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Commit f66bd7fd by maarten
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backup -- met nieuwe Cif++ optimalisaties 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@341 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 7f234272
Showing with 238 additions and 72 deletions
include/cif++/Cif++.h
...@@ -611,6 +611,7 @@ struct ConditionImpl ...@@ -611,6 +611,7 @@ struct ConditionImpl
{ {
virtual ~ConditionImpl() {} virtual ~ConditionImpl() {}
virtual void prepare(const Category& c) {}
virtual bool test(const Category& c, const Row& r) const = 0; virtual bool test(const Category& c, const Row& r) const = 0;
virtual std::string str() const = 0; virtual std::string str() const = 0;
}; };
...@@ -638,9 +639,16 @@ struct Condition ...@@ -638,9 +639,16 @@ struct Condition
delete mImpl; delete mImpl;
} }
void prepare(const Category& c)
{
mImpl->prepare(c);
mPrepared = true;
}
bool operator()(const Category& c, const Row& r) const bool operator()(const Category& c, const Row& r) const
{ {
assert(mImpl); assert(mImpl);
assert(mPrepared);
return mImpl->test(c, r); return mImpl->test(c, r);
} }
...@@ -650,6 +658,7 @@ struct Condition ...@@ -650,6 +658,7 @@ struct Condition
} }
detail::ConditionImpl* mImpl; detail::ConditionImpl* mImpl;
bool mPrepared = false;
}; };
namespace detail namespace detail
...@@ -659,10 +668,12 @@ struct KeyIsEmptyConditionImpl : public ConditionImpl ...@@ -659,10 +668,12 @@ struct KeyIsEmptyConditionImpl : public ConditionImpl
{ {
KeyIsEmptyConditionImpl(const string& ItemTag) KeyIsEmptyConditionImpl(const string& ItemTag)
: mItemTag(ItemTag) {} : mItemTag(ItemTag) {}
virtual void prepare(const Category& c);
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return r[mItemTag].empty(); return r[mItemIx].empty();
} }
virtual std::string str() const virtual std::string str() const
...@@ -671,6 +682,7 @@ struct KeyIsEmptyConditionImpl : public ConditionImpl ...@@ -671,6 +682,7 @@ struct KeyIsEmptyConditionImpl : public ConditionImpl
} }
string mItemTag; string mItemTag;
size_t mItemIx;
}; };
template<typename T> template<typename T>
...@@ -681,9 +693,11 @@ struct KeyIsConditionImpl : public ConditionImpl ...@@ -681,9 +693,11 @@ struct KeyIsConditionImpl : public ConditionImpl
KeyIsConditionImpl(const string& ItemTag, const valueType& value) KeyIsConditionImpl(const string& ItemTag, const valueType& value)
: mItemTag(ItemTag), mValue(value) {} : mItemTag(ItemTag), mValue(value) {}
virtual void prepare(const Category& c);
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return r[mItemTag].template compare<valueType>(mValue) == 0; return r[mItemIx].template compare<valueType>(mValue) == 0;
} }
virtual std::string str() const virtual std::string str() const
...@@ -692,6 +706,7 @@ struct KeyIsConditionImpl : public ConditionImpl ...@@ -692,6 +706,7 @@ struct KeyIsConditionImpl : public ConditionImpl
} }
string mItemTag; string mItemTag;
size_t mItemIx;
valueType mValue; valueType mValue;
}; };
...@@ -703,9 +718,11 @@ struct KeyIsNotConditionImpl : public ConditionImpl ...@@ -703,9 +718,11 @@ struct KeyIsNotConditionImpl : public ConditionImpl
