libXpertMass Developer Documentation
  • libXpertMass
  • ChemicalGroupRule

    • Contents

    ChemicalGroupRule Class

    class MsXpS::libXpertMass::ChemicalGroupRule

    The ChemicalGroupRule class provides a model for refining the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object. More...

    Header: #include <ChemicalGroupRule.hpp>

    Public Functions

    ChemicalGroupRule(QString name = QString(), QString entity = QString(), ChemicalGroupRuleFate fate = ChemicalGroupRuleFate::LOST)
    QString entity()
    ChemicalGroupRuleFate fate()
    QString name()
    bool renderXmlElement(const QDomElement &element)
    void setEntity(QString entity)
    void setFate(ChemicalGroupRuleFate fate)
    void setName(QString name)

    Protected Variables

    ChemicalGroupRuleFate m_chemicalGroupFate
    QString m_entity
    QString m_name

    Detailed Description

    In an pkaphpidata definition file, the following xml structure is encountered:

    <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>
    .....
  <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>

    See also ChemicalGroup.

    Member Function Documentation

    ChemicalGroupRule::ChemicalGroupRule(QString name = QString(), QString entity = QString(), ChemicalGroupRuleFate fate = ChemicalGroupRuleFate::LOST)

    Constructs a ChemicalGroupRule instance.

    QString ChemicalGroupRule::entity()

    Returns the entity.

    See also setEntity().

    ChemicalGroupRuleFate ChemicalGroupRule::fate()

    Returns the fate.

    See also setFate().

    QString ChemicalGroupRule::name()

    Returns the name.

    See also setName().

    bool ChemicalGroupRule::renderXmlElement(const QDomElement &element)

    Parses the ChemicalGroupRule XML element.

    Upon parsing of the element, its data are validated and set to this ChemicalGroupRule instance, thus essentially initializing it.

    Returns true if parsing and validation were successful, false otherwise.

    void ChemicalGroupRule::setEntity(QString entity)

    Sets the entity.

    See also entity().

    void ChemicalGroupRule::setFate(ChemicalGroupRuleFate fate)

    Sets the fate.

    See also fate().

    void ChemicalGroupRule::setName(QString name)

    Sets the name.

    See also name().

    Member Variable Documentation

    ChemicalGroupRuleFate ChemicalGroupRule::m_chemicalGroupFate

    This variable holds the fate of the ChemicalGroupRule instance.

    See also MsXpS::libXpertMass::ChemicalGroupRuleFate.

    QString ChemicalGroupRule::m_entity

    This variable holds the entity of the ChemicalGroupRule instance, like LE_PLM_MODIF for left end polymer modification.

    QString ChemicalGroupRule::m_name

    This variable holds the name of the ChemicalGroupRule instance.

    Filippo Rusconi