ChemicalGroup Class

<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>

Member Function Documentation

ChemicalGroup::ChemicalGroup(const QString &name = QString(), float pka = 7.0, bool is_acid_charged = true, MsXpS::libXpertMassCore::Enums::ChemicalGroupTrapped polymerization_rule = Enums::ChemicalGroupTrapped::NEVER)

Constructs a ChemicalGroup instance.

name The name of this ChemicalGroup. pka The pKa value of this ChemicalGroup. is_acid_charged Tells if the ChemicalGroup bears a charge when in acidic conditions. polymerization_rule Specifies the polymerization rule.

Upon construction the object is validated and m_isValid is set to the result of that validation.

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

Construct a ChemicalGroup instance as a copy of other.

There is no checking of the validity of other.

[noexcept] ChemicalGroup::~ChemicalGroup()

Destructs this ChemicalGroup instance.

MsXpS::libXpertMassCore::ChemicalGroupRuleSPtr ChemicalGroup::findRuleByEntity(const QString &entity, std::size_t &index) const

Searches by entity for a ChemicalGroupRule instance.

Returns the index of the ChemicalGroupRule instance in the member list of ChemicalGroupRule instances or -1 if not found.

MsXpS::libXpertMassCore::ChemicalGroupRuleSPtr ChemicalGroup::findRuleByEntityAndName(const QString &entity, const QString &name, std::size_t &index) const

Searches by entity and name for a ChemicalGroupRule instance.

Returns the index of the ChemicalGroupRule instance in the member list of ChemicalGroupRule instances or -1 if not found.

MsXpS::libXpertMassCore::ChemicalGroupRuleSPtr ChemicalGroup::findRuleByName(const QString &name, std::size_t &index) const

Searches by name for a ChemicalGroupRule instance.

Returns the index of the ChemicalGroupRule instance in the member list of ChemicalGroupRule instances or -1 if not found.

QString ChemicalGroup::getName() const

Returns the name.

float ChemicalGroup::getPka() const

Returns the pKa.

MsXpS::libXpertMassCore::Enums::ChemicalGroupTrapped ChemicalGroup::getPolRule() const

Returns the polymerization rule.

const std::vector<MsXpS::libXpertMassCore::ChemicalGroupRuleSPtr> &ChemicalGroup::getRulesCstRef() const

Returns a const reference to the container of ChemicalGroupRule instances.

std::vector<MsXpS::libXpertMassCore::ChemicalGroupRuleSPtr> &ChemicalGroup::getRulesRef()

Returns a reference to the container of ChemicalGroupRule instances.

bool ChemicalGroup::isAcidCharged() const

Returns the charge condition in acidic conditions.

If true, the group bears a charge when the pH is less than the pKa.

bool ChemicalGroup::isValid() const

Returns the validity status of this instance.

bool ChemicalGroup::renderXmlMdfElement(const QDomElement &element)

Parses the ChemicalGroup XML element related to a Modif.

Upon parsing of the element (tag <mnmchemgroup>), its data are validated and set to this ChemicalGroup instance, thus essentially initializing it.

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>
    .......
  </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>

Upon parsing of the element, all the data are validated and set to this ChemicalGroup instance, thus essentially initializing it. If there are ChemicalGroupRules associated to the ChemicalGroup element, these are rendered also.

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

bool ChemicalGroup::renderXmlMnmElement(const QDomElement &element)

Parses the ChemicalGroup XML element related to a Monomer.

Upon parsing of the element (tag

are validated and set to this ChemicalGroup instance, thus essentially
initializing it.

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

\code
<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>

Upon parsing of the element, all the data are validated and set to this ChemicalGroup instance, thus essentially initializing it. If there are ChemicalGroupRules associated to the ChemicalGroup element, these are rendered also.

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

void ChemicalGroup::setAcidCharged(bool acid_charged)

Sets the charge condition in acidic conditions to acid_charged.

If true, the group bears a charge when the pH is less than the pKa.

See also isAcidCharged().

void ChemicalGroup::setName(QString name)

Sets the name.

void ChemicalGroup::setPka(float pka)

Sets the pKa to pka.

void ChemicalGroup::setPolRule(MsXpS::libXpertMassCore::Enums::ChemicalGroupTrapped pol_rule)

Sets the polymerization rule to pol_rule.

The polymerization rule determines if the chemical group is trapped upon formation of a Monomer-to-Monomer bond.

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

Validates this instance, setting eventual error messages in error_list_p.

If the validation is successful, m_isValid is set to true, otherwise it is set to false. That result is returned.

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

Assigns other to this ChemicalGroup instance.

Returns a reference to this ChemicalGroup instance.