KeyIsNotConditionImpl(const string& ItemTag, const valueType& value) KeyIsNotConditionImpl(const string& ItemTag, const valueType& value)
: mItemTag(ItemTag), mValue(value) {} : mItemTag(ItemTag), mValue(value) {}
virtual void prepare(const Category& c);
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return r[mItemTag].template compare<valueType>(mValue) != 0; return r[mItemIx].template compare<valueType>(mValue) != 0;
} }
virtual std::string str() const virtual std::string str() const
...@@ -714,6 +731,7 @@ struct KeyIsNotConditionImpl : public ConditionImpl ...@@ -714,6 +731,7 @@ struct KeyIsNotConditionImpl : public ConditionImpl
} }
string mItemTag; string mItemTag;
size_t mItemIx;
valueType mValue; valueType mValue;
}; };
...@@ -723,6 +741,8 @@ struct KeyCompareConditionImpl : public ConditionImpl ...@@ -723,6 +741,8 @@ struct KeyCompareConditionImpl : public ConditionImpl
KeyCompareConditionImpl(const string& ItemTag, COMP&& comp) KeyCompareConditionImpl(const string& ItemTag, COMP&& comp)
: mItemTag(ItemTag), mComp(std::move(comp)) {} : mItemTag(ItemTag), mComp(std::move(comp)) {}
virtual void prepare(const Category& c);
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return mComp(c, r); return mComp(c, r);
...@@ -734,6 +754,7 @@ struct KeyCompareConditionImpl : public ConditionImpl ...@@ -734,6 +754,7 @@ struct KeyCompareConditionImpl : public ConditionImpl
} }
string mItemTag; string mItemTag;
size_t mItemIx;
COMP mComp; COMP mComp;
}; };
...@@ -742,9 +763,11 @@ struct KeyMatchesConditionImpl : public ConditionImpl ...@@ -742,9 +763,11 @@ struct KeyMatchesConditionImpl : public ConditionImpl
KeyMatchesConditionImpl(const string& ItemTag, const std::regex& rx) KeyMatchesConditionImpl(const string& ItemTag, const std::regex& rx)
: mItemTag(ItemTag), mRx(rx) {} : mItemTag(ItemTag), mRx(rx) {}
virtual void prepare(const Category& c);
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return std::regex_match(r[mItemTag].as<string>(), mRx); return std::regex_match(r[mItemIx].as<string>(), mRx);
} }
virtual std::string str() const virtual std::string str() const
...@@ -753,6 +776,7 @@ struct KeyMatchesConditionImpl : public ConditionImpl ...@@ -753,6 +776,7 @@ struct KeyMatchesConditionImpl : public ConditionImpl
} }
string mItemTag; string mItemTag;
size_t mItemIx;
std::regex mRx; std::regex mRx;
}; };
...@@ -804,6 +828,12 @@ struct andConditionImpl : public ConditionImpl ...@@ -804,6 +828,12 @@ struct andConditionImpl : public ConditionImpl
delete mB; delete mB;
} }
virtual void prepare(const Category& c)
{
mA->prepare(c);
mB->prepare(c);
}
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return mA->test(c, r) and mB->test(c, r); return mA->test(c, r) and mB->test(c, r);
...@@ -833,6 +863,12 @@ struct orConditionImpl : public ConditionImpl ...@@ -833,6 +863,12 @@ struct orConditionImpl : public ConditionImpl
delete mB; delete mB;
} }
virtual void prepare(const Category& c)
{
mA->prepare(c);
mB->prepare(c);
}
virtual bool test(const Category& c, const Row& r) const virtual bool test(const Category& c, const Row& r) const
{ {
return mA->test(c, r) or mB->test(c, r); return mA->test(c, r) or mB->test(c, r);
...@@ -842,7 +878,7 @@ struct orConditionImpl : public ConditionImpl ...@@ -842,7 +878,7 @@ struct orConditionImpl : public ConditionImpl
