Monomer Class

Member Function Documentation

Monomer::Monomer(PolChemDefCstSPtr pol_chem_def_csp, QString name, QString code = QString(), QString formula = QString())

Constructs a monomer with its member data set to name, code, formula.

The pol_chem_def_csp polymer chemistry definition is set to the PolChemDefEntity base class' member.

Monomer::Monomer(const Monomer &other)

Constructs a monomer as a copy of other.

[virtual noexcept] Monomer::~Monomer()

Destroys the monomer.

[override virtual] bool Monomer::accountMasses(double *mono = 0, double *avg = 0, int times = 1) const

Reimplements: Ponderable::accountMasses(double *mono, double *avg, int times) const.

Accounts this monomer's masses in mono and avg.

The mono and avg masses are updated only if they are non-nullptr.

This monomer's masses are stored in member data m_mono and m_avg. This monomer's masses multiplied by times before setting the values to mono and avg.

Returns true.

bool Monomer::accountMasses(Ponderable *ponderable, int times) const

Accounts this monomer's masses in ponderable's mono and avg masses.

This monomer's masses are stored in member data m_mono and m_avg. These masses are multiplied by times before setting the values to ponderable. ponderable cannot be nullptr.

Returns true.

[virtual] bool Monomer::calculateMasses(int monomer_chemical_entities)

Calculates this monomer's monoisotopic and avg masses.

The calculation is performed by computing the masses of this monomer's formula.

If monomer_chemical_entities & MONOMER_CHEMENT_MODIF is true, then the masses are updated to account for the mass of modifications.

Returns true if the calculations were successful, false otherwise.

See also Formula::accountMasses().

bool Monomer::checkCodeSyntax() const

Checks the code's syntactic validity.

The monomer code is verified and has to verify these criteria:

• It must be non-empty
• Its character length has to be less or equal to the code length parameter in the polymer chemistry definition (see PolChemDef::m_codeLength)
• The first character is uppercase
• All the remaining characters are lowercase

Returns true if the code syntax checked successfully, false otherwise.

See also validate().

QString Monomer::code() const

Returns the code

See also setCode().

void Monomer::debugPutStdErr() const

Outputs a string representing this monomer using qDebug().

QString *Monomer::formatXmlMnmElement(int offset, const QString &indent = QString(" "))

Formats this monomer's data as a string suitable to be used as an XML element in the polymer chemistry definition.

The typical monomer element that is generated in this function looks like this:

<monomers>
<mnm>
  <name>Glycine</name>
  <code>G</code>
  <formula>C2H3N1O1</formula>
</mnm>

The formatting of the XML element takes into account offset and indent by prepending the string with offset * indent character substring.

indent defaults to two spaces.

Returns a dynamically allocated string that needs to be freed after use.

QString *Monomer::formatXmlMonomerElement(int offset, const QString &indent = QString(" ")) const

Formats a string suitable to be used as an XML element in a polymer sequence file.

The typical monomer element that is generated in this function looks like this:

<monomer>
<code>S</code>
<prop>
<name>MODIF</name>
<data>Phosphorylation</data>
</prop>
<prop>
<name>COMMENT</name>
<data>Phosphorylation is only partial</data>
</prop>
</monomer>

The formatting of the XML element takes into account offset and indent by prepending the string with offset * indent character substring.

indent defaults to two spaces.

Returns a dynamically allocated string that needs to be freed after use.

[static] int Monomer::isCodeInList(const QString &code, const QList<Monomer *> &refList, Monomer *monomer_p = 0)

Tells if a monomer by the monomer code is in refList.

The monomers in refList are searched through for the monomer code.

If a monomer is found and monomer_p is non-nullptr, the monomer pointed to by monomer_p is set to the contents of the found monomer.

Returns the index of the found monomer or -1 either if m_code is empty or if the monomer was not found.

int Monomer::isCodeKnown() const

Tells if a monomer by this monomer's code is known in the polymer chemistry definition.

The monomers in the list of monomers of the polymer chemistry definition (mcsp_polChemDef) are searched through for this monomer's code (m_code).

Returns the index of the found monomer or -1 either if m_code is empty or if the monomer was not found.

bool Monomer::isModified() const

Returns true if this monomer has at least one modification, false otherwise.

