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Commit f5016403 by Maarten L. Hekkelman
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refactored mmcif::File

parent c8f66ae6
Showing with 277 additions and 333 deletions
changelog
Version 3.0.5
- mmcif::Structure redesign. It is now a wrapper around a cif::Datablock.
Version 3.0.4
- Fix in mmCIF parser, now correctly handles the unquoted
string ??
......
include/cif++/Cif++.hpp
......@@ -2169,17 +2169,21 @@ class File
File();
File(std::istream &is, bool validate = false);
File(const std::filesystem::path &path, bool validate = false);
File(const char *data, size_t length); // good luck trying to find out what it is...
File(File &&rhs);
File(const File &rhs) = delete;
File &operator=(const File &rhs) = delete;
~File();
virtual ~File();
virtual void load(const std::filesystem::path &p);
virtual void save(const std::filesystem::path &p);
void load(const std::filesystem::path &p);
void save(const std::filesystem::path &p);
virtual void load(std::istream &is);
virtual void save(std::ostream &os);
void load(std::istream &is);
void save(std::ostream &os);
virtual void load(const char *data, std::size_t length);
/// \brief Load only the data block \a datablock from the mmCIF file
void load(std::istream &is, const std::string &datablock);
......@@ -2211,6 +2215,12 @@ class File
void append(Datablock *e);
Datablock &emplace(std::string_view name)
{
append(new Datablock(name));
return back();
}
Datablock *get(std::string_view name) const;
Datablock &operator[](std::string_view name);
......@@ -2248,6 +2258,9 @@ class File
iterator begin() const;
iterator end() const;
Datablock &front();
Datablock &back();
bool empty() const { return mHead == nullptr; }
const Validator &getValidator() const;
......
include/cif++/Point.hpp
......@@ -221,7 +221,7 @@ struct PointF
FType length() const
{
return sqrt(mX * mX + mY * mY + mZ * mZ);
return std::sqrt(mX * mX + mY * mY + mZ * mZ);
}
};
......@@ -285,7 +285,7 @@ inline double DistanceSquared(const PointF<F> &a, const PointF<F> &b)
template <typename F>
inline double Distance(const PointF<F> &a, const PointF<F> &b)
{
return sqrt(
return std::sqrt(
(a.mX - b.mX) * (a.mX - b.mX) +
(a.mY - b.mY) * (a.mY - b.mY) +
(a.mZ - b.mZ) * (a.mZ - b.mZ));
......@@ -332,10 +332,10 @@ double DihedralAngle(const PointF<F> &p1, const PointF<F> &p2, const PointF<F> &
double result = 360;
if (u > 0 and v > 0)
{
u = DotProduct(p, x) / sqrt(u);
v = DotProduct(p, y) / sqrt(v);
u = DotProduct(p, x) / std::sqrt(u);
v = DotProduct(p, y) / std::sqrt(v);
if (u != 0 or v != 0)
result = atan2(v, u) * 180 / kPI;
result = std::atan2(v, u) * 180 / kPI;
}
return result;
......@@ -351,7 +351,7 @@ double CosinusAngle(const PointF<F> &p1, const PointF<F> &p2, const PointF<F> &p
double x = DotProduct(v12, v12) * DotProduct(v34, v34);
if (x > 0)
result = DotProduct(v12, v34) / sqrt(x);
result = DotProduct(v12, v34) / std::sqrt(x);
return result;
}
......@@ -436,9 +436,9 @@ class SphericalDots
double lat = std::asin((2.0 * i) / P);
double lon = std::fmod(i, kGoldenRatio) * 2 * kPI / kGoldenRatio;
p->mX = sin(lon) * cos(lat);
p->mY = cos(lon) * cos(lat);
p->mZ = sin(lat);
p->mX = std::sin(lon) * std::cos(lat);
p->mY = std::cos(lon) * std::cos(lat);
p->mZ = std::sin(lat);
++p;
}
......
include/cif++/Structure.hpp
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
......@@ -34,16 +34,16 @@
#include "cif++/Point.hpp"
/*
To modify a structure, you will have to use actions.
The currently supported actions are:
To modify a structure, you will have to use actions.
