PkaPhPi Class

Member Function Documentation

PkaPhPi::PkaPhPi(Polymer &polymer, CalcOptions &calc_options, QList<Monomer *> *monomer_list_p = 0, QList<Modif *> *modif_list_p = 0)

Constructs a PkaPhPi instance.

• polymer: .The polymer within the context of which the calculations are performed.
• calc_options: The options driving the calculations.
• monomer_list_p: .The list of Monomer instances.
• modif_list_p: .The list of Modif instances.

[virtual noexcept] PkaPhPi::~PkaPhPi()

Destructs this PkaPhPi instance.

int PkaPhPi::accountMonomerModif(const Monomer &monomer, 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(PolymerChemEnt end_modif, const ChemicalGroup &chemical_group)

Accounts for the chemical_group in the context of the Polymer end_modif.

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 coordinates 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 libXpertMass::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().

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 CalcOptions &calc_options)

Sets the calculation options to calc_options.

void PkaPhPi::setModifList(QList<Modif *> *modif_list_p)

Sets the modification list to modif_list_p.

The list and its contents are now owned by this PkaPhPi instance.

void PkaPhPi::setMonomerList(QList<Monomer *> *monomer_list_p)

Sets the monomer list to monomer_list_p.

The list and its contents are now owned by this PkaPhPi instance.

void PkaPhPi::setPh(double ph)

Sets the pH to ph.

See also ph().