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Sourcecode: massxpert version File versions

massXpert::CleaveRule Class Reference

#include <cleaveRule.hpp>

Inheritance diagram for massXpert::CleaveRule:


List of all members.

Detailed Description

The CleaveRule class provides a cleavage rule.

Cleavage rules help refine the description of the chemical reaction that is the basis of a cleavage(either enzymatic or chemical).

While a number of cleavage agent(like a number of enzymes) do not make unexpected reactions upon cleavage(enzyme usually hydrolyze their substrates), chemical agents sometimes make a cleavage, and in the process of the cleavage reaction modify chemically the ends of the generaed oligomers. One notorious example is the case of cyanogen bromide, that cleaves proteins right of methionyl residues. Upon such cleavage, the monomer at the right side of the generated oligomer (methionyl residue) get modified according to this formula: "-CH2S+O".

Cleavage rules are designed to be able to model such complex reactions.

Definition at line 72 of file cleaveRule.hpp.

Public Member Functions

 CleaveRule (const CleaveRule &)
 Constructs a copy of other.
 CleaveRule (const PolChemDef *, QString, QString=QString(), QString=QString(), QString=QString(), QString=QString())
 Construct a cleavage rule.
virtual PolChemDefEntityclone () const
 Creates a new polymer chemistry definition entity.
virtual void clone (PolChemDefEntity *) const
 Modifies other to be identical to this.
void clone (CleaveRule *)
 Modifies other to be identical to this.
QString * formatXmlClrElement (int, const QString &=QString(" "))
 Formats a string suitable to use as an XML element.
const QString & leftCode ()
 Returns the left code.
const FormulaleftFormula ()
 Returns the left formula.
virtual void mold (const PolChemDefEntity &)
 Modifies this to be identical to other.
void mold (const CleaveRule &)
 Modifies this to be identical to other.
QString name () const
 Returns the name.
virtual bool operator!= (const PolChemDefEntity &) const
 Tests inequality.
CleaveRuleoperator= (const CleaveRule &)
 Assigns other to this cleavage rule.
virtual bool operator== (const PolChemDefEntity &) const
 Tests equality.
const PolChemDefpolChemDef () const
 Returns the polymer chemistry definition.
bool renderXmlClrElement (const QDomElement &, int)
 Parses a cleavage rule XML element.
const QString & rightCode ()
 Returns the right code.
const FormularightFormula ()
 Returns the right formula.
void setAtomRefList (const QList< Atom * > *)
void setLeftCode (const QString &)
 Sets the left code.
void setLeftFormula (const Formula &)
 Sets the left formula.
void setMonomerRefList (const QList< Monomer * > *)
void setName (const QString &)
 Sets the name.
void setPolChemDef (PolChemDef *)
void setRightCode (const QString &)
 Sets the right code.
void setRightFormula (const Formula &)
 Sets the right formula.
virtual bool validate () const
bool validate ()
 Validates the cleavage rule.
 ~CleaveRule ()
 Destroys the cleavage rule.

Static Public Member Functions

static int isNameInList (const QString &, const QList< CleaveRule * > &, CleaveRule *other=0)

Protected Attributes

QString m_name
const PolChemDefmp_polChemDef
 Pointer to the reference polymer chemistry definition.

Private Attributes

QString m_leftCode
 Left code.
Formula m_leftFormula
 Left formula.
QString m_rightCode
 Right code.
Formula m_rightFormula
 Right formula.

The documentation for this class was generated from the following files:

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