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libcifpp
Commit 88879a5d by Maarten L. Hekkelman
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for usage with clipper

parent 52919f96
Showing with 64 additions and 120 deletions
include/cif++/Point.hpp
......@@ -28,6 +28,10 @@
#include <functional>
#if HAVE_LIBCLIPPER
#include <clipper/core/coords.h>
#endif
#include "cif++/Config.hpp"
#include <boost/math/quaternion.hpp>
......@@ -58,21 +62,24 @@ struct PointF
PointF() : mX(0), mY(0), mZ(0) {}
PointF(FType x, FType y, FType z) : mX(x), mY(y), mZ(z) {}
// PointF(const clipper::Coord_orth& pt): mX(pt[0]), mY(pt[1]), mZ(pt[2]) {}
template<typename PF>
PointF(const PointF<PF>& pt)
: mX(static_cast<F>(pt.mX))
, mY(static_cast<F>(pt.mY))
, mZ(static_cast<F>(pt.mZ)) {}
// PointF& operator=(const clipper::Coord_orth& rhs)
// {
// mX = rhs[0];
// mY = rhs[1];
// mZ = rhs[2];
// return *this;
// }
#if HAVE_LIBCLIPPER
PointF(const clipper::Coord_orth& pt): mX(pt[0]), mY(pt[1]), mZ(pt[2]) {}
PointF& operator=(const clipper::Coord_orth& rhs)
{
mX = rhs[0];
mY = rhs[1];
mZ = rhs[2];
return *this;
}
#endif
template<typename PF>
PointF& operator=(const PointF<PF>& rhs)
......@@ -169,11 +176,13 @@ struct PointF
mZ = p.R_component_4();
}
// operator clipper::Coord_orth() const
// {
// return clipper::Coord_orth(mX, mY, mZ);
// }
#if HAVE_LIBCLIPPER
operator clipper::Coord_orth() const
{
return clipper::Coord_orth(mX, mY, mZ);
}
#endif
operator std::tuple<const FType&, const FType&, const FType&>() const
{
return std::make_tuple(std::ref(mX), std::ref(mY), std::ref(mZ));
......@@ -379,8 +388,7 @@ class SphericalDots
SphericalDots()
{
using namespace std;
const double
kGoldenRatio = (1 + std::sqrt(5.0)) / 2;
......
include/cif++/Structure.hpp
......@@ -66,6 +66,9 @@ class Atom
Atom(struct AtomImpl* impl);
Atom(const Atom& rhs);
// a special constructor to create symmetry copies
Atom(const Atom& rhs, const Point& symmmetry_location);
~Atom();
explicit operator bool() const { return mImpl_ != nullptr; }
......@@ -81,6 +84,10 @@ class Atom
Point location() const;
void location(Point p);
// for direct access to underlying data, be careful!
const cif::Row getRow() const;
const cif::Row getRowAniso() const;
// Atom symmetryCopy(const Point& d, const clipper::RTop_orth& rt);
// bool isSymmetryCopy() const;
// std::string symmetry() const;
......
