PkaPhPi Class

Member Function Documentation

PkaPhPi::PkaPhPi(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp, MsXpS::libXpertMassCore::PolymerCstQSPtr polymer_cqsp, const MsXpS::libXpertMassCore::CalcOptions &calc_options)

Constructs a PkaPhPi instance with a number of parameters.

• pol_chem_def_csp: The polymer chemistry definition
• polymer_cqsp: The polymer within the context of which the calculations are performed.
• calc_options: The options driving the calculations.

[virtual noexcept] PkaPhPi::~PkaPhPi()

Destructs this PkaPhPi instance.

int PkaPhPi::accountMonomerModif(const MsXpS::libXpertMassCore::Monomer &monomer, MsXpS::libXpertMassCore::ChemicalGroup &chemical_group)

Accounts for the chemical_group in the context of the monomer.

A chemical group is described as follows:

<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>

Returns the count of rules that were accounted for, or -1 if none was.

int PkaPhPi::accountPolymerEndModif(MsXpS::libXpertMassCore::Enums::ChemicalEntity polymer_chem_ent, const MsXpS::libXpertMassCore::ChemicalGroup &chemical_group)

Accounts for the chemical_group according the the polymer chemical entities defined in polymer_chem_ent.

A chemical group is described as follows:

<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>

Returns the count of rules that were accounted for, or -1 if none was.

double PkaPhPi::calculateChargeRatio(double pka, bool is_acid_charged)

Returns the ratio between the charged and the uncharged forms of the chemical entity using pka and is_acid_charged. If the charge is negative, the returned ratio is negative, positive otherwise.

The charged and uncharged species are the AH an A- species of the acido-basic theory.

The calculation is based on the use of the m_ph member variable value.

int PkaPhPi::calculateCharges()

Calculates the charges (positive and negative).

The general scheme is :

Get the list of the iter_index_range of the different Polymer region selections. For each first monomer and end monomer of a given region selection, check if the the region is an oligomer or a residual chain (m_selectionType of libXpertMassCore::CalcOptions); act accordingly. Also, check for each selection region if it encompasses the polymer left/right end. If the left/right end modifications are to be taken into account, act accordingly.

The positive and negative charges are stored in the member m_positiveCharges and m_negativeCharges variables.

Returns the count of chemical groups that have been processed.

See also calculatePi().

int PkaPhPi::calculatePi()

Calculates the isoelectric point.

The isoelectric point is the pH at which a given analyte will have a net charge of 0, that is, when the count of negative charges will be equal to the count of positive charges.

The pI will be stored in the m_pi member variable.

Returns the count of chemical groups that have been processed.

See also calculateCharges().

const std::vector<MsXpS::libXpertMassCore::ModifCstSPtr> &PkaPhPi::getModifs() const

Returns a const reference to the container of Modif instances.

const std::vector<MsXpS::libXpertMassCore::MonomerCstSPtr> &PkaPhPi::getMonomersCstRef() const

Returns a const reference to the container of Monomer instances.

MsXpS::libXpertMassCore::PolChemDefCstSPtr PkaPhPi::getPolChemDefCstSPtr() const

Returns the PolChemDef.

double PkaPhPi::negativeCharges()

Returns the negative charges.

double PkaPhPi::ph()

Returns the pH.

See also setPh().

double PkaPhPi::pi()

Returns the pI.

double PkaPhPi::positiveCharges()

Returns the positive charges.

void PkaPhPi::setCalcOptions(const MsXpS::libXpertMassCore::CalcOptions &calc_options)

Sets the calculation options to calc_options.

void PkaPhPi::setModifs(std::vector<MsXpS::libXpertMassCore::ModifCstSPtr> &modifs)

Copies the Modif instances in modifs to the member container.

This is a shallow copy with only the pointers being copied.

void PkaPhPi::setModifs(std::vector<MsXpS::libXpertMassCore::ModifCstSPtr> &&modifs)

Moves the Modif instances from modifs to the member container.

void PkaPhPi::setModifs(std::vector<MsXpS::libXpertMassCore::ModifSPtr> &&modifs)

Moves the Modif instances from modifs to the member container.

void PkaPhPi::setMonomers(std::vector<MsXpS::libXpertMassCore::MonomerCstSPtr> &monomers)

Copies the Monomer instances in monomers to the member container.

This is a shallow copy with only the pointers being copied.

void PkaPhPi::setMonomers(std::vector<MsXpS::libXpertMassCore::MonomerCstSPtr> &&monomers)

Moves the Monomer instances from monomers to the member container.

void PkaPhPi::setMonomers(std::vector<MsXpS::libXpertMassCore::MonomerSPtr> &&monomers)

Moves the Monomer instances from monomers to the member container.

void PkaPhPi::setPh(double ph)

Sets the pH to ph.

See also ph().

void PkaPhPi::setPolChemDefCstSPtr(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp)

Sets the PolChemDef to pol_chem_def_csp.