Ionizable Class

Member Function Documentation

Ionizable::Ionizable(PolChemDefCstSPtr pol_chem_def_csp, const QString &name = QString("NOT_SET"), const Ponderable &ponderable = Ponderable(), const IonizeRule &ionize_rule = IonizeRule(), bool is_ionized = false)

Constructs an Ionizable.

The Ionizable instance will be an ionized entity if is_ionized is true. The ponderable's mono and avg masses must thus be masses which take (is_ionized is true) or do not take (is_ionized is false) into account the data located in ionize_rule. If is_ionized is true, the ionize_rule is validated and the level of the ionization must not be 0. If one of these two tests fails, this is an error and the program aborts.

pol_chem_def_csp Polymer chemistry definition (cannot be nullptr);

name Name of this Ionizable (defaults to "NOT_SET");

ponderable Ponderable (mono and avg masses);

ionize_rule IonizeRule (defaults to IonizeRule(), that is, an invalid IonizeRule).

is_ionized Tells if the Ionizable to be constructed should be considered as an ionized chemical entity.

Ionizable::Ionizable(const Ionizable &other)

Constructs an Ionizable as a copy of other.

No assumption should be made as to the status of the created Ionizable. The caller should characterize the ionization status of the Ionizable with isIonized().

[virtual noexcept] Ionizable::~Ionizable()

Destructs this Ionizable.

[override virtual] bool Ionizable::calculateMasses()

Calculates the masses of this Ionizable.

If this Ionizable is ionized, the masses of the Ponderable base class are let unchanged. If this Ionizable is not ionized and the IonizeRule is valid, perform the ionization, which calculates the masses.

This function returns false if the member IonizeRule is not valid or if the ionization failed, true otherwise.

See also ionize().

[virtual] int Ionizable::charge() const

Returns the ionization charge of this Ionizable.

The charge is returned as a positive number (0 allowed) or as -1 if the IonizeRule is not valid or if m_isIonized is false.

See also setCharge().

[virtual] int Ionizable::deionize()

Deionizes this Ionizable.

This Ionizable is deionized using its member m_ionizeRule. The following logic is applied:

1. If this Ionizable is not ionized, this function returns 0.
2. If the member ionizeRule is not valid, this function returns -1 because it does not make sense to try to change the ionization of an Ionizable if its member IonizeRule is not valid.
4. The deionization process is carried out. If the process is successful, 1 is returned, otherwise -1 is returned.

[virtual] int Ionizable::ionize()

Ionizes this Ionizable.

Ionization is performed on this Ionizable using the member IonizeRule.

The following logic is applied:

1. If the member ionizeRule is not valid, this function returns -1 because it does not make sense to try to change the charge of an Ionizable if its member IonizeRule is not valid.
2. If this Ionizable is ionized, return 0 (already ionized, then nothing to do).
3. The mass status of this Ionizable (Ponderable base class) is stored for later comparison.
4. The ionization process is carried out and the new mass status is compared to the older one. If the new status differs from the previous one, than 1 is returned, otherwise -1 is returned.

[virtual] int Ionizable::ionize(const IonizeRule &ionize_rule)

Ionizes this Ionizable using ionize_rule.

The following logic is applied:

1. If ionize_rule is not valid, this function returns -1 because it does not make sense to try to change the charge of an Ionizable if that ionization rule is not valid.
2. If this Ionizable is ionized, first deionize() it. If this step fails, returns -1.
3. The ionization process is carried out. If the process is successful, 1 is returned, otherwise -1 is returned.

See also ionize().

[static] int Ionizable::ionize(Ionizable *ionizable, const IonizeRule &ionize_rule)

Ionizes the ionizable using ionize_rule.

The following logic is applied:

1. If ionize_rule is not valid, this function returns -1 because it does not make sense to try to change the charge of an Ionizable if that ionization rule is not valid.
2. If ionizable is ionized, first deionize() it. If this step fails, returns -1.
3. The ionization process is carried out. If the process is successful, 1 is returned, otherwise -1 is returned.

See also ionize().

const IonizeRule &Ionizable::ionizeRule() const

Returns a constant reference to this IonizeRule.

IonizeRule *Ionizable::ionizeRule()

Returns a pointer to this IonizeRule.

bool Ionizable::isIonized() const

Returns true if this Ionizable is ionized, false otherwise.

The ionization status is returned on the basis of the m_isIonized member boolean value.

[virtual] double Ionizable::molecularMass(MassType mass_type)

Returns the molecular mass (either monoisotopic or average, depending on mass_type)

A copy of this Ionizable is first made, then it is deionized and its mass is returned.

int Ionizable::setCharge(int charge)

Sets the charge of this Ionizable to charge.

The charge of an ionizable is the compound product of m_charge and m_level in its IonizeRule member. The value passed as charge is that compound product. Thus, the member IonizeRule is updated to reflect the new charge using the following code:

int level = charge / m_ionizeRule.charge();
m_ionizeRule.setLevel(level);

Only the level value of IonizeRule is changed to reflect the change of the charge because the chemistry of the ionization rule itself must not be changed.

The following logic is applied:

1. If the member ionizeRule is not valid, this function returns -1 because it does not make sense to try to change the charge of an Ionizable if its member IonizeRule is not valid.
2. This Ionizable is first deionized if it is ionized. If the deionization fails -1 is returned.
3. This Ionizable is ionized with the level value in its member IonizeRule. If that ionization fails, -1 is returned.

At this point all the process went fine and 1 is returned.

See also charge().

QString Ionizable::toString()

Returns a string describing this Ionizable.

[virtual] bool Ionizable::validate()

Validates this Ionizable.

The member IonizeRule needs to validate successfully.

Returns true if the validation is successfull, false otherwise.

[virtual] bool Ionizable::operator!=(const Ionizable &other) const

Returns true if this Ionizable is different than other, false otherwise.

[virtual] Ionizable &Ionizable::operator=(const Ionizable &other)

Assigns other to this Ionizable.

Return A reference to this Ionizable instance.

[virtual] bool Ionizable::operator==(const Ionizable &other) const

Returns true if this Ionizable is identical to other, false otherwise.