The currently supported actions are:
// - Move atom to new location
- Remove atom
- Remove atom
// - Add new atom that was formerly missing
// - Add alternate Residue
-
-
*/
namespace mmcif
......@@ -61,7 +61,6 @@ class File;
class Atom
{
private:
struct AtomImpl : public std::enable_shared_from_this<AtomImpl>
{
AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row);
......@@ -99,7 +98,7 @@ class Atom
int mRefcount;
cif::Row mRow;
mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
mutable std::vector<std::tuple<std::string, cif::detail::ItemReference>> mCachedRefs;
mutable const Compound *mCompound = nullptr;
......@@ -110,14 +109,17 @@ class Atom
};
public:
Atom() {}
Atom(std::shared_ptr<AtomImpl> impl)
: mImpl(impl) {}
: mImpl(impl)
{
}
Atom(const Atom &rhs)
: mImpl(rhs.mImpl) {}
: mImpl(rhs.mImpl)
{
}
Atom(cif::Datablock &db, cif::Row &row);
......@@ -152,10 +154,10 @@ class Atom
set_property(name, std::to_string(value));
}
const std::string &id() const { return impl().mID; }
AtomType type() const { return impl().mType; }
const std::string &id() const { return impl().mID; }
AtomType type() const { return impl().mType; }
Point location() const { return impl().mLocation; }
Point location() const { return impl().mLocation; }
void location(Point p)
{
if (not mImpl)
......@@ -176,33 +178,33 @@ class Atom
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
// for direct access to underlying data, be careful!
const cif::Row getRow() const { return impl().mRow; }
const cif::Row getRow() const { return impl().mRow; }
const cif::Row getRowAniso() const;
bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
std::string symmetry() const { return impl().mSymmetryOperator; }
bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
std::string symmetry() const { return impl().mSymmetryOperator; }
const Compound &comp() const { return impl().comp(); }
bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
const Compound &comp() const { return impl().comp(); }
bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
int charge() const;
float uIso() const;
bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
float occupancy() const;
// specifications
const std::string& labelAtomID() const { return impl().mAtomID; }
const std::string& labelCompID() const { return impl().mCompID; }
const std::string& labelAsymID() const { return impl().mAsymID; }
const std::string &labelAtomID() const { return impl().mAtomID; }
const std::string &labelCompID() const { return impl().mCompID; }
const std::string &labelAsymID() const { return impl().mAsymID; }
std::string labelEntityID() const;
int labelSeqID() const { return impl().mSeqID; }
const std::string& labelAltID() const { return impl().mAltID; }
bool isAlternate() const { return not impl().mAltID.empty(); }
int labelSeqID() const { return impl().mSeqID; }
const std::string &labelAltID() const { return impl().mAltID; }
bool isAlternate() const { return not impl().mAltID.empty(); }
std::string authAtomID() const;
std::string authCompID() const;
std::string authAsymID() const;
const std::string& authSeqID() const { return impl().mAuthSeqID; }
const std::string &authSeqID() const { return impl().mAuthSeqID; }
std::string pdbxAuthInsCode() const;
std::string pdbxAuthAltID() const;
......@@ -225,7 +227,7 @@ class Atom
std::swap(mImpl, b.mImpl);
}
int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
bool operator<(const Atom &rhs) const
{
......@@ -487,31 +489,33 @@ class Polymer : public std::vector<Monomer>
// file is a reference to the data stored in e.g. the cif file.
// This object is not copyable.
class File : public std::enable_shared_from_this<File>
class File : public cif::File
{
public:
File();
File(const std::filesystem::path &path);
File(const char *data, size_t length); // good luck trying to find out what it is...
