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libcifpp
Commit c4f3b1cd by Maarten L. Hekkelman
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delay loading atoms in residues

parent a490b19d
Showing with 70 additions and 132 deletions
include/cif++/Structure.hpp
...@@ -241,6 +241,11 @@ class Residue ...@@ -241,6 +241,11 @@ class Residue
const Compound &compound() const; const Compound &compound() const;
const AtomView &atoms() const; const AtomView &atoms() const;
void addAtom(const Atom &atom)
{
mAtoms.push_back(atom);
}
/// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id. /// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id.
AtomView unique_atoms() const; AtomView unique_atoms() const;
...@@ -291,6 +296,8 @@ class Residue ...@@ -291,6 +296,8 @@ class Residue
friend std::ostream &operator<<(std::ostream &os, const Residue &res); friend std::ostream &operator<<(std::ostream &os, const Residue &res);
friend Structure;
protected: protected:
Residue() {} Residue() {}
......
src/Structure.cpp
...@@ -764,27 +764,27 @@ Residue::Residue(const Structure &structure, const std::string &compoundID, ...@@ -764,27 +764,27 @@ Residue::Residue(const Structure &structure, const std::string &compoundID,
, mAsymID(asymID) , mAsymID(asymID)
, mAuthSeqID(authSeqID) , mAuthSeqID(authSeqID)
{ {
for (auto &a : mStructure->atoms()) // for (auto &a : mStructure->atoms())
{ // {
if (a.labelAsymID() != mAsymID or // if (a.labelAsymID() != mAsymID or
a.labelCompID() != mCompoundID) // a.labelCompID() != mCompoundID)
continue; // continue;
if (compoundID == "HOH") // if (compoundID == "HOH")
{ // {
if (not mAuthSeqID.empty() and a.authSeqID() != mAuthSeqID) // if (not mAuthSeqID.empty() and a.authSeqID() != mAuthSeqID)
continue; // continue;
} // }
else // else
{ // {
if (mSeqID > 0 and a.labelSeqID() != mSeqID) // if (mSeqID > 0 and a.labelSeqID() != mSeqID)
continue; // continue;
} // }
mAtoms.push_back(a); // mAtoms.push_back(a);
} // }
assert(not mAtoms.empty()); // assert(not mAtoms.empty());
} }
Residue::Residue(const Structure &structure, const std::string &compoundID, const std::string &asymID) Residue::Residue(const Structure &structure, const std::string &compoundID, const std::string &asymID)
...@@ -802,17 +802,17 @@ Residue::Residue(const Structure &structure, const std::string &compoundID, ...@@ -802,17 +802,17 @@ Residue::Residue(const Structure &structure, const std::string &compoundID,
{ {
assert(mCompoundID != "HOH"); assert(mCompoundID != "HOH");
for (auto &a : mStructure->atoms()) // for (auto &a : mStructure->atoms())
{ // {
if (mSeqID > 0 and a.labelSeqID() != mSeqID) // if (mSeqID > 0 and a.labelSeqID() != mSeqID)
continue; // continue;
if (a.labelAsymID() != mAsymID or // if (a.labelAsymID() != mAsymID or
a.labelCompID() != mCompoundID) // a.labelCompID() != mCompoundID)
continue; // continue;
mAtoms.push_back(a); // mAtoms.push_back(a);
} // }
} }
Residue::Residue(Residue &&rhs) Residue::Residue(Residue &&rhs)
...@@ -1103,11 +1103,6 @@ std::ostream &operator<<(std::ostream &os, const Residue &res) ...@@ -1103,11 +1103,6 @@ std::ostream &operator<<(std::ostream &os, const Residue &res)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// monomer // monomer
//Monomer::Monomer(Monomer&& rhs)
// : Residue(std::move(rhs)), mPolymer(rhs.mPolymer), mIndex(rhs.mIndex)
//{
//}
Monomer::Monomer(const Polymer &polymer, size_t index, int seqID, const std::string &authSeqID, const std::string &compoundID) Monomer::Monomer(const Polymer &polymer, size_t index, int seqID, const std::string &authSeqID, const std::string &compoundID)
: Residue(*polymer.structure(), compoundID, polymer.asymID(), seqID, authSeqID) : Residue(*polymer.structure(), compoundID, polymer.asymID(), seqID, authSeqID)
, mPolymer(&polymer) , mPolymer(&polymer)
...@@ -1120,23 +1115,11 @@ Monomer::Monomer(Monomer &&rhs) ...@@ -1120,23 +1115,11 @@ Monomer::Monomer(Monomer &&rhs)
, mPolymer(rhs.mPolymer) , mPolymer(rhs.mPolymer)
, mIndex(rhs.mIndex) , mIndex(rhs.mIndex)
{ {
std::cerr << "move constructor monomer" << std::endl;
// mStructure = rhs.mStructure; rhs.mStructure = nullptr;
// mCompoundID = std::move(rhs.mCompoundID);
// mAsymID = std::move(rhs.mAsymID);
// mSeqID = rhs.mSeqID;
// mAtoms = std::move(rhs.mAtoms);
//
// mPolymer = rhs.mPolymer; rhs.mPolymer = nullptr;
// mIndex = rhs.mIndex;
