CleaveSpec Class

Member Function Documentation

CleaveSpec::CleaveSpec(PolChemDefCstSPtr pol_chem_def_csp, QString name, QString pattern = QString())

Constructs a CleaveSpec instance.

• pol_chem_def_csp: The polymer chemistry definition.
• name: The name of the CleaveSpec.
• pattern: The pattern of the CleaveSpec, like ("Lys/;Arg/;-Lys/Pro").

CleaveSpec::CleaveSpec(const CleaveSpec &other)

Constructs a CleaveSpec instance as a copy of other.

[virtual noexcept] CleaveSpec::~CleaveSpec()

Destructs this CleaveSpec instance.

QString *CleaveSpec::formatXmlClsElement(int offset, const QString &indent = QString(" "))

Formats a string describing this CleaveSpec instance suitable to be used as an XML element.

The XML element is typically used in a polymer chemistry defintion and looks like this:

<cls>
<name>CyanogenBromide</name>
<pattern>M/</pattern>
<clr>
<re-mnm-code>M</re-mnm-code>
<re-formula>-CH2S+O</re-formula>
</clr>
</cls>

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 CleaveSpec::isNameInList(const QString &name, const QList<CleaveSpec *> &cleave_spec_list, CleaveSpec *other = nullptr)

Searches for a CleaveSpec instance by name in cleave_spec_list.

If the CleaveSpec instance is found, it is copied into other.

Returns the index of the found cleavage specification or -1 if none is found or if other is empty.

QList<CleaveMotif *> *CleaveSpec::motifList()

Returns the list of CleaveMotif instances.

bool CleaveSpec::parse()

Parses this CleaveSpec instance.

The parsing involves separating the components found in the m_pattern string and making CleaveMotif instances out of them.

Starting from a pattern "Lys/;Arg/;-Lys/Pro", the parsing would first split it into three site strings:

• "Lys/";
• "Arg/";
• "-Lys/Pro"

Each of these site strings will be deconstructed into motifs, stored in CleaveMotif objects:

• First motif has a code list "[0] Lys", an offset of 1 and is for cleavage;
• Second motif has a code list "[0] Arg", an offset of 1 and is for cleavage;
• Third motif has a code list "[0] Lys, [1] Pro", an offset of 1 and is not for cleavage (see the '-')

Returns true if parsing is successful, false otherwise.

const QString &CleaveSpec::pattern()

Returns the pattern.

See also setPattern().

bool CleaveSpec::renderXmlClsElement(const QDomElement &element, int version)

Parses a cleavage specification XML element using a versioned function.

The data in the element are validated and if successful they are set to this instance, thus initializing it.

Returns true upon success, false otherwise.

QList<CleaveRule *> *CleaveSpec::ruleList()

Returns the list of CleaveRule instances.

void CleaveSpec::setPattern(const QString &pattern)

Sets the pattern.

See also pattern().

bool CleaveSpec::validate()

Validates this CleaveSpec instance.

The validation involves checking that:

• The name is not empty.
• The pattern is nt empty.
• The parsing of the pattern is successful.
• Each CleaveRule instance (if any) validates successfully.

Returns true if the validation is successful, false otherwise.

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

Assigns other to this CleaveSpec instance.

Returns a reference to this CleaveSpec instance.