{ {
return "(" + mA->str() + ") or (" + mB->str() + ")"; return "(" + mA->str() + ") or (" + mB->str() + ")";
} }
ConditionImpl* mA; ConditionImpl* mA;
ConditionImpl* mB; ConditionImpl* mB;
}; };
...@@ -1218,22 +1254,40 @@ inline bool anyMatchesConditionImpl::test(const Category& c, const Row& r) const ...@@ -1218,22 +1254,40 @@ inline bool anyMatchesConditionImpl::test(const Category& c, const Row& r) const
} }
} // these should be here, as I learned today
namespace std
{
template<>
inline void swap(cif::Row& a, cif::Row& b) inline void swap(cif::Row& a, cif::Row& b)
{ {
a.swap(b); a.swap(b);
} }
template<>
inline void swap(cif::detail::ItemReference& a, cif::detail::ItemReference& b) inline void swap(cif::detail::ItemReference& a, cif::detail::ItemReference& b)
{ {
a.swap(b); a.swap(b);
} }
namespace detail
{
template<typename T>
void KeyIsConditionImpl<T>::prepare(const Category& c)
{
mItemIx = c.getColumnIndex(mItemTag);
}
template<typename T>
void KeyIsNotConditionImpl<T>::prepare(const Category& c)
{
mItemIx = c.getColumnIndex(mItemTag);
}
template<typename T>
void KeyCompareConditionImpl<T>::prepare(const Category& c)
{
mItemIx = c.getColumnIndex(mItemTag);
}
}
} }
include/cif++/Structure.h
...@@ -151,11 +151,21 @@ class Atom ...@@ -151,11 +151,21 @@ class Atom
return labelAtomId() == "N" or labelAtomId() == "O" or return labelAtomId() == "N" or labelAtomId() == "O" or
labelAtomId() == "C" or labelAtomId() == "CA"; labelAtomId() == "C" or labelAtomId() == "CA";
} }
void swap(Atom& b)
{
std::swap(mImpl, b.mImpl);
}
private: private:
struct AtomImpl* mImpl; struct AtomImpl* mImpl;
}; };
inline void swap(mmcif::Atom& a, mmcif::Atom& b)
{
a.swap(b);
}
inline double Distance(const Atom& a, const Atom& b) inline double Distance(const Atom& a, const Atom& b)
{ {
return Distance(a.location(), b.location()); return Distance(a.location(), b.location());
...@@ -187,7 +197,7 @@ class Residue ...@@ -187,7 +197,7 @@ class Residue
, mAsymID(asymID), mAltID(altID), mSeqID(seqID) {} , mAsymID(asymID), mAltID(altID), mSeqID(seqID) {}
const Compound& compound() const; const Compound& compound() const;
AtomView atoms() const; const AtomView& atoms() const;
Atom atomByID(const std::string& atomID) const; Atom atomByID(const std::string& atomID) const;
...@@ -385,7 +395,7 @@ class Structure ...@@ -385,7 +395,7 @@ class Structure
File& getFile() const; File& getFile() const;
AtomView atoms() const; const AtomView& atoms() const;
AtomView waters() const; AtomView waters() const;
std::vector<Polymer> polymers() const; std::vector<Polymer> polymers() const;
......
src/Cif++.cpp
...@@ -485,6 +485,24 @@ void Datablock::write(ostream& os, const vector<string>& order) ...@@ -485,6 +485,24 @@ void Datablock::write(ostream& os, const vector<string>& order)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// //
namespace detail
{
void KeyIsEmptyConditionImpl::prepare(const Category& c)
{
mItemIx = c.getColumnIndex(mItemTag);
}
void KeyMatchesConditionImpl::prepare(const Category& c)
{
mItemIx = c.getColumnIndex(mItemTag);
}
}
// --------------------------------------------------------------------
//
// class to compare two rows based on their keys. // class to compare two rows based on their keys.