~File();
File() {}
File(const File &) = delete;
File &operator=(const File &) = delete;
cif::Datablock& createDatablock(const std::string_view name);
File(const std::filesystem::path &path)
{
load(path);
}
void load(const std::filesystem::path &path);
void save(const std::filesystem::path &path);
File(const char *data, size_t length)
{
load(data, length);
}
Structure *model(size_t nr = 1);
File(const File &) = delete;
File &operator=(const File &) = delete;
struct FileImpl &impl() const { return *mImpl; }
void load(const std::filesystem::path &p) override;
void save(const std::filesystem::path &p) override;
cif::Datablock &data();
cif::File &file();
void load(std::istream &is) override;
using cif::File::save;
using cif::File::load;
private:
struct FileImpl *mImpl;
cif::Datablock &data() { return front(); }
};
// --------------------------------------------------------------------
......@@ -531,14 +535,18 @@ inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
class Structure
{
public:
Structure(File &p, size_t modelNr = 1, StructureOpenOptions options = {});
Structure &operator=(const Structure &) = delete;
~Structure();
Structure(File &p, size_t modelNr = 1, StructureOpenOptions options = {})
: Structure(p.firstDatablock(), modelNr, options)
{
}
Structure(cif::Datablock &db, size_t modelNr = 1, StructureOpenOptions options = {});
// Create a read-only clone of the current structure (for multithreaded calculations that move atoms)
Structure(const Structure &);
File &getFile() const;
Structure &operator=(const Structure &) = delete;
~Structure();
const AtomView &atoms() const { return mAtoms; }
AtomView waters() const;
......@@ -655,8 +663,15 @@ class Structure
void cleanupEmptyCategories();
/// \brief Direct access to underlying data
cif::Category &category(std::string_view name) const;
cif::Datablock &datablock() const;
cif::Category &category(std::string_view name) const
{
return mDb[name];
}
cif::Datablock &datablock() const
{
return mDb;
}
private:
friend Polymer;
......@@ -671,7 +686,7 @@ class Structure
void loadAtomsForModel(StructureOpenOptions options);
File &mFile;
cif::Datablock &mDb;
size_t mModelNr;
AtomView mAtoms;
std::vector<size_t> mAtomIndex;
......
src/BondMap.cpp
......@@ -233,7 +233,7 @@ BondMap::BondMap(const Structure &p)
link[b].insert(a);
};
cif::Datablock &db = p.getFile().data();
cif::Datablock &db = p.datablock();
// collect all compounds first
std::set<std::string> compounds;
......
src/Cif++.cpp
......@@ -2408,7 +2408,7 @@ namespace detail
size_t writeValue(std::ostream &os, std::string value, size_t offset, size_t width)
{
if (value.find('\n') != std::string::npos or width == 0 or value.length() >= 132) // write as text field
if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field
{
ba::replace_all(value, "\n;", "\n\\;");
......@@ -2511,7 +2511,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
if (not isUnquotedString(v->mText))
l += 2;
if (l >= 132)
if (l > 132)
continue;
if (columnWidths[v->mColumnIndex] < l + 1)
......@@ -2547,7 +2547,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
if (l < w)
l = w;
if (offset + l >= 132 and offset > 0)
if (offset + l > 132 and offset > 0)
{
os << std::endl;
offset = 0;
......@@ -2555,7 +2555,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
offset = detail::writeValue(os, s, offset, w);
if (offset >= 132)
if (offset > 132)
{
os << std::endl;
offset = 0;
......@@ -3367,6 +3367,11 @@ File::File(const std::filesystem::path &path, bool validate)
}
}
File::File(const char *data, std::size_t length)
{
load(data, length);
}
File::File(File &&rhs)
: mHead(nullptr)
, mValidator(nullptr)
......@@ -3483,6 +3488,25 @@ void File::load(std::istream &is, const std::string &datablock)
}
}
void File::load(const char *data, std::size_t length)
{
bool gzipped = length > 2 and data[0] == static_cast<char>(0x1f) and data[1] == static_cast<char>(0x8b);
struct membuf : public std::streambuf
{
membuf(char *data, size_t length) { this->setg(data, data, data + length); }
} buffer(const_cast<char *>(data), length);
std::istream is(&buffer);
io::filtering_stream<io::input> in;
if (gzipped)
in.push(io::gzip_decompressor());
in.push(is);
load(is);
}
void File::save(std::ostream &os)
{
Datablock *e = mHead;
......@@ -3523,6 +3547,21 @@ Datablock &File::operator[](std::string_view name)
return *result;
}
Datablock &File::front()
{
assert(mHead);
return *mHead;
}
Datablock &File::back()
{
assert(mHead);
auto *block = mHead;
while (block->mNext != nullptr)
block = block->mNext;
return *block;
}
bool File::isValid()
{
if (mValidator == nullptr)
......
