cif::CCP4_compound_factory_impl Class Reference

Inheritance diagram for cif::CCP4_compound_factory_impl:

Collaboration diagram for cif::CCP4_compound_factory_impl:

Public Member Functions
	CCP4_compound_factory_impl (const fs::path &clibd_mon, std::shared_ptr< compound_factory_impl > next=nullptr)
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)

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 564 of file compound.cpp.

Constructor & Destructor Documentation

CCP4_compound_factory_impl()

cif::CCP4_compound_factory_impl::CCP4_compound_factory_impl	(	const fs::path &	clibd_mon,
		std::shared_ptr< compound_factory_impl >	next = nullptr
	)

Definition at line 576 of file compound.cpp.

    : compound_factory_impl(next)
    , m_file((clibd_mon / "list" / "mon_lib_list.cif").string())
    , m_CLIBD_MON(clibd_mon)
{
    const std::regex peptideRx("(?:[lmp]-)?peptide", std::regex::icase);

    auto &chemComps = m_file["comp_list"]["chem_comp"];

    for (const auto &[group, threeLetterCode] : chemComps.rows<std::string, std::string>("group", "three_letter_code"))
    {
        if (std::regex_match(group, peptideRx))
            m_known_peptides.insert(threeLetterCode);
        else if (cif::iequals(group, "DNA") or cif::iequals(group, "RNA"))
            m_known_bases.insert(threeLetterCode);
    }
}

Member Function Documentation

create()

compound * cif::CCP4_compound_factory_impl::create ( const std::string &  id )

overridevirtual

Reimplemented from cif::compound_factory_impl.

Definition at line 594 of file compound.cpp.

{
    compound *result = nullptr;

    auto &cat = m_file["comp_list"]["chem_comp"];

    auto rs = cat.find(cif::key("three_letter_code") == id);

    if (rs.size() == 1)
    {
        auto row = rs.front();

        std::string name, group;
        uint32_t numberAtomsAll, numberAtomsNh;
        cif::tie(name, group, numberAtomsAll, numberAtomsNh) =
            row.get("name", "group", "number_atoms_all", "number_atoms_nh");

        fs::path resFile = m_CLIBD_MON / cif::to_lower_copy(id.substr(0, 1)) / (id + ".cif");

        if (not fs::exists(resFile) and (id == "COM" or id == "CON" or "PRN")) // seriously...
            resFile = m_CLIBD_MON / cif::to_lower_copy(id.substr(0, 1)) / (id + '_' + id + ".cif");

        if (fs::exists(resFile))
        {
            cif::file cf(resFile.string());

            // locate the datablock
            auto &db = cf["comp_" + id];

            std::string type;

            // known groups are (counted from ccp4 monomer dictionary)

            //  D-pyranose
            //  DNA
            //  L-PEPTIDE LINKING
            //  L-SACCHARIDE
            //  L-peptide
            //  L-pyranose
            //  M-peptide
            //  NON-POLYMER
            //  P-peptide
            //  RNA
            //  furanose
            //  non-polymer
            //  non_polymer
            //  peptide
            //  pyranose
            //  saccharide

            if (cif::iequals(id, "gly"))
                type = "peptide linking";
            else if (cif::iequals(group, "l-peptide") or cif::iequals(group, "L-peptide linking") or cif::iequals(group, "peptide") or cif::iequals(group, "p-peptide"))
                type = "L-peptide linking";
            else if (cif::iequals(group, "DNA"))
                type = "DNA linking";
            else if (cif::iequals(group, "RNA"))
                type = "RNA linking";
            else
                type = "non-polymer";

            m_compounds.push_back(new compound(db, id, name, type, group));
            result = m_compounds.back();
        }
    }

    return result;
}

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

• libcifpp/src/compound.cpp