cif::pdb::PDBFileParser Class Reference

Public Member Functions
	PDBFileParser ()
	~PDBFileParser ()
void	Parse (std::istream &is, cif::file &result)

Detailed Description

Definition at line 435 of file pdb2cif.cpp.

Constructor & Destructor Documentation

PDBFileParser()

cif::pdb::PDBFileParser::PDBFileParser ( )

inline

Definition at line 438 of file pdb2cif.cpp.

        : mData(nullptr)
        , mRec(nullptr)
    {
    }

~PDBFileParser()

cif::pdb::PDBFileParser::~PDBFileParser ( )

inline

Definition at line 444 of file pdb2cif.cpp.

    {
        PDBRecord *r = mData;
        while (r != nullptr)
        {
            PDBRecord *d = r;
            r = d->mNext;
            delete d;
        }
    }

Member Function Documentation

Parse()

void cif::pdb::PDBFileParser::Parse	(	std::istream &	is,
		cif::file &	result
	)

Definition at line 5719 of file pdb2cif.cpp.

{
    try
    {
        mDatablock.set_validator(result.get_validator());

        PreParseInput(is);

        mRec = mData;

        ParseTitle();

        ParseRemarks();
        ParsePrimaryStructure();
        ParseHeterogen();

        ConstructEntities();

        ParseRemark350();

        ParseSecondaryStructure();
        ParseConnectivtyAnnotation();
        ParseMiscellaneousFeatures();
        ParseCrystallographic();
        ParseCoordinateTransformation();

        uint32_t modelNr = 1;
        bool hasAtoms = false;

        while (mRec->is("MODEL ") or mRec->is("ATOM  ") or mRec->is("HETATM"))
        {
            bool model = false;
            if (mRec->is("MODEL "))
            {
                model = true;

                modelNr = vI(11, 14);

                GetNextRecord();
            }

            hasAtoms = hasAtoms or mRec->is("ATOM  ") or mRec->is("HETATM");

            ParseCoordinate(modelNr);

            if (model)
            {
                Match("ENDMDL", true);
                GetNextRecord();
            }
        }

        if (not hasAtoms)
            throw std::runtime_error("Either the PDB file has no atom records, or the field " + std::string(mRec->mName) + " is not at the correct location");

        for (auto e : mAtomTypes)
            getCategory("atom_type")->emplace({
                { "symbol", e } });

        // in V5, atom_type is sorted
        getCategory("atom_type")->reorder_by_index();

        ParseConnectivty();
        ParseBookkeeping();

        // almost done, now fix some outstanding issued that could not be done before

        try
        {
            auto r = FindRecord("REMARK   3");

            if (r != nullptr and Remark3Parser::parse(mExpMethod, r, mDatablock))
            {
                // make sure the "exptl" category is created
                auto exptl = getCategory("exptl");
                if (exptl->empty())
                {
                    exptl->emplace({
                        { "entry_id", mStructureID },
                        { "method", mExpMethod },
                        { "crystals_number", mRemark200["NUMBER OF CRYSTALS USED"] } });
                }
            }
        }
        catch (const std::exception &ex)
        {
            if (cif::VERBOSE >= 0)
                std::cerr << "Error parsing REMARK 3" << std::endl;
            throw;
        }
        //
        //      auto cat = getCategory("pdbx_refine_tls_group");
        //      for (Row r: *cat)
        //      {
        //          // add the mapped locations
        //
        //          try
        //          {
        //              std::string asymID;
        //              int resNum;
        //
        //              cif::tie(asymID, resNum) = r.get("beg_auth_asym_id", "beg_auth_seq_id");
        //
        //              r["beg_label_asym_id"] = asymID;
        //              r["beg_label_seq_id"] = resNum;
        //
        //              cif::tie(asymID, resNum) = r.get("end_auth_asym_id", "end_auth_seq_id");
        //
        //              r["end_label_asym_id"] = asymID;
        //              r["end_label_seq_id"] = resNum;
        //          }
        //          catch (const std::exception& ex)
        //          {
        //              continue;
        //          }
        //      }

        using namespace cif::literals;

        auto &atom_site = *getCategory("atom_site");

        for (auto r : getCategory("struct_conn")->find("pdbx_dist_value"_key == 0 or "pdbx_dist_value"_key == cif::null))
        {
            const auto &[asym1, seq1, atom1, symm1, asym2, seq2, atom2, symm2] = r.get<std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string>(
                "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
                    "ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry");

            float distance = 1.0f;

            try
            {
                auto a1 = atom_site.find1("label_asym_id"_key == asym1 and "label_seq_id"_key == seq1 and "label_atom_id"_key == atom1);
                auto a2 = atom_site.find1("label_asym_id"_key == asym2 and "label_seq_id"_key == seq2 and "label_atom_id"_key == atom2);

                if (not a1 or not a2)
                    throw std::runtime_error("cannot find atom");

                const auto &[x1, y1, z1] = a1.get<float, float, float>("cartn_x", "cartn_y", "cartn_z");
                const auto &[x2, y2, z2] = a2.get<float, float, float>("cartn_x", "cartn_y", "cartn_z");

                if ((symm1.empty() or symm1 == "1_555") and (symm2.empty() or symm2 == "1_555"))
                    distance = std::sqrt(
                        (x1 - x2) * (x1 - x2) +
                        (y1 - y2) * (y1 - y2) +
                        (z1 - z2) * (z1 - z2)
                    );
                else if (cif::VERBOSE > 0)
                    std::cerr << "Cannot calculate distance for link since one of the atoms is in another dimension" << std::endl;
            }
            catch (std::exception &ex)
            {
                if (cif::VERBOSE > 0)
                    std::cerr << "Error finding atom for LINK distance calculation: " << ex.what() << std::endl;
            }

            r["pdbx_dist_value"] = distance;
        }

        result.emplace_back(std::move(mDatablock));
    }
    catch (const std::exception &ex)
    {
        if (cif::VERBOSE >= 0)
        {
            std::cerr << "Error parsing PDB";
            if (mRec != nullptr)
                std::cerr << " at line " << mRec->mLineNr;
            std::cerr << std::endl;
        }
        throw;
    }
}

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

• libcifpp/src/pdb/pdb2cif.cpp