src/Point.cpp
......@@ -301,7 +301,7 @@ std::tuple<double,Point> QuaternionToAngleAxis(Quaternion q)
q = Normalize(q);
// angle:
double angle = 2 * acos(q.R_component_1());
double angle = 2 * std::acos(q.R_component_1());
angle = angle * 180 / kPI;
// axis:
......
src/Secondary.cpp
......@@ -535,7 +535,7 @@ double CalculateHBondEnergy(Res &inDonor, Res &inAcceptor)
result = kCouplingConstant / distanceHO - kCouplingConstant / distanceHC + kCouplingConstant / distanceNC - kCouplingConstant / distanceNO;
// DSSP compatibility mode:
result = round(result * 1000) / 1000;
result = std::round(result * 1000) / 1000;
if (result < kMinHBondEnergy)
result = kMinHBondEnergy;
......@@ -1230,7 +1230,7 @@ DSSPImpl::DSSPImpl(const Structure &s, int min_poly_proline_stretch_length)
void DSSPImpl::calculateSecondaryStructure()
{
auto &db = mStructure.getFile().data();
auto &db = mStructure.datablock();
for (auto r : db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
{
std::string asym1, asym2;
......
src/Structure.cpp
......@@ -50,157 +50,6 @@ namespace mmcif
{
// --------------------------------------------------------------------
// FileImpl
struct FileImpl
{
cif::File mData;
cif::Datablock *mDb = nullptr;
void load_data(const char *data, size_t length);
void load(const std::filesystem::path &path);
void save(const std::filesystem::path &path);
};
void FileImpl::load_data(const char *data, size_t length)
{
bool gzipped = length > 2 and data[0] == static_cast<char>(0x1f) and data[1] == static_cast<char>(0x8b);
try
{
// First try mmCIF
struct membuf : public std::streambuf
{
membuf(char *data, size_t length) { this->setg(data, data, data + length); }
} buffer(const_cast<char *>(data), length);
std::istream is(&buffer);
io::filtering_stream<io::input> in;
if (gzipped)
in.push(io::gzip_decompressor());
in.push(is);
mData.load(in);
}
catch (const cif::CifParserError &e)
{
// First try mmCIF
struct membuf : public std::streambuf
{
membuf(char *data, size_t length) { this->setg(data, data, data + length); }
} buffer(const_cast<char *>(data), length);
std::istream is(&buffer);
io::filtering_stream<io::input> in;
if (gzipped)
in.push(io::gzip_decompressor());
in.push(is);
ReadPDBFile(in, mData);
}
// Yes, we've parsed the data. Now locate the datablock.
mDb = &mData.firstDatablock();
// And validate, otherwise lots of functionality won't work
// if (mData.getValidator() == nullptr)
mData.loadDictionary("mmcif_pdbx_v50");
if (not mData.isValid() and cif::VERBOSE >= 0)
std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
}
void FileImpl::load(const std::filesystem::path &path)
{
std::ifstream inFile(path, std::ios_base::in | std::ios_base::binary);
if (not inFile.is_open())
throw std::runtime_error("No such file: " + path.string());
io::filtering_stream<io::input> in;
std::string ext = path.extension().string();
if (path.extension() == ".gz")
{
in.push(io::gzip_decompressor());
ext = path.stem().extension().string();
}
in.push(inFile);
try
{
// OK, we've got the file, now create a protein
if (ext == ".cif")
mData.load(in);
else if (ext == ".pdb" or ext == ".ent")
ReadPDBFile(in, mData);
else
{
try
{
if (cif::VERBOSE > 0)
std::cerr << "unrecognized file extension, trying cif" << std::endl;
mData.load(in);
}
catch (const cif::CifParserError &e)
{
if (cif::VERBOSE > 0)
std::cerr << "Not cif, trying plain old PDB" << std::endl;
// pffft...
in.reset();
if (inFile.is_open())
inFile.seekg(0);
else
inFile.open(path, std::ios_base::in | std::ios::binary);
if (path.extension() == ".gz")
in.push(io::gzip_decompressor());
in.push(inFile);
ReadPDBFile(in, mData);
}
}
}
catch (const std::exception &ex)
{
if (cif::VERBOSE >= 0)
std::cerr << "Error trying to load file " << path << std::endl;
throw;
}
// Yes, we've parsed the data. Now locate the datablock.