src/Structure.cpp
......@@ -216,6 +216,16 @@ struct AtomImpl
// mLocation -= d;
// }
AtomImpl(const AtomImpl& impl, const Point& loc)
: mFile(impl.mFile), mID(impl.mID), mType(impl.mType), mAtomID(impl.mAtomID)
, mCompID(impl.mCompID), mAsymID(impl.mAsymID), mSeqID(impl.mSeqID)
, mAltID(impl.mAltID), mLocation(loc), mRefcount(1)
, mRow(impl.mRow), mCompound(impl.mCompound), mRadius(impl.mRadius)
, mCachedProperties(impl.mCachedProperties)
, mSymmetryCopy(true)
{
}
void prefetch()
{
// Prefetch some data
......@@ -237,53 +247,6 @@ struct AtomImpl
mCompound = Compound::create(compID);
}
// clipper::Atom toClipper() const
// {
// clipper::Atom result;
// result.set_coord_orth(mLocation);
// if (mRow["occupancy"].empty())
// result.set_occupancy(1.0);
// else
// result.set_occupancy(mRow["occupancy"].as<float>());
// std::string element = mRow["type_symbol"].as<std::string>();
// if (not mRow["pdbx_formal_charge"].empty())
// {
// int charge = mRow["pdbx_formal_charge"].as<int>();
// if (abs(charge) > 1)
// element += std::to_string(charge);
// if (charge < 0)
// element += '-';
// else
// element += '+';
// }
// result.set_element(element);
// if (not mRow["U_iso_or_equiv"].empty())
// result.set_u_iso(mRow["U_iso_or_equiv"].as<float>());
// else if (not mRow["B_iso_or_equiv"].empty())
// result.set_u_iso(mRow["B_iso_or_equiv"].as<float>() / (8 * kPI * kPI));
// else
// throw std::runtime_error("Missing B_iso or U_iso");
// auto& db = *mFile.impl().mDb;
// auto& cat = db["atom_site_anisotrop"];
// auto r = cat[cif::Key("id") == mID];
// if (r.empty())
// result.set_u_aniso_orth(clipper::U_aniso_orth(nan("0"), 0, 0, 0, 0, 0));
// else
// {
// float u11, u12, u13, u22, u23, u33;
// cif::tie(u11, u12, u13, u22, u23, u33) =
// r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]");
// result.set_u_aniso_orth(clipper::U_aniso_orth(u11, u22, u33, u12, u13, u23));
// }
// return result;
// }
void reference()
{
++mRefcount;
......@@ -396,14 +359,14 @@ struct AtomImpl
}
const File& mFile;
std::string mID;
std::string mID;
AtomType mType;
std::string mAtomID;
std::string mCompID;
std::string mAsymID;
std::string mAtomID;
std::string mCompID;
std::string mAsymID;
int mSeqID;
std::string mAltID;
std::string mAltID;
Point mLocation;
int mRefcount;
......@@ -455,6 +418,11 @@ Atom Atom::clone() const
return Atom(mImpl_ ? new AtomImpl(*mImpl_) : nullptr);
}
Atom::Atom(const Atom& rhs, const Point& loc)
: mImpl_(new AtomImpl(*rhs.mImpl_, loc))
{
}
Atom::Atom(const Atom& rhs)
: mImpl_(rhs.mImpl_)
{
......@@ -482,6 +450,18 @@ Atom& Atom::operator=(const Atom& rhs)
return *this;
}
const cif::Row Atom::getRow() const
{
return mImpl_->mRow;
}
const cif::Row Atom::getRowAniso() const
{
auto& db = *mImpl_->mFile.impl().mDb;
auto& cat = db["atom_site_anisotrop"];
return cat[cif::Key("id") == mImpl_->mID];
}
template<>
std::string Atom::property<std::string>(const std::string& name) const
{
......@@ -1583,57 +1563,6 @@ File::~File()
void File::load(const std::string& p)
{
mImpl->load(p);
// // all data is now in mFile, construct atoms and others
//
// auto& db = mFile.firstDatablock();
//
// // the entities
//
// struct entity
// {
// std::string id;
// std::string type;
// };
// std::vector<entity> entities;
//
// for (auto& _e: db["entity"])
// {
// std::string type = _e["type"];
// ba::to_lower(type);
// entities.push_back({ _e["id"], type });
// }
//
// auto& atomSites = db["atom_site"];
// for (auto& atomSite: atomSites)
// {
// AtomPtr ap(new Atom(this, atom_site));
//
// std::string entity_id = atom_site["entity_id"];
//
// auto e = find_if(entities.begin(), entities.end(), [=](entity& e) -> bool { return e.id == entity_id; });
// if (e == entities.end())
// throw std::runtime_error("Entity " + entity_id + " is not defined");
//
// std::string comp_id, asym_id, seq_id;
// cif::tie(comp_id, seq_id) = atom_site.get("label_comp_id", "label_asym_id", "label_seq_id");
//
// auto r = find_if(m_residues.begin(), m_residues.end(), [=](residue_ptr& res) -> bool
// {
//// return res.entities
// return false;
// });
//
// if (e->type == "water")
// ;
// else if (e->type == "polymer")
// ;
// else
// ;
//
// m_atoms.push_back(ap);
// }
}
void File::save(const std::string& file)
......
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