class RowComparator class RowComparator
...@@ -1228,6 +1246,8 @@ void Category::drop(const string& field) ...@@ -1228,6 +1246,8 @@ void Category::drop(const string& field)
Row Category::operator[](Condition&& cond) Row Category::operator[](Condition&& cond)
{ {
Row result; Row result;
cond.prepare(*this);
for (auto r: *this) for (auto r: *this)
{ {
...@@ -1244,6 +1264,9 @@ Row Category::operator[](Condition&& cond) ...@@ -1244,6 +1264,9 @@ Row Category::operator[](Condition&& cond)
RowSet Category::find(Condition&& cond) RowSet Category::find(Condition&& cond)
{ {
RowSet result(*this); RowSet result(*this);
cond.prepare(*this);
for (auto r: *this) for (auto r: *this)
{ {
if (cond(*this, r)) if (cond(*this, r))
...@@ -1255,6 +1278,8 @@ RowSet Category::find(Condition&& cond) ...@@ -1255,6 +1278,8 @@ RowSet Category::find(Condition&& cond)
bool Category::exists(Condition&& cond) bool Category::exists(Condition&& cond)
{ {
bool result = false; bool result = false;
cond.prepare(*this);
for (auto r: *this) for (auto r: *this)
{ {
...@@ -1379,6 +1404,8 @@ tuple<Row,bool> Category::emplace(Row r) ...@@ -1379,6 +1404,8 @@ tuple<Row,bool> Category::emplace(Row r)
void Category::erase(Condition&& cond) void Category::erase(Condition&& cond)
{ {
RowSet remove(*this); RowSet remove(*this);
cond.prepare(*this);
for (auto r: *this) for (auto r: *this)
{ {
...@@ -2201,8 +2228,8 @@ File::File(boost::filesystem::path p, bool validate) ...@@ -2201,8 +2228,8 @@ File::File(boost::filesystem::path p, bool validate)
File::File(File&& rhs) File::File(File&& rhs)
: mHead(nullptr), mValidator(nullptr) : mHead(nullptr), mValidator(nullptr)
{ {
swap(mHead, rhs.mHead); std::swap(mHead, rhs.mHead);
swap(mValidator, rhs.mValidator); std::swap(mValidator, rhs.mValidator);
} }
File::~File() File::~File()
......
src/Compound.cpp
...@@ -1118,7 +1118,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(fs::path file, CompoundFactoryImpl* nex ...@@ -1118,7 +1118,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(fs::path file, CompoundFactoryImpl* nex
//{ //{
// const char* clibdMon = getenv("CLIBD_MON"); // const char* clibdMon = getenv("CLIBD_MON");
// if (clibdMon == nullptr) // if (clibdMon == nullptr)
// throw runtime_error("Cannot locate peptide list, please souce the CCP4 environment"); // throw runtime_error("Cannot locate peptide list, please source the CCP4 environment");
// mClibdMon = clibdMon; // mClibdMon = clibdMon;
//} //}
// //
...@@ -1305,7 +1305,7 @@ CompoundFactory::CompoundFactory() ...@@ -1305,7 +1305,7 @@ CompoundFactory::CompoundFactory()
{ {
const char* clibdMon = getenv("CLIBD_MON"); const char* clibdMon = getenv("CLIBD_MON");
if (clibdMon == nullptr) if (clibdMon == nullptr)
throw runtime_error("Cannot locate peptide list, please souce the CCP4 environment"); throw runtime_error("Cannot locate peptide list, please source the CCP4 environment");
fs::path db = fs::path(clibdMon) / "list" / "mon_lib_list.cif"; fs::path db = fs::path(clibdMon) / "list" / "mon_lib_list.cif";
......
src/DistanceMap.cpp
...@@ -253,7 +253,7 @@ float DistanceMap::operator()(const Atom& a, const Atom& b) const ...@@ -253,7 +253,7 @@ float DistanceMap::operator()(const Atom& a, const Atom& b) const
} }
if (ixb < ixa) if (ixb < ixa)
swap(ixa, ixb); std::swap(ixa, ixb);
tuple<size_t,size_t> k{ ixa, ixb }; tuple<size_t,size_t> k{ ixa, ixb };
......
