libXpertMassCore and libXpertMassGui Developer Documentation
  • libXpertMassCore
  • CleavageConfig

    • Contents

    CleavageConfig Class

    class MsXpS::libXpertMassCore::CleavageConfig

    The CleavageConfig class derives from CleavageAgent to provide a model for specifying aqueous cleavage specifications (patterns) of Polymer Sequences along with instructions on the way the cleavage must occur. More...

    Header: #include <CleavageConfig.hpp>
    Inherits: MsXpS::libXpertMassCore::CleavageAgent

    Public Functions

    CleavageConfig(QObject *parent = nullptr)
    CleavageConfig(const MsXpS::libXpertMassCore::CleavageAgent &cleavage_agent, int partials = 0, bool is_sequence_embedded = false, QObject *parent = nullptr)
    CleavageConfig(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp, const QString &name, const QString &pattern, int partials = 0, bool is_sequence_embedded = false, QObject *parent = nullptr)
    CleavageConfig(const MsXpS::libXpertMassCore::CleavageConfig &other, QObject *parent = nullptr)
    virtual ~CleavageConfig()
    int getPartials() const
    int getStartIonizeLevel() const
    int getStopIonizeLevel() const
    bool initialize(const MsXpS::libXpertMassCore::CleavageConfig &other)
    bool isSequenceEmbedded() const
    bool setCleavageAgent(const MsXpS::libXpertMassCore::CleavageAgent &cleavage_agent)
    void setIonizeLevels(int value1, int value2)
    void setPartials(int value)
    void setSequenceEmbedded(bool is_sequence_embedded)
    void setStartIonizeLevel(int value)
    void setStopIonizeLevel(int value)
    bool operator!=(const MsXpS::libXpertMassCore::CleavageConfig &other) const
    bool operator==(const MsXpS::libXpertMassCore::CleavageConfig &other) const

    Protected Variables

    int m_partials
    bool m_sequenceEmbedded
    int m_startIonizeLevel
    int m_stopIonizeLevel

    Detailed Description

    Cleavage agent specifications determine the specificity of cleavage in a polymer sequence using a simple syntax. For example, Trypsin is able to cleave after lysyl and arginyl residues. Its cleavage pattern is thus "Lys/;Arg/". However, it is known that Trypsin fails to cleave after Lys if that monomer is followed by a Prolyl residue, thus the complete cleavage agent pattern specification for Trypsin is the following: "Lys/;Arg/;-Lys/Pro".

    A cleavage agent specification might not be enough information to determine the manner in which a polymer is cleaved. Cleavage rules might be required to refine the specification. A cleavage agent specification might hold as many cleavage rules as required.

    See also CleavageMotif and CleavageRule.

    Member Function Documentation

    [invokable] CleavageConfig::CleavageConfig(QObject *parent = nullptr)

    Constructs an empty CleavageConfig instance.

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    [invokable] CleavageConfig::CleavageConfig(const MsXpS::libXpertMassCore::CleavageAgent &cleavage_agent, int partials = 0, bool is_sequence_embedded = false, QObject *parent = nullptr)

    Constructs a CleavageConfig instance starting using a limited set of parameters.

    cleavage_agent: CleavageAgent to be used to initialize the base class.

    partials: the partial cleavages;

    is_sequence_embedded: indicates if the Oligomer sequence needs to be stored.

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    [invokable] CleavageConfig::CleavageConfig(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp, const QString &name, const QString &pattern, int partials = 0, bool is_sequence_embedded = false, QObject *parent = nullptr)

    Constructs a CleavageConfig instance using a full set of parameters.

    pol_chem_def_csp: the polymer chemistry definition.

    name: the name of CleavageAgent;

    pattern: the cleavage pattern of the CleavageAgent;

    partials: the partial cleavages;

    is_sequence_embedded: indicates if the Oligomer sequence needs to be stored.

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    [invokable] CleavageConfig::CleavageConfig(const MsXpS::libXpertMassCore::CleavageConfig &other, QObject *parent = nullptr)

    Constructs a CleavageConfig instance as a copy of other

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    [virtual noexcept] CleavageConfig::~CleavageConfig()

    Destructs this CleavageConfig instance.

    int CleavageConfig::getPartials() const

    Returns the partial cleavages.

    Note: Getter function for property partials.

    int CleavageConfig::getStartIonizeLevel() const

    Returns the ionization start level.

    Note: Getter function for property startIonizeLevel.

    int CleavageConfig::getStopIonizeLevel() const

    Returns the ionization stop level.

    Note: Getter function for property stopIonizeLevel.

    [invokable] bool CleavageConfig::initialize(const MsXpS::libXpertMassCore::CleavageConfig &other)

    Initializes this CleavageConfig instance using other.

    If no initialization error occurred, return true, false otherwise.

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    bool CleavageConfig::isSequenceEmbedded() const

    Returns the sequence embedded boolean value.

    Note: Getter function for property sequenceEmbedded.

    [invokable] bool CleavageConfig::setCleavageAgent(const MsXpS::libXpertMassCore::CleavageAgent &cleavage_agent)

    Sets this instance's CleavageAgent base class to cleavage_agent.

    Returns true the CleavageAgent initialization succeeded, false otherwise.

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    [invokable] void CleavageConfig::setIonizeLevels(int value1, int value2)

    Sets both the ionization start and stop levels to value1 and value2, respectively.

    Note: This function can be invoked via the meta-object system and from QML. See Q_INVOKABLE.

    void CleavageConfig::setPartials(int value)

    Set the partial cleavages to value.

    Note: Setter function for property partials.

    void CleavageConfig::setSequenceEmbedded(bool is_sequence_embedded)

    Sets the sequence embedded boolean value to is_sequence_embedded.

    Note: Setter function for property sequenceEmbedded.

    See also isSequenceEmbedded().

    void CleavageConfig::setStartIonizeLevel(int value)

    Sets the ionization start level to value.

    Note: Setter function for property startIonizeLevel.

    void CleavageConfig::setStopIonizeLevel(int value)

    Sets the ionization stop level to value.

    Note: Setter function for property stopIonizeLevel.

    bool CleavageConfig::operator!=(const MsXpS::libXpertMassCore::CleavageConfig &other) const

    Returns true if this instance and other differ, false otherwise. Returns the negative value of opearator==().

    See also operator==().

    bool CleavageConfig::operator==(const MsXpS::libXpertMassCore::CleavageConfig &other) const

    Returns true if this CleavageConfig instance and other are identical, false otherwise.

    See also operator!=().

    Member Variable Documentation

    int CleavageConfig::m_partials

    This variable holds the partial cleavages accepted.

    bool CleavageConfig::m_sequenceEmbedded

    Tells if the sequence of the obtained Oligomer instance need to embed their sequence.

    int CleavageConfig::m_startIonizeLevel

    This variable holds the first ionization level of the range.

    int CleavageConfig::m_stopIonizeLevel

    This variable holds the last ionization level of the range.

    Filippo Rusconi