CrossLink Class

Member Function Documentation

CrossLink::CrossLink(PolChemDefCstSPtr pol_chem_def_csp, Polymer *polymer, const QString &name, const QString &formula, const QString &comment = QString())

Constructs a CrossLink instance

• pol_chem_def_csp: the polymer chemistry definition (PolChemDef).
• polymer: the Polymer instance in which this CrossLink was formed.
• name: the name of this CrossLink instance.
• formula: the Formula that describes the reaction that is the basis of the chemical reaction leading to the formation of this CrossLink.
• comment: a comment that might be associated to this CrossLink.

CrossLink::CrossLink(const CrossLinker &cross_linker, Polymer *polymer, const QString &comment = QString())

Constructs a CrossLink instance

• cross_linker: CrossLinker instance used to initialize this CrossLink.
• polymer: the Polymer instance in which this CrossLink was formed
• comment: a comment that might be associated to this CrossLink

CrossLink::CrossLink(const CrossLink &other)

Constructs a CrossLink instance as a copy of other.

[virtual noexcept] CrossLink::~CrossLink()

Destructs this CrossLink instance.

No entity needs to be destructed, since the Monomer instances in the list are not owned by this CrossLinker instance.

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

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

Adds the member m_mono and m_avg masses to mono and avg, as compounded by the times factor.

Returns true.

[override virtual] bool CrossLink::accountMasses(Ponderable *ponderable, int times = 1)

Reimplements: CrossLinker::accountMasses(Ponderable *ponderable, int times).

Adds the member m_mono and m_avg masses to ponderable, as compounded by the times factor.

Returns true.

bool CrossLink::appendMonomer(const Monomer *monomer)

Adds monomer to the member list of Monomer instances.

monomer cannot be nullptr.

Returns true.

[override virtual] bool CrossLink::calculateMasses()

Reimplements: CrossLinker::calculateMasses().

Calculates the masses of this CrossLink and set them anew to the member masses (Ponderable base class).

Returns true.

const QString &CrossLink::comment() const

Returns the member comment.

See also setComment().

int CrossLink::encompassedBy(int start, int end, int *in = 0, int *out = 0)

Tells if this CrossLink instance is encompassed (partially or fully) or not at all by the Polymer sequence region defined by the [start - end ] Monomer index range.

The count of monomers involved in this cross-link that:

• Are contained in the range is stored in in.
• Are not contained in the range is stored in out.

If all the monomers are listed as in, then this CrossLink is fully encompassed by the Polymer sequence region defined by the [start - end ] Monomer index range and CROSS_LINK_ENCOMPASSED_FULL is returned.

If all the monomers are listed as out, then this CrossLink is not at all encompassed by the Polymer sequence region and CROSS_LINK_ENCOMPASSED_NO is returned.

If both kinds of monmers were found, then CROSS_LINK_ENCOMPASSED_PARTIAL is returned.

int CrossLink::encompassedBy(const CoordinateList &coordinate_list, int *in = 0, int *out = 0)

Tells if this CrossLink instance is encompassed (partially or fully) or not at all by various Coordinates instances in the coordinate_list CoordinateList.

The count of monomers involved in this cross-link that:

• Are contained in the regions defined in coordinate_list is stored in in.
• Are not contained in the range is stored in out.

If all the monomers are listed as in, then this CrossLink is fully encompassed by the Polymer sequence regions defined in coordinate_list and CROSS_LINK_ENCOMPASSED_FULL is returned.

If all the monomers are listed as out, then this CrossLink is not at all encompassed by the Polymer sequence region and CROSS_LINK_ENCOMPASSED_NO is returned.

If both kinds of monmers were found, then CROSS_LINK_ENCOMPASSED_PARTIAL is returned.

const Monomer *CrossLink::firstMonomer() const

Returns the first Monomer instance listed in the member list of monomers. If the list is empty; returns nullptr.

int CrossLink::involvesMonomer(const Monomer *monomer) const

Returns the index of monomer found in the member Polymer sequence that is involved in this CrossLink, or -1 if that is not found.

const Monomer *CrossLink::monomerAt(int index)

Returns the monomer at index in the member list of Monomer instances.

index cannot be out-of-bounds.

See also setMonomerAt().

int CrossLink::monomerIndexList(QList<int> *list)

Lists in list the indices of all the monomers involved in this CrossLink instance.

Returns the count of indices set to list.

QString CrossLink::monomerIndexText()

Returns a string containing a ';'-separated list of the indices of all the Monomer instances involved in this CrossLink.

QList<const Monomer *> *CrossLink::monomerList()

Returns the member list of Monomer instances.

QString CrossLink::monomerPosText()

Returns a string containing a ';'-separated list of the positions of all the Monomer instances involved in this CrossLink.

Polymer *CrossLink::polymer()

Returns the Polymer instance in which this CrossLink has been formed.

See also setPolymer().

int CrossLink::populateMonomerList(QString text)

Sets to the member monomer list all the Monomer instances referenced in text as indices to monomer in the Polymer sequence.

text contains a list of Monomer instance indices separated by ';' characters. The corresponding monomers found in the member Polymer are copied to the member list of Monomer instances, effectively documenting a CrossLink in that member Polymer sequence.

This CrossLink instance does not own the Monomer instances pointers, as they effectively point to monomer that belong to the member Polymer.

QString *CrossLink::prepareResultsTxtString()

Returns an allocated string describing this CrossLink instance.

bool CrossLink::removeMonomerAt(int index)

Removes the monomer at index in the member list of Monomer instances.

index cannot be out-of-bounds.

Returns true.

void CrossLink::setComment(const QString &comment)

Set the member comment to comment.

See also comment().

bool CrossLink::setMonomerAt(Monomer *monomer, int index)

Sets monomer to this CrossLink at index of the member list of Monomer instances, effectively replacing the monomer instance currently at that index.

monomer cannot be nullptr and index cannot be out-of-bounds.

This CrossLinker instance does not take ownership of monomer.

Returns true.

See also monomerAt().

void CrossLink::setPolymer(Polymer *polymer)

Set polymer as the Polymer sequence in which this CrossLink has been formed.

polymer cannot be nullptr.

See also polymer().

bool CrossLink::validate()

Returns true if this CrossLink instance validates successfully, false otherwise.

The validation is successful if:

• The count of Monomer instances listed in the member list is > 1.
• The member Polymer instance exists.
• The count of Monomer instances listed in the member list is equal to the number of Modif instance in the CrossLinker base class.
• If the list of Modif instances in the CrossLinker base class is not empty, there must be a colinearity between the order in which these instances are listed and the order in which the Monomer instances are listed in the member list. The monomer instance must be a target of the modification.

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

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