[static] int Monomer::isNameInList(const QString &name, const QList<Monomer *> &refList, Monomer *monomer_p = 0)

Tells if a monomer by the monomer name is in refList.

The monomers in refList are searched through for the monomer name.

If a monomer is found and monomer_p is non-nullptr, the monomer pointed to by monomer_p is set to the contents of the found monomer.

Returns the index of the found monomer or -1 either if m_name is empty or if the monomer was not found.

int Monomer::isNameKnown() const

Tells if a monomer by this monomer's name is known in the polymer chemistry definition.

The monomers in the list of monomers of the polymer chemistry definition (mcsp_polChemDef) are searched through for this monomer's name (m_name).

Returns the index of the found monomer or -1 either if m_name is empty or if the monomer was not found.

int Monomer::modifCount(const QString &modif_name)

Returns the count of modifications by name modif_name in this monomer.

QList<Modif *> *Monomer::modifList() const

Returns the modification list

bool Monomer::modify(Modif *modif, bool override, QStringList &errorList)

Modifies this monomer using modif.

The two verifications that are done:

• This monomer must be a modif target;
• The count of modif modifications in this monomer must be at most the authorized count - 1, to accomodate this new modification [see Modif::maxCount()].

The two restriction above can be overridden by setting override to true.

If errors are encountered, these are reported as strings in errorList.

The modif's ownership is taken by this monomer.

Returns true on success, false otherwise.

bool Monomer::renderXmlMnmElement(const QDomElement &element, int version)

Parses the monomer XML element specifically for version.

Parses the monomer XML element passed as argument and for each encountered data will set the data to this monomer (this is called XML rendering).The parsing is delegated to a function that is specific for for version of the polymer chemistry definition.

The XML element is found in the polymer chemistry definition and has the following form:

<monomers>
  <mnm>
    <name>Glycine</name>
    <code>G</code>
    <formula>C2H3N1O1</formula>
  </mnm>
  <mnm>
    <name>Alanine</name>
    <code>A</code>
    <formula>C3H5N1O1</formula>
  </mnm>

After setting all the data, this monomer calculates it masses and validates itself. If any of these steps fails, the error is reported by returning false.

See also validate().

bool Monomer::renderXmlMonomerElement(const QDomElement &element, int version)

Parses into this monomer the XML monomer element passed as argument.

The XML element comes from a polymer sequence file, where the monomer is singled out (not in a sequence string) because it might be modified.

version indicates the format version of this XML element.

As soon as the monomer code is known, while parsing the element, the corresponding monomer is searched in the list of monomers in the member polymer chemistry definition (mcsp_polChemDef). Then, the found monomer is copied into this monomer so that both monomers are identical, effectively initializing this monomer to the monomer described by the element.

If the element contains one or more mdf modifications, these modifications are allocated as Modif's and validated. If these modifications validate successfully, they are appended to this monomer's list of modifications.

Returns true if initializationt of his monomer with the contents of element succeeded, false otherwise.

See also formatXmlMonomerElement(int offset, const QString &indent).

void Monomer::setCode(const QString &code)

Sets the code to code

See also code().

bool Monomer::unmodify()

Removes all the modification from this monomer.

Returns true.

bool Monomer::unmodify(Modif *modif)

Removes modif from this monomer.

The member list of modifications must exist (it is a heap-allocated list that is allocated upon the first modification of the monomer) and must be non-empty.

Returns true.

bool Monomer::validate()

Returns true if this monomer is valid, false otherwise.

Validation of the monomer occurs if:

• Its name is not empty
• Its code is not empty and its syntax is correct
• Its formula validates
• Its modifications (if any) validate

See also checkCodeSyntax().

bool Monomer::operator!=(const Monomer &other) const

Returns true if this monomer and other differ, false otherwise.

The comparison involves also the comparison of the Modif objects in mpa_modifList.

Monomer &Monomer::operator=(const Monomer &other)

Assigns other's member data to this monomer.

The copy is deep, in particular with the mpa_modifList being copied.

Returns a reference to this monomer.

bool Monomer::operator==(const Monomer &other) const

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

The comparison involves also the comparison of the Modif objects in mpa_modifList.