rhs.mPolymer = nullptr; rhs.mPolymer = nullptr;
} }
Monomer &Monomer::operator=(Monomer &&rhs) Monomer &Monomer::operator=(Monomer &&rhs)
{ {
std::cerr << "move assignment monomer" << std::endl;
Residue::operator=(std::move(rhs)); Residue::operator=(std::move(rhs));
mPolymer = rhs.mPolymer; mPolymer = rhs.mPolymer;
rhs.mPolymer = nullptr; rhs.mPolymer = nullptr;
...@@ -1508,94 +1491,6 @@ bool Monomer::isCis(const mmcif::Monomer &a, const mmcif::Monomer &b) ...@@ -1508,94 +1491,6 @@ bool Monomer::isCis(const mmcif::Monomer &a, const mmcif::Monomer &b)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// polymer // polymer
//
//Polymer::iterator::iterator(const Polymer& p, uint32_t index)
// : mPolymer(&p), mIndex(index), mCurrent(p, index)
//{
// auto& polySeq = mPolymer->mPolySeq;
//
// if (index < polySeq.size())
// {
// int seqID;
// std::string asymID, monID;
// cif::tie(asymID, seqID, monID) =
// polySeq[mIndex].get("asym_id", "seq_id", "mon_id");
//
// mCurrent = Monomer(*mPolymer, index, seqID, monID, "");
// }
//}
//
//Monomer Polymer::operator[](size_t index) const
//{
// if (index >= mPolySeq.size())
// throw out_of_range("Invalid index for residue in polymer");
//
// std::string compoundID;
// int seqID;
//
// auto r = mPolySeq[index];
//
// cif::tie(seqID, compoundID) =
// r.get("seq_id", "mon_id");
//
// return Monomer(const_cast<Polymer&>(*this), index, seqID, compoundID, "");
//}
//
//Polymer::iterator::iterator(const iterator& rhs)
// : mPolymer(rhs.mPolymer), mIndex(rhs.mIndex), mCurrent(rhs.mCurrent)
//{
//}
//
//Polymer::iterator& Polymer::iterator::operator++()
//{
// auto& polySeq = mPolymer->mPolySeq;
//
// if (mIndex < polySeq.size())
// ++mIndex;
//
// if (mIndex < polySeq.size())
// {
// int seqID;
// std::string asymID, monID;
// cif::tie(asymID, seqID, monID) =
// polySeq[mIndex].get("asym_id", "seq_id", "mon_id");
//
// mCurrent = Monomer(*mPolymer, mIndex, seqID, monID, "");
// }
//
// return *this;
//}
//Polymer::Polymer(const Structure& s, const std::string& asymID)
// : mStructure(const_cast<Structure*>(&s)), mAsymID(asymID)
// , mPolySeq(s.category("pdbx_poly_seq_scheme").find(cif::Key("asym_id") == mAsymID))
//{
// mEntityID = mPolySeq.front()["entity_id"].as<std::string>();
//
//#if DEBUG
// for (auto r: mPolySeq)
// assert(r["entity_id"] == mEntityID);
//#endif
//
//}
//Polymer::Polymer(Polymer&& rhs)
// : std::vector<Monomer>(std::move(rhs))
// , mStructure(rhs.mStructure)
// , mEntityID(std::move(rhs.mEntityID)), mAsymID(std::move(rhs.mAsymID)), mPolySeq(std::move(rhs.mPolySeq))
//{
// rhs.mStructure = nullptr;
//}
//
//Polymer& Polymer::operator=(Polymer&& rhs)
//{
// std::vector<Monomer>::operator=(std::move(rhs));
// mStructure = rhs.mStructure; rhs.mStructure = nullptr;
// mEntityID = std::move(rhs.mEntityID);
// mAsymID = std::move(rhs.mAsymID);
// mPolySeq = std::move(rhs.mPolySeq);
// return *this;
//}
Polymer::Polymer(const Structure &s, const std::string &entityID, const std::string &asymID) Polymer::Polymer(const Structure &s, const std::string &entityID, const std::string &asymID)
: mStructure(const_cast<Structure *>(&s)) : mStructure(const_cast<Structure *>(&s))
...@@ -1856,6 +1751,42 @@ void Structure::loadData() ...@@ -1856,6 +1751,42 @@ void Structure::loadData()
mBranchResidues.emplace_back(*this, monID, asymID, num); mBranchResidues.emplace_back(*this, monID, asymID, num);
} }
// place atoms in residues
using key_type = std::tuple<std::string,std::string,int>;
using map_type = std::map<key_type,Residue*>;
map_type resMap;
for (auto &poly : mPolymers)
{
for (auto &res : poly)
resMap[{ res.asymID(), res.compoundID(), res.seqID() }] = &res;
}
for (auto &res : mNonPolymers)
resMap[{ res.asymID(), res.compoundID(), (res.isWater() ? std::stoi(res.mAuthSeqID) : res.seqID()) }] = &res;
for (auto &res : mBranchResidues)
resMap[{ res.asymID(), res.compoundID(), res.seqID() }] = &res;
for (auto &atom: mAtoms)
{
key_type k(atom.labelAsymID(), atom.labelCompID(), atom.isWater() ? std::stoi(atom.authSeqID()) : atom.labelSeqID());
auto ri = resMap.find(k);
if (ri == resMap.end())
{
if (cif::VERBOSE)
std::cerr << "Missing residue for atom " << atom << std::endl;
assert(false);
continue;
}
ri->second->addAtom(atom);
}
} }
void Structure::updateAtomIndex() void Structure::updateAtomIndex()
......
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