cif::CCD_compound_factory_impl Class Reference

Inheritance diagram for cif::CCD_compound_factory_impl:

Collaboration diagram for cif::CCD_compound_factory_impl:

Public Member Functions
	CCD_compound_factory_impl (std::shared_ptr< compound_factory_impl > next, const fs::path &file)
	CCD_compound_factory_impl (std::shared_ptr< compound_factory_impl > next)
compound *	create (const std::string &id) override
Public Member Functions inherited from cif::compound_factory_impl
	compound_factory_impl (std::shared_ptr< compound_factory_impl > next)
	compound_factory_impl (const fs::path &file, std::shared_ptr< compound_factory_impl > next)
virtual	~compound_factory_impl ()
compound *	get (std::string id)
std::shared_ptr< compound_factory_impl >	next () const
bool	is_known_peptide (const std::string &resName)
bool	is_known_base (const std::string &resName)

Public Attributes
cif::parser::datablock_index	mIndex
fs::path	mCompoundsFile

Additional Inherited Members
Protected Attributes inherited from cif::compound_factory_impl
std::shared_timed_mutex	mMutex
std::vector< compound * >	m_compounds
std::set< std::string >	m_known_peptides
std::set< std::string >	m_known_bases
std::set< std::string >	m_missing
std::shared_ptr< compound_factory_impl >	m_next

Detailed Description

Definition at line 465 of file compound.cpp.

Constructor & Destructor Documentation

CCD_compound_factory_impl() [1/2]

cif::CCD_compound_factory_impl::CCD_compound_factory_impl ( std::shared_ptr< compound_factory_impl >  next, const fs::path &  file  )

inline

Definition at line 468 of file compound.cpp.

        : compound_factory_impl(next)
        , mCompoundsFile(file)
    {
    }

CCD_compound_factory_impl() [2/2]

cif::CCD_compound_factory_impl::CCD_compound_factory_impl ( std::shared_ptr< compound_factory_impl >  next )

inline

Definition at line 474 of file compound.cpp.

        : compound_factory_impl(next)
    {
    }

Member Function Documentation

create()

compound * cif::CCD_compound_factory_impl::create ( const std::string &  id )

overridevirtual

Reimplemented from cif::compound_factory_impl.

Definition at line 485 of file compound.cpp.

{
    compound *result = nullptr;

    std::unique_ptr<std::istream> ccd;

    if (mCompoundsFile.empty())
    {
        ccd = cif::load_resource("components.cif");
        if (not ccd)
        {
            std::cerr << "Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data." << std::endl;
            return nullptr;
        }
    }
    else
        ccd.reset(new std::ifstream(mCompoundsFile));

    cif::file file;

    if (mIndex.empty())
    {
        if (cif::VERBOSE > 1)
        {
            std::cout << "Creating component index "
                      << "...";
            std::cout.flush();
        }

        cif::parser parser(*ccd, file);
        mIndex = parser.index_datablocks();

        if (cif::VERBOSE > 1)
            std::cout << " done" << std::endl;

        // reload the resource, perhaps this should be improved...
        if (mCompoundsFile.empty())
        {
            ccd = cif::load_resource("components.cif");
            if (not ccd)
                throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data.");
        }
        else
            ccd.reset(new std::ifstream(mCompoundsFile));
    }

    if (cif::VERBOSE > 1)
    {
        std::cout << "Loading component " << id << "...";
        std::cout.flush();
    }

    cif::parser parser(*ccd, file);
    parser.parse_single_datablock(id, mIndex);

    if (cif::VERBOSE > 1)
        std::cout << " done" << std::endl;

    if (not file.empty())
    {
        auto &db = file.front();
        if (db.name() == id)
        {
            result = new compound(db);

            std::shared_lock lock(mMutex);
            m_compounds.push_back(result);
        }
    }

    if (result == nullptr and cif::VERBOSE > 0)
        std::cerr << "Could not locate compound " << id << " in the CCD components file" << std::endl;

    return result;
}

Member Data Documentation

mCompoundsFile

fs::path cif::CCD_compound_factory_impl::mCompoundsFile

Definition at line 482 of file compound.cpp.

mIndex

cif::parser::datablock_index cif::CCD_compound_factory_impl::mIndex

Definition at line 481 of file compound.cpp.

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The documentation for this class was generated from the following file:

• libcifpp/src/compound.cpp