mDb = &mData.firstDatablock();
// And validate, otherwise lots of functionality won't work
// if (mData.getValidator() == nullptr)
mData.loadDictionary("mmcif_pdbx_v50");
if (not mData.isValid() and cif::VERBOSE >= 0)
std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
}
void FileImpl::save(const std::filesystem::path &path)
{
std::ofstream outFile(path, std::ios_base::out | std::ios_base::binary);
io::filtering_stream<io::output> out;
if (path.extension() == ".gz")
out.push(io::gzip_compressor());
out.push(outFile);
if (path.extension() == ".pdb")
WritePDBFile(out, mData);
else
mData.save(out);
}
// --------------------------------------------------------------------
// Atom
Atom::AtomImpl::AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row)
......@@ -1131,10 +980,10 @@ bool Monomer::areBonded(const Monomer &a, const Monomer &b, float errorMargin)
auto distanceCACA = Distance(atoms[0], atoms[3]);
double omega = DihedralAngle(atoms[0], atoms[1], atoms[2], atoms[3]);
bool cis = abs(omega) <= 30.0;
bool cis = std::abs(omega) <= 30.0;
float maxCACADistance = cis ? 3.0f : 3.8f;
result = abs(distanceCACA - maxCACADistance) < errorMargin;
result = std::abs(distanceCACA - maxCACADistance) < errorMargin;
}
catch (...)
{
......@@ -1242,7 +1091,7 @@ int Polymer::Distance(const Monomer &a, const Monomer &b) const
ixb = ix, ++f;
if (f == 2)
{
result = abs(ixa - ixb);
result = std::abs(ixa - ixb);
break;
}
}
......@@ -1254,81 +1103,120 @@ int Polymer::Distance(const Monomer &a, const Monomer &b) const
// --------------------------------------------------------------------
// File
File::File()
: mImpl(new FileImpl)
void File::load(const std::filesystem::path &path)
{
}
std::ifstream inFile(path, std::ios_base::in | std::ios_base::binary);
if (not inFile.is_open())
throw std::runtime_error("No such file: " + path.string());
File::File(const char *data, size_t length)
: mImpl(new FileImpl)
{
mImpl->load_data(data, length);
}
io::filtering_stream<io::input> in;
std::string ext = path.extension().string();
File::File(const std::filesystem::path &File)
: mImpl(new FileImpl)
{
load(File);
}
if (path.extension() == ".gz")
{
in.push(io::gzip_decompressor());
ext = path.stem().extension().string();
}
File::~File()
{
delete mImpl;
}
in.push(inFile);
cif::Datablock &File::createDatablock(const std::string_view name)
{
auto db = new cif::Datablock(name);
try
{
// OK, we've got the file, now create a protein
if (ext == ".cif")
load(in);
else if (ext == ".pdb" or ext == ".ent")
ReadPDBFile(in, *this);
else
{
try
{
if (cif::VERBOSE > 0)
std::cerr << "unrecognized file extension, trying cif" << std::endl;
mImpl->mData.append(db);
mImpl->mDb = db;
cif::File::load(in);
}
catch (const cif::CifParserError &e)
{
if (cif::VERBOSE > 0)
std::cerr << "Not cif, trying plain old PDB" << std::endl;
return *mImpl->mDb;
}
// pffft...