src/Secondary.cpp
...@@ -8,6 +8,8 @@ ...@@ -8,6 +8,8 @@
#include "cif++/Config.h" #include "cif++/Config.h"
#include <numeric> #include <numeric>
#include <chrono>
#include <iomanip>
#include <boost/algorithm/string.hpp> #include <boost/algorithm/string.hpp>
...@@ -775,20 +777,62 @@ struct DSSPImpl ...@@ -775,20 +777,62 @@ struct DSSPImpl
vector<Res> mResidues; vector<Res> mResidues;
}; };
ostream& operator<<(ostream& os, const chrono::duration<double>& t)
{
uint64 s = static_cast<uint64>(trunc(t.count()));
if (s > 24 * 60 * 60)
{
uint32 days = s / (24 * 60 * 60);
os << days << "d ";
s %= 24 * 60 * 60;
}
if (s > 60 * 60)
{
uint32 hours = s / (60 * 60);
os << hours << "h ";
s %= 60 * 60;
}
if (s > 60)
{
uint32 minutes = s / 60;
os << minutes << "m ";
s %= 60;
}
double ss = s + 1e-6 * (t.count() - s);
os << fixed << setprecision(1) << ss << 's';
return os;
}
DSSPImpl::DSSPImpl(const Structure& s) DSSPImpl::DSSPImpl(const Structure& s)
: mStructure(s) : mStructure(s)
, mPolymers(mStructure.polymers()) , mPolymers(mStructure.polymers())
{ {
if (VERBOSE)
cerr << "Calculating DSSP ";
size_t nRes = accumulate(mPolymers.begin(), mPolymers.end(), size_t nRes = accumulate(mPolymers.begin(), mPolymers.end(),
0.0, [](double s, auto& p) { return s + p.size(); }); 0.0, [](double s, auto& p) { return s + p.size(); });
mResidues.reserve(nRes); mResidues.reserve(nRes);
cerr << "starting to copy atoms for DSSP" << endl;
auto start = std::chrono::system_clock::now();
for (auto& p: mPolymers) for (auto& p: mPolymers)
{ {
for (auto m: p) for (auto m: p)
mResidues.emplace_back(move(m)); mResidues.emplace_back(move(m));
} }
auto end = std::chrono::system_clock::now();
chrono::duration<double> diff = end - start;
cerr << "Copying atoms took " << diff << " seconds" << endl;
for (size_t i = 0; i + 1 < mResidues.size(); ++i) for (size_t i = 0; i + 1 < mResidues.size(); ++i)
{ {
...@@ -798,11 +842,18 @@ DSSPImpl::DSSPImpl(const Structure& s) ...@@ -798,11 +842,18 @@ DSSPImpl::DSSPImpl(const Structure& s)
mResidues[i + 1].assignHydrogen(); mResidues[i + 1].assignHydrogen();
} }
if (VERBOSE) cerr << ".";
CalculateHBondEnergies(mResidues); CalculateHBondEnergies(mResidues);
if (VERBOSE) cerr << ".";
CalculateBetaSheets(mResidues); CalculateBetaSheets(mResidues);
if (VERBOSE) cerr << ".";
CalculateAlphaHelices(mResidues); CalculateAlphaHelices(mResidues);
if (VERBOSE) if (VERBOSE) cerr << endl;
if (VERBOSE > 1)
{ {
for (auto& r: mResidues) for (auto& r: mResidues)
{ {
...@@ -823,7 +874,7 @@ DSSPImpl::DSSPImpl(const Structure& s) ...@@ -823,7 +874,7 @@ DSSPImpl::DSSPImpl(const Structure& s)
string id = m.asymID() + ':' + to_string(m.seqID()) + '/' + m.compoundID(); string id = m.asymID() + ':' + to_string(m.seqID()) + '/' + m.compoundID();
cout << id << string(12 - id.length(), ' ') cerr << id << string(12 - id.length(), ' ')
<< char(r.mSecondaryStructure) << ' ' << char(r.mSecondaryStructure) << ' '
<< helix << helix
<< endl; << endl;
......
