m_index + 1);
if (m_seq_id + 1 == next.m_seq_id)
result = static_cast<float>(dihedral_angle(N().get_location(), CAlpha().get_location(), C().get_location(), next.N().get_location()));
auto a1 = N();
auto a2 = CAlpha();
auto a3 = C();
auto a4 = next.N();
if (a1 and a2 and a3 and a4)
result = dihedral_angle(a1.get_location(), a2.get_location(), a3.get_location(), a4.get_location());
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
return result;
}
......@@ -935,17 +935,17 @@ float monomer::omega(const monomer &a, const monomer &b)
{
float result = 360;
try
{
auto a1 = a.get_atom_by_atom_id("CA");
auto a2 = a.get_atom_by_atom_id("C");
auto a3 = b.get_atom_by_atom_id("N");
auto a4 = b.get_atom_by_atom_id("CA");
if (a1 and a2 and a3 and a4)
result = static_cast<float>(dihedral_angle(
a.get_atom_by_atom_id("CA").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("CA").get_location()));
}
catch (...)
{
}
a1.get_location(),
a2.get_location(),
a3.get_location(),
a4.get_location()));
return result;
}
......@@ -974,8 +974,12 @@ polymer::polymer(structure &s, const std::string &entityID, const std::string &a
for (auto r : poly_seq_scheme.find("asym_id"_key == asym_id))
{
int seqID;
std::optional<int> pdbSeqNum;
std::string compoundID, authSeqID, pdbInsCode;
cif::tie(seqID, authSeqID, compoundID, pdbInsCode) = r.get("seq_id", "auth_seq_num", "mon_id", "pdb_ins_code");
cif::tie(seqID, authSeqID, compoundID, pdbInsCode, pdbSeqNum) = r.get("seq_id", "auth_seq_num", "mon_id", "pdb_ins_code", "pdb_seq_num");
if (authSeqID.empty() and pdbSeqNum.has_value())
authSeqID = std::to_string(*pdbSeqNum);
size_t index = size();
......
src/pdb/pdb2cif.cpp
......@@ -3819,41 +3819,48 @@ void PDBFileParser::ConstructEntities()
for (std::string monID : monIds)
{
std::string authMonID, authSeqNum, authInsCode;
std::string authMonID, authSeqNum, authInsCode{'.'};
if (res.mSeen)
{
authMonID = monID;
authSeqNum = std::to_string(res.mSeqNum);
if (res.mIcode != ' ' and res.mIcode != 0)
authInsCode = std::string{ res.mIcode };
cat->emplace({
{ "asym_id", asymID },
{ "entity_id", mMolID2EntityID[chain.mMolID] },
{ "seq_id", seqID },
{ "mon_id", monID },
{ "ndb_seq_num", seqID },
{ "pdb_seq_num", res.mSeqNum },
{ "auth_seq_num", authSeqNum },
{ "pdb_mon_id", authMonID },
{ "auth_mon_id", authMonID },
{ "pdb_strand_id", std::string{ chain.mDbref.chainID } },
{ "pdb_ins_code", authInsCode },
{ "hetero", res.mAlts.empty() ? "n" : "y" } });
}
else
{
authMonID = res.mMonID;
authSeqNum = std::to_string(res.mSeqNum);
if (res.mIcode != ' ' and res.mIcode != 0)
authInsCode = std::string{ res.mIcode } + "A";
else
authInsCode = "A";
}
if (authInsCode.empty())
authInsCode = ".";
cat->emplace({
{ "asym_id", asymID },
{ "entity_id", mMolID2EntityID[chain.mMolID] },
{ "seq_id", seqID },
{ "mon_id", monID },
{ "ndb_seq_num", seqID },
{ "pdb_seq_num", res.mSeqNum },
{ "auth_seq_num", authSeqNum },
{ "pdb_mon_id", authMonID },
{ "auth_mon_id", authMonID },
{ "pdb_strand_id", std::string{ chain.mDbref.chainID } },
{ "pdb_ins_code", authInsCode },
{ "hetero", res.mAlts.empty() ? "n" : "y" } });
cat->emplace({
{ "asym_id", asymID },
{ "entity_id", mMolID2EntityID[chain.mMolID] },
{ "seq_id", seqID },
{ "mon_id", monID },
{ "ndb_seq_num", seqID },
{ "pdb_seq_num", res.mSeqNum },
{ "auth_seq_num", "." },
{ "pdb_mon_id", "." },
{ "auth_mon_id", "." },
{ "pdb_strand_id", std::string{ chain.mDbref.chainID } },
{ "pdb_ins_code", authInsCode },
{ "hetero", res.mAlts.empty() ? "n" : "y" } });
}
}
}
}
......
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