in.reset();
void File::load(const std::filesystem::path &p)
{
mImpl->load(p);
}
if (inFile.is_open())
inFile.seekg(0);
else
inFile.open(path, std::ios_base::in | std::ios::binary);
void File::save(const std::filesystem::path &file)
{
mImpl->save(file);
if (path.extension() == ".gz")
in.push(io::gzip_decompressor());
in.push(inFile);
ReadPDBFile(in, *this);
}
}
}
catch (const std::exception &ex)
{
if (cif::VERBOSE >= 0)
std::cerr << "Error trying to load file " << path << std::endl;
throw;
}
// validate, otherwise lots of functionality won't work
loadDictionary("mmcif_pdbx_v50");
if (not isValid() and cif::VERBOSE >= 0)
std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
}
cif::Datablock &File::data()
void File::load(std::istream &is)
{
assert(mImpl);
assert(mImpl->mDb);
if (mImpl == nullptr or mImpl->mDb == nullptr)
throw std::runtime_error("No data loaded");
try
{
cif::File::load(is);
}
catch (const cif::CifParserError &e)
{
ReadPDBFile(is, *this);
}
return *mImpl->mDb;
// validate, otherwise lots of functionality won't work
loadDictionary("mmcif_pdbx_v50");
if (not isValid() and cif::VERBOSE >= 0)
std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
}
cif::File &File::file()
void File::save(const std::filesystem::path &path)
{
assert(mImpl);
fs::path file = path.filename();
std::ofstream outFile(path, std::ios_base::out | std::ios_base::binary);
io::filtering_stream<io::output> out;
if (file.extension() == ".gz")
{
out.push(io::gzip_compressor());
file.replace_extension("");
}
if (mImpl == nullptr)
throw std::runtime_error("No data loaded");
out.push(outFile);
return mImpl->mData;
if (file.extension() == ".pdb")
WritePDBFile(out, *this);
else
cif::File::save(out);
}
// --------------------------------------------------------------------
// Structure
Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
: mFile(f)
Structure::Structure(cif::Datablock &db, size_t modelNr, StructureOpenOptions options)
: mDb(db)
, mModelNr(modelNr)
{
auto db = mFile.impl().mDb;
if (db == nullptr)
throw std::logic_error("Empty file!");
auto &atomCat = (*db)["atom_site"];
auto &atomCat = db["atom_site"];
loadAtomsForModel(options);
......@@ -1357,8 +1245,8 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
void Structure::loadAtomsForModel(StructureOpenOptions options)
{
auto db = mFile.impl().mDb;
auto &atomCat = (*db)["atom_site"];
auto &db = datablock();
auto &atomCat = db["atom_site"];
for (auto &a : atomCat)
{
......@@ -1373,12 +1261,12 @@ void Structure::loadAtomsForModel(StructureOpenOptions options)
if ((options bitand StructureOpenOptions::SkipHydrogen) and type_symbol == "H")
continue;
mAtoms.emplace_back(std::make_shared<Atom::AtomImpl>(*db, id, a));
mAtoms.emplace_back(std::make_shared<Atom::AtomImpl>(db, id, a));
}
}
Structure::Structure(const Structure &s)
: mFile(s.mFile)
: mDb(s.mDb)
, mModelNr(s.mModelNr)
{
mAtoms.reserve(s.mAtoms.size());
......@@ -1677,21 +1565,10 @@ const Residue &Structure::getResidue(const mmcif::Atom &atom) const
return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID());
}
File &Structure::getFile() const
{
return mFile;
}
cif::Category &Structure::category(std::string_view name) const
{
auto &db = datablock();
return db[name];
}
std::tuple<char, int, char> Structure::MapLabelToAuth(
const std::string &asymID, int seqID) const
{
auto &db = *getFile().impl().mDb;
auto &db = datablock();
std::tuple<char, int, char> result;
bool found = false;
......@@ -1841,11 +1718,6 @@ std::tuple<std::string, int, std::string> Structure::MapPDBToLabel(const std::st
return result;
}
cif::Datablock &Structure::datablock() const
{
return *mFile.impl().mDb;
}
std::string Structure::insertCompound(const std::string &compoundID, bool isEntity)
{
using namespace cif::literals;
......@@ -1854,7 +1726,7 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
if (compound == nullptr)
throw std::runtime_error("Trying to insert unknown compound " + compoundID + " (not found in CCD)");
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
auto &chemComp = db["chem_comp"];
auto r = chemComp.find(cif::Key("id") == compoundID);
......@@ -1899,7 +1771,7 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
void Structure::removeAtom(Atom &a)
{
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
auto &atomSites = db["atom_site"];
......@@ -1922,12 +1794,11 @@ void Structure::removeAtom(Atom &a)
