PkaPhPiDataParser Class

The PkaPhPiDataParser class provides a file reader for the pKa, pH, pI data XML file. More...

Public Functions

	PkaPhPiDataParser(const MsXpS::libXpertMassCore::PolChemDefCstSPtr &pol_chem_def_csp, const QString &file_path = QString())
	~PkaPhPiDataParser()
const QString &	filePath()
bool	renderXmlFile(std::vector<MsXpS::libXpertMassCore::MonomerSPtr> &monomers, std::vector<MsXpS::libXpertMassCore::ModifSPtr> &modifs)
void	setFilePath(const QString &file_path)

Protected Variables

Detailed Description

The format is the following:

<pkaphpidata>
  <monomers>
    <monomer>
      <code>A</code>
      <mnmchemgroup>
        <name>N-term NH2</name>
        <pka>9.6</pka>
        <acidcharged>TRUE</acidcharged>
        <polrule>left_trapped</polrule>
        <chemgrouprule>
          <entity>LE_PLM_MODIF</entity>
          <name>Acetylation</name>
          <outcome>LOST</outcome>
        </chemgrouprule>
      </mnmchemgroup>
      <mnmchemgroup>
        <name>C-term COOH</name>
        <pka>2.35</pka>
        <acidcharged>FALSE</acidcharged>
        <polrule>right_trapped</polrule>
      </mnmchemgroup>
    </monomer>
    [...]
    <monomer>
      <code>C</code>
      <mnmchemgroup>
        <name>N-term NH2</name>
        <pka>9.6</pka>
        <acidcharged>TRUE</acidcharged>
        <polrule>left_trapped</polrule>
        <chemgrouprule>
          <entity>LE_PLM_MODIF</entity>
          <name>Acetylation</name>
          <outcome>LOST</outcome>
        </chemgrouprule>
      </mnmchemgroup>
      <mnmchemgroup>
        <name>C-term COOH</name>
        <pka>2.35</pka>
        <acidcharged>FALSE</acidcharged>
        <polrule>right_trapped</polrule>
      </mnmchemgroup>
      <mnmchemgroup>
        <name>Lateral SH2</name>
        <pka>8.3</pka>
        <acidcharged>FALSE</acidcharged>
        <polrule>never_trapped</polrule>
      </mnmchemgroup>
    </monomer>
  </monomers>
  <modifs>
    <modif>
      <name>Phosphorylation</name>
      <mdfchemgroup>
        <name>none_set</name>
        <pka>1.2</pka>
        <acidcharged>FALSE</acidcharged>
      </mdfchemgroup>
      <mdfchemgroup>
        <name>none_set</name>
        <pka>6.5</pka>
        <acidcharged>FALSE</acidcharged>
      </mdfchemgroup>
    </modif>
  </modifs>
</pkaphpidata>

Member Function Documentation

PkaPhPiDataParser::PkaPhPiDataParser(const MsXpS::libXpertMassCore::PolChemDefCstSPtr &pol_chem_def_csp, const QString &file_path = QString())

Constructs a PkaPhPiDataParser instance.

pol_chem_def_csp: The polymer chemistry definition (cannot be nullptr).
file_path: the specification file path.

`[noexcept]` PkaPhPiDataParser::~PkaPhPiDataParser()

Destructs this PkaPhPiDataParser instance

const QString &PkaPhPiDataParser::filePath()

Returns the file path.

See also setFilePath().

bool PkaPhPiDataParser::renderXmlFile(std::vector<MsXpS::libXpertMassCore::MonomerSPtr> &monomers, std::vector<MsXpS::libXpertMassCore::ModifSPtr> &modifs)

Parses the file and fills-in the monomers and the modifs containers.

The two container hold specific Monomer and Modif instances as desribed in the loaded file.

Returns true upon success, false otherwise.

void PkaPhPiDataParser::setFilePath(const QString &file_path)

Sets the file_path.

See also filePath().

Member Variable Documentation

QString PkaPhPiDataParser::m_filePath

This variable holds the path of the file that contains all the specifications for chemical groups and chemical rules.

MsXpS::libXpertMassCore::PolChemDefCstSPtr PkaPhPiDataParser::mcsp_polChemDef

This variable holds the polymer chemistry definition context in which this PkaPhPiDataParser instance exists.

QString	m_filePath
MsXpS::libXpertMassCore::PolChemDefCstSPtr	mcsp_polChemDef

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