libXpertMassCore and libXpertMassGui Developer Documentation
  • libXpertMassCore
  • ChemicalGroupRule

    • Contents

    ChemicalGroupRule Class

    class MsXpS::libXpertMassCore::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(const QString &name = QString(), const QString &entity = QString(), MsXpS::libXpertMassCore::Enums::ChemicalGroupFate fate = Enums::ChemicalGroupFate::LOST)
    ChemicalGroupRule(const MsXpS::libXpertMassCore::ChemicalGroupRule &other)
    ~ChemicalGroupRule()
    QString getEntity()
    MsXpS::libXpertMassCore::Enums::ChemicalGroupFate getFate()
    QString getName()
    bool isValid() const
    bool renderXmlElement(const QDomElement &element)
    void setEntity(const QString &entity)
    void setFate(MsXpS::libXpertMassCore::Enums::ChemicalGroupFate fate)
    void setName(const QString &name)
    bool validate(MsXpS::libXpertMassCore::ErrorList *error_list_p) const
    MsXpS::libXpertMassCore::ChemicalGroupRule &operator=(const MsXpS::libXpertMassCore::ChemicalGroupRule &other)

    Protected Variables

    MsXpS::libXpertMassCore::Enums::ChemicalGroupFate 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(const QString &name = QString(), const QString &entity = QString(), MsXpS::libXpertMassCore::Enums::ChemicalGroupFate fate = Enums::ChemicalGroupFate::LOST)

    Constructs a ChemicalGroupRule instance.

    ChemicalGroupRule::ChemicalGroupRule(const MsXpS::libXpertMassCore::ChemicalGroupRule &other)

    Constructs a ChemicalGroupRule instance as a copy of other.

    [noexcept] ChemicalGroupRule::~ChemicalGroupRule()

    brief Constructs this ChemicalGroupRule

    QString ChemicalGroupRule::getEntity()

    Returns the entity.

    MsXpS::libXpertMassCore::Enums::ChemicalGroupFate ChemicalGroupRule::getFate()

    Returns the fate.

    QString ChemicalGroupRule::getName()

    Returns the name.

    bool ChemicalGroupRule::isValid() const

    Returns the validity status of this instance.

    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(const QString &entity)

    Sets the entity.

    void ChemicalGroupRule::setFate(MsXpS::libXpertMassCore::Enums::ChemicalGroupFate fate)

    Sets the fate.

    void ChemicalGroupRule::setName(const QString &name)

    Sets the name.

    bool ChemicalGroupRule::validate(MsXpS::libXpertMassCore::ErrorList *error_list_p) const

    Validates this instance, setting eventual error messages to error_list_p.

    Note: error_list_p is not cleared.

    Following a successful validation, m_isValid is set to true, to false otherwise and that result is returned.

    MsXpS::libXpertMassCore::ChemicalGroupRule &ChemicalGroupRule::operator=(const MsXpS::libXpertMassCore::ChemicalGroupRule &other)

    Assigns other to this instance.

    Member Variable Documentation

    MsXpS::libXpertMassCore::Enums::ChemicalGroupFate ChemicalGroupRule::m_chemicalGroupFate

    This variable holds the fate of the ChemicalGroupRule instance.

    See also MsXpS::libXpertMassCore::Enums::ChemicalGroupFate.

    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