src/Structure.cpp
...@@ -631,13 +631,14 @@ const Compound& Residue::compound() const ...@@ -631,13 +631,14 @@ const Compound& Residue::compound() const
return *result; return *result;
} }
AtomView Residue::atoms() const const AtomView& Residue::atoms() const
{ {
if (mStructure == nullptr) if (mStructure == nullptr)
throw runtime_error("Invalid Residue object"); throw runtime_error("Invalid Residue object");
if (mAtoms.empty()) if (mAtoms.empty())
{ {
#if 0
for (auto& a: mStructure->atoms()) for (auto& a: mStructure->atoms())
{ {
if (mSeqID > 0 and a.labelSeqId() != mSeqID) if (mSeqID > 0 and a.labelSeqId() != mSeqID)
...@@ -652,28 +653,22 @@ AtomView Residue::atoms() const ...@@ -652,28 +653,22 @@ AtomView Residue::atoms() const
mAtoms.push_back(a); mAtoms.push_back(a);
} }
// #else
// auto& atomSites = mStructure->category("atom_site"); auto& atomSites = mStructure->category("atom_site");
//
// auto query = cif::Key("label_asym_id") == mAsymID and cif::Key("label_comp_id") == mCompoundID; auto query = cif::Key("label_asym_id") == mAsymID and cif::Key("label_comp_id") == mCompoundID;
//
// if (not mSeqID.empty()) if (mSeqID != 0)
// query = move(query) and cif::Key("label_seq_id") == mSeqID; query = move(query) and cif::Key("label_seq_id") == mSeqID;
//
// if (not mAltID.empty()) if (not mAltID.empty())
// query = move(query) and (cif::Key("label_alt_id") == cif::Empty() or cif::Key("label_alt_id") == mAltID); query = move(query) and (cif::Key("label_alt_id") == cif::Empty() or cif::Key("label_alt_id") == mAltID);
//
// auto cifAtoms = atomSites.find(move(query)); auto cifAtoms = atomSites.find(move(query));
//
// set<string> ids; for (auto cifAtom: cifAtoms)
// for (auto cifAtom: cifAtoms) mAtoms.push_back(mStructure->getAtomById(cifAtom["id"].as<string>()));
// ids.insert(cifAtom["id"].as<string>()); #endif
//
// for (auto& a: mStructure->atoms())
// {
// if (ids.count(a.id()))
// mAtoms.push_back(a);
// }
} }
return mAtoms; return mAtoms;
...@@ -785,24 +780,43 @@ Monomer::Monomer(const Polymer& polymer, uint32 index, int seqID, const string& ...@@ -785,24 +780,43 @@ Monomer::Monomer(const Polymer& polymer, uint32 index, int seqID, const string&
float Monomer::phi() const float Monomer::phi() const
{ {
float result = 360; float result = 360;
if (mIndex > 0)
try
{
if (mIndex > 0)
{
Monomer prev = mPolymer->operator[](mIndex - 1);
if (prev.mSeqID + 1 == mSeqID)
result = DihedralAngle(prev.C().location(), N().location(), CAlpha().location(), C().location());
}
}
catch (const exception& ex)
{ {
Monomer prev = mPolymer->operator[](mIndex - 1); if (VERBOSE)
if (prev.mSeqID + 1 == mSeqID) cerr << ex.what() << endl;
result = DihedralAngle(prev.C().location(), N().location(), CAlpha().location(), C().location());
} }
return result; return result;
} }
float Monomer::psi() const float Monomer::psi() const
{ {
float result = 360; float result = 360;
if (mIndex + 1 < mPolymer->size())
try
{ {
Monomer next = mPolymer->operator[](mIndex + 1); if (mIndex + 1 < mPolymer->size())
if (mSeqID + 1 == next.mSeqID) {
result = DihedralAngle(N().location(), CAlpha().location(), C().location(), next.N().location()); Monomer next = mPolymer->operator[](mIndex + 1);
if (mSeqID + 1 == next.mSeqID)
result = DihedralAngle(N().location(), CAlpha().location(), C().location(), next.N().location());
}
}
catch (const exception& ex)
{
if (VERBOSE)
cerr << ex.what() << endl;
} }
return result; return result;