void Structure::removeResidue(const std::string &asym_id, int seq_id)
{
}
void Structure::swapAtoms(Atom &a1, Atom &a2)
{
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
auto &atomSites = db["atom_site"];
auto rs1 = atomSites.find(cif::Key("id") == a1.id());
......@@ -1963,7 +1834,7 @@ void Structure::changeResidue(Residue &res, const std::string &newCompound,
{
using namespace cif::literals;
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
std::string asymID = res.asymID();
const auto compound = CompoundFactory::instance().create(newCompound);
......@@ -2073,7 +1944,7 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
{
using namespace cif::literals;
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
auto &struct_asym = db["struct_asym"];
std::string asym_id = struct_asym.getUniqueID();
......@@ -2093,8 +1964,7 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
{
auto atom_id = atom_site.getUniqueID("");
auto &&[row, inserted] = atom_site.emplace({
{"group_PDB", atom.get_property<std::string>("group_PDB")},
auto &&[row, inserted] = atom_site.emplace({{"group_PDB", atom.get_property<std::string>("group_PDB")},
{"id", atom_id},
{"type_symbol", atom.get_property<std::string>("type_symbol")},
{"label_atom_id", atom.get_property<std::string>("label_atom_id")},
......@@ -2127,7 +1997,7 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
{
using namespace cif::literals;
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
auto &struct_asym = db["struct_asym"];
std::string asym_id = struct_asym.getUniqueID();
......@@ -2143,23 +2013,27 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
auto &res = mNonPolymers.emplace_back(*this, comp_id, asym_id);
auto appendUnlessSet = [](std::vector<cif::Item> &ai, cif::Item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](cif::Item &ci) { return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
for (auto &atom : atom_info)
{
auto atom_id = atom_site.getUniqueID("");
atom.insert(atom.end(), {
{"group_PDB", "HETATM"},
{"id", atom_id},
{"label_comp_id", comp_id},
{"label_asym_id", asym_id},
{"label_seq_id", ""},
{"label_entity_id", entity_id},
{"auth_comp_id", comp_id},
{"auth_asym_id", asym_id},
{"auth_seq_id", ""},
{"pdbx_PDB_model_num", 1},
{"label_alt_id", ""}
});
appendUnlessSet(atom, { "group_PDB", "HETATM"} );
appendUnlessSet(atom, { "id", atom_id} );
appendUnlessSet(atom, { "label_comp_id", comp_id} );
appendUnlessSet(atom, { "label_asym_id", asym_id} );
appendUnlessSet(atom, { "label_seq_id", ""} );
appendUnlessSet(atom, { "label_entity_id", entity_id} );
appendUnlessSet(atom, { "auth_comp_id", comp_id} );
appendUnlessSet(atom, { "auth_asym_id", asym_id} );
appendUnlessSet(atom, { "auth_seq_id", ""} );
appendUnlessSet(atom, { "pdbx_PDB_model_num", 1} );
appendUnlessSet(atom, { "label_alt_id", ""} );
auto &&[row, inserted] = atom_site.emplace(atom.begin(), atom.end());
......@@ -2174,7 +2048,7 @@ void Structure::cleanupEmptyCategories()
{
using namespace cif::literals;
cif::Datablock &db = *mFile.impl().mDb;
cif::Datablock &db = datablock();
auto &atomSite = db["atom_site"];
......
test/rename-compound-test.cpp
......@@ -37,7 +37,7 @@ int main(int argc, char* argv[])
structure.cleanupEmptyCategories();
f.file().save(std::cout);
f.save(std::cout);
}
catch (const std::exception& e)
{
......
test/structure-test.cpp
......@@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1)
cif::VERBOSE = 1;
mmcif::File file;
file.file().loadDictionary("mmcif_pdbx_v50.dic");
file.createDatablock("TEST"); // create a datablock
file.loadDictionary("mmcif_pdbx_v50.dic");
file.emplace("TEST"); // create a datablock
mmcif::Structure structure(file);
......@@ -171,12 +171,12 @@ _struct_asym.details ?
expected.loadDictionary("mmcif_pdbx_v50.dic");
if (not (expected.firstDatablock() == structure.getFile().data()))
if (not (expected.firstDatablock() == structure.datablock()))
{
BOOST_TEST(false);
std::cout << expected.firstDatablock() << std::endl
<< std::endl
<< structure.getFile().data() << std::endl;
<< structure.datablock() << std::endl;
}
}
......
test/unit-test.cpp
......@@ -1626,7 +1626,7 @@ PRO OXT HXT SING N N 17
mmcif::File file(example.string());
mmcif::Structure structure(file);
(void)file.file().isValid();
(void)file.isValid();
mmcif::BondMap bm(structure);
......
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