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massXpert::Modif Class Reference

#include <modif.hpp>

Inheritance diagram for massXpert::Modif:

massXpert::PolChemDefEntity massXpert::Formula massXpert::Ponderable massXpert::PropListHolder

List of all members.


Detailed Description

The Modif class provides a chemical modification.

Chemical modifications are found very often in biopolymers. These can be phophorylations of seryl residues or acetylation of lysyl residues or methylation of DNA bases, for example.

Monomers and polymers are typical substrates for chemical modifications.

Definition at line 64 of file modif.hpp.


Public Member Functions

bool accountAtoms (const QList< Atom * > &, int)
 Accounts the atoms in the formula times times.
bool accountInList (AtomCount *, int *=0)
 Accounts the atomCount instance into the list.
virtual bool accountMasses (double *=0, double *=0, int=1) const
 Increments the masses in the arguments.
virtual bool accountMasses (const QList< Atom * > &, Ponderable *, int=1)
 Accounts this formula's mono/avg masses.
virtual bool accountMasses (const QList< Atom * > &, double *=0, double *=0, int=1)
 Accounts this formula's mono/avg masses.
bool accountMasses (double *mono=0, double *avg=0, int times=1)
 Increments the masses in the arguments.
QChar actions () const
 Tells the actions found in the formula.
QChar actions (const QString &) const
 Tells the actions found in the formula.
bool appendProp (Prop *)
const QList< AtomCount * > & atomCountList () const
 Returns the list of atom count objects.
QString avg (const QLocale &, int=10) const
 Returns the average mass as a string.
double avg () const
 Returns the average mass.
bool calculateMasses ()
 Calculates the net masses.
bool checkSyntax ()
 Checks the syntax of the formula.
void clearMasses ()
 Clears the monoisotopic and average masses by setting both to 0.
virtual void clone (PropListHolder *) const
virtual void clone (Ponderable *) const
 Modifies other to be identical to this.
virtual void clone (Formula *) const
 Modifies other to be identical to this.
virtual void clone (PolChemDefEntity *) const
 Modifies other to be identical to this.
void clone (Modif *) const
 Modifies other to be identical to this.
Modifclone () const
 Creates a new modification.
void debugPutStdErr ()
 Outputs a string to the standard error console.
void decrementAvg (double)
 Decrements the average mass by mass.
void decrementMono (double)
 Decrements the monoisotopic mass by mass.
bool deepAtomCopy (const QList< Atom * > &refList)
 Performs a deep copy of the atom count objects.
QString elementalComposition () const
 Computes a formula string.
QString * formatXmlMdfElement (int, const QString &=QString(" "))
 Formats a string suitable to use as an XML element.
QString formula () const
 Returns the formula.
bool hasMonomerTarget (QString) const
void incrementAvg (double)
 Increments the average mass by mass.
void incrementMass (double, MassType)
void incrementMono (double)
 Increments the monoisotopic mass by mass.
int isNameKnown ()
 Searches this modification in the reference list.
double mass (MassType) const
void masses (double *=0, double *=0) const
 Updates the arguments with the monoisotopic and average masses.
int maxCount ()
 Modif (const Modif &)
 Constructs a copy of other.
 Modif (const PolChemDef *, QString, QString=QString())
 Constructs a modification.
virtual void mold (const PropListHolder &)
virtual void mold (const Ponderable &)
 Modifies this to be identical to other.
virtual void mold (const Formula &)
 Modifies this to be identical to other.
virtual void mold (const PolChemDefEntity &)
 Modifies this to be identical to other.
void mold (const Modif &)
 Modifies this to be identical to other.
QString mono (const QLocale &, int=10) const
 Returns the monoisotopic mass as a string.
double mono () const
 Returns the monoisotopic mass.
QString name () const
 Returns the name.
virtual bool operator!= (const Ponderable &) const
 Inquality operator.
virtual bool operator!= (const Formula &) const
 Tests inequality.
virtual bool operator!= (const PolChemDefEntity &) const
 Tests inequality.
bool operator!= (const Modif &)
 Tests inequality.
Modifoperator= (const Modif &)
 Assigns other to this modification.
virtual bool operator== (const Ponderable &) const
 Equality operator.
virtual bool operator== (const Formula &) const
 Tests equality.
virtual bool operator== (const PolChemDefEntity &) const
 Tests equality.
bool operator== (const Modif &)
 Tests equality.
const PolChemDefpolChemDef () const
 Returns the polymer chemistry definition.
Propprop (const QString &, int *=0)
int propIndex (const QString &, Prop *=0)
QList< Prop * > & propList ()
const QList< Prop * > & propList () const
int propListSize () const
double & ravg ()
 Returns a reference to the average mass.
bool removeProp (const QString &)
bool removeProp (Prop *)
bool renderXmlFormulaElement (const QDomElement