...@@ -811,16 +825,24 @@ float Monomer::psi() const ...@@ -811,16 +825,24 @@ float Monomer::psi() const
float Monomer::alpha() const float Monomer::alpha() const
{ {
float result = 360; float result = 360;
if (mIndex > 1 and mIndex + 2 < mPolymer->size()) try
{ {
Monomer prev = mPolymer->operator[](mIndex - 1); if (mIndex > 1 and mIndex + 2 < mPolymer->size())
Monomer next = mPolymer->operator[](mIndex + 1); {
Monomer nextNext = mPolymer->operator[](mIndex + 2); Monomer prev = mPolymer->operator[](mIndex - 1);
Monomer next = mPolymer->operator[](mIndex + 1);
result = DihedralAngle(prev.CAlpha().location(), CAlpha().location(), next.CAlpha().location(), nextNext.CAlpha().location()); Monomer nextNext = mPolymer->operator[](mIndex + 2);
result = DihedralAngle(prev.CAlpha().location(), CAlpha().location(), next.CAlpha().location(), nextNext.CAlpha().location());
}
} }
catch (const exception& ex)
{
if (VERBOSE)
cerr << ex.what() << endl;
}
return result; return result;
} }
...@@ -1162,6 +1184,8 @@ struct StructureImpl ...@@ -1162,6 +1184,8 @@ struct StructureImpl
if (modelNr.empty() or modelNr.as<uint32>() == mModelNr) if (modelNr.empty() or modelNr.as<uint32>() == mModelNr)
mAtoms.emplace_back(new AtomImpl(f, a["id"].as<string>(), a)); mAtoms.emplace_back(new AtomImpl(f, a["id"].as<string>(), a));
} }
sort(mAtoms.begin(), mAtoms.end(), [](auto& a, auto& b) { return a.id() < b.id(); });
} }
StructureImpl(const StructureImpl& si) StructureImpl(const StructureImpl& si)
...@@ -1180,9 +1204,9 @@ struct StructureImpl ...@@ -1180,9 +1204,9 @@ struct StructureImpl
void insertCompound(const string& compoundID, bool isEntity); void insertCompound(const string& compoundID, bool isEntity);
File* mFile; File* mFile;
uint32 mModelNr; uint32 mModelNr;
AtomView mAtoms; AtomView mAtoms;
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1268,11 +1292,11 @@ void StructureImpl::swapAtoms(Atom& a1, Atom& a2) ...@@ -1268,11 +1292,11 @@ void StructureImpl::swapAtoms(Atom& a1, Atom& a2)
auto l1 = r1.front()["label_atom_id"]; auto l1 = r1.front()["label_atom_id"];
auto l2 = r2.front()["label_atom_id"]; auto l2 = r2.front()["label_atom_id"];
swap(l1, l2); std::swap(l1, l2);
auto l3 = r1.front()["auth_atom_id"]; auto l3 = r1.front()["auth_atom_id"];
auto l4 = r2.front()["auth_atom_id"]; auto l4 = r2.front()["auth_atom_id"];
swap(l3, l4); std::swap(l3, l4);
} }
void StructureImpl::moveAtom(Atom& a, Point p) void StructureImpl::moveAtom(Atom& a, Point p)
...@@ -1346,7 +1370,7 @@ Structure::Structure(const Structure& rhs) ...@@ -1346,7 +1370,7 @@ Structure::Structure(const Structure& rhs)
{ {
} }
AtomView Structure::atoms() const const AtomView& Structure::atoms() const
{ {
return mImpl->mAtoms; return mImpl->mAtoms;
} }
...@@ -1420,13 +1444,13 @@ vector<Residue> Structure::nonPolymers() const ...@@ -1420,13 +1444,13 @@ vector<Residue> Structure::nonPolymers() const
Atom Structure::getAtomById(string id) const Atom Structure::getAtomById(string id) const
{ {
for (auto& a: mImpl->mAtoms) auto i = lower_bound(mImpl->mAtoms.begin(), mImpl->mAtoms.end(),
{ id, [](auto& a, auto& b) { return a.id() < b; });
if (a.id() == id)
return a; if (i == mImpl->mAtoms.end() or i->id() != id)
} throw out_of_range("Could not find atom with id " + id);
throw out_of_range("Could not find atom with id " + id); return *i;
} }
File& Structure::getFile() const File& Structure::getFile() const
......
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