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libcifpp
Commit 3ebf4338 by Maarten L. Hekkelman
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Do not crash on uninitialized Atoms

parent 2eb4b7b3
Showing with 43 additions and 26 deletions
CMakeLists.txt
...@@ -43,10 +43,10 @@ set(CXX_EXTENSIONS OFF) ...@@ -43,10 +43,10 @@ set(CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_STANDARD_REQUIRED ON)
# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
find_package(Filesystem REQUIRED) find_package(Filesystem REQUIRED)
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
elseif(MSVC) elseif(MSVC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
......
include/cif++/Structure.hpp
...@@ -141,6 +141,8 @@ class Atom ...@@ -141,6 +141,8 @@ class Atom
void set_property(const std::string_view name, const std::string &value) void set_property(const std::string_view name, const std::string &value)
{ {
if (not mImpl)
throw std::logic_error("Error trying to modify an uninitialized atom");
mImpl->set_property(name, value); mImpl->set_property(name, value);
} }
...@@ -150,11 +152,16 @@ class Atom ...@@ -150,11 +152,16 @@ class Atom
set_property(name, std::to_string(value)); set_property(name, std::to_string(value));
} }
const std::string &id() const { return mImpl->mID; } const std::string &id() const { return impl().mID; }
AtomType type() const { return mImpl->mType; } AtomType type() const { return impl().mType; }
Point location() const { return mImpl->mLocation; } Point location() const { return impl().mLocation; }
void location(Point p) { mImpl->moveTo(p); } void location(Point p)
{
if (not mImpl)
throw std::logic_error("Error trying to modify an uninitialized atom");
mImpl->moveTo(p);
}
/// \brief Translate the position of this atom by \a t /// \brief Translate the position of this atom by \a t
void translate(Point t); void translate(Point t);
...@@ -169,33 +176,33 @@ class Atom ...@@ -169,33 +176,33 @@ class Atom
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2); void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
// for direct access to underlying data, be careful! // for direct access to underlying data, be careful!
const cif::Row getRow() const { return mImpl->mRow; } const cif::Row getRow() const { return impl().mRow; }
const cif::Row getRowAniso() const; const cif::Row getRowAniso() const;
bool isSymmetryCopy() const { return mImpl->mSymmetryCopy; } bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
std::string symmetry() const { return mImpl->mSymmetryOperator; } std::string symmetry() const { return impl().mSymmetryOperator; }
const Compound &comp() const { return mImpl->comp(); } const Compound &comp() const { return impl().comp(); }
bool isWater() const { return mImpl->mCompID == "HOH" or mImpl->mCompID == "H2O" or mImpl->mCompID == "WAT"; } bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
int charge() const; int charge() const;
float uIso() const; float uIso() const;
bool getAnisoU(float anisou[6]) const { return mImpl->getAnisoU(anisou); } bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
float occupancy() const; float occupancy() const;
// specifications // specifications
const std::string& labelAtomID() const { return mImpl->mAtomID; } const std::string& labelAtomID() const { return impl().mAtomID; }
const std::string& labelCompID() const { return mImpl->mCompID; } const std::string& labelCompID() const { return impl().mCompID; }
const std::string& labelAsymID() const { return mImpl->mAsymID; } const std::string& labelAsymID() const { return impl().mAsymID; }
std::string labelEntityID() const; std::string labelEntityID() const;
int labelSeqID() const { return mImpl->mSeqID; } int labelSeqID() const { return impl().mSeqID; }
const std::string& labelAltID() const { return mImpl->mAltID; } const std::string& labelAltID() const { return impl().mAltID; }
bool isAlternate() const { return not mImpl->mAltID.empty(); } bool isAlternate() const { return not impl().mAltID.empty(); }
std::string authAtomID() const; std::string authAtomID() const;
std::string authCompID() const; std::string authCompID() const;
std::string authAsymID() const; std::string authAsymID() const;
const std::string& authSeqID() const { return mImpl->mAuthSeqID; } const std::string& authSeqID() const { return impl().mAuthSeqID; }
std::string pdbxAuthInsCode() const; std::string pdbxAuthInsCode() const;
std::string pdbxAuthAltID() const; std::string pdbxAuthAltID() const;
...@@ -218,7 +225,7 @@ class Atom ...@@ -218,7 +225,7 @@ class Atom
std::swap(mImpl, b.mImpl); std::swap(mImpl, b.mImpl);
} }
int compare(const Atom &b) const { return mImpl->compare(*b.mImpl); } int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
bool operator<(const Atom &rhs) const bool operator<(const Atom &rhs) const
{ {
...@@ -232,26 +239,33 @@ class Atom ...@@ -232,26 +239,33 @@ class Atom
void setID(int id); void setID(int id);
const AtomImpl &impl() const
{
if (not mImpl)
throw std::runtime_error("Uninitialized atom, not found?");
return *mImpl;
}
std::shared_ptr<AtomImpl> mImpl; std::shared_ptr<AtomImpl> mImpl;
}; };
template <> template <>
inline std::string Atom::get_property<std::string>(const std::string_view name) const inline std::string Atom::get_property<std::string>(const std::string_view name) const
{ {
return mImpl->get_property(name); return impl().get_property(name);
} }
template <> template <>
inline int Atom::get_property<int>(const std::string_view name) const inline int Atom::get_property<int>(const std::string_view name) const
{ {
auto v = mImpl->get_property(name); auto v = impl().get_property(name);
return v.empty() ? 0 : stoi(v); return v.empty() ? 0 : stoi(v);
} }
template <> template <>
inline float Atom::get_property<float>(const std::string_view name) const inline float Atom::get_property<float>(const std::string_view name) const
{ {
return stof(mImpl->get_property(name)); return stof(impl().get_property(name));
} }
inline void swap(mmcif::Atom &a, mmcif::Atom &b) inline void swap(mmcif::Atom &a, mmcif::Atom &b)
......
src/PDB2Cif.cpp
...@@ -657,7 +657,7 @@ class PDBFileParser ...@@ -657,7 +657,7 @@ class PDBFileParser
int mSeqNum; int mSeqNum;
char mIcode; char mIcode;
int mDbSeqNum; int mDbSeqNum = 0;
bool mSeen = false; bool mSeen = false;
std::set<std::string> mAlts; std::set<std::string> mAlts;
...@@ -941,7 +941,10 @@ class PDBFileParser ...@@ -941,7 +941,10 @@ class PDBFileParser
std::string pdb2cifDate(std::string s) std::string pdb2cifDate(std::string s)
{ {
std::error_code ec; std::error_code ec;
return pdb2cifDate(s, ec); auto result = pdb2cifDate(s, ec);
if (ec and cif::VERBOSE > 0)
std::cerr << "Invalid date(" << s << "): " << ec.message() << std::endl;
return result;
} }
std::string pdb2cifAuth(std::string author) std::string pdb2cifAuth(std::string author)
......
test/unit-test.cpp
...@@ -1735,12 +1735,12 @@ BOOST_AUTO_TEST_CASE(t1) ...@@ -1735,12 +1735,12 @@ BOOST_AUTO_TEST_CASE(t1)
auto p2 = p1; auto p2 = p1;
Point c1 = CenterPoints(p1); CenterPoints(p1);
for (auto &p : p2) for (auto &p : p2)
p.rotate(q); p.rotate(q);
Point c2 = CenterPoints(p2); CenterPoints(p2);
auto q2 = AlignPoints(p1, p2); auto q2 = AlignPoints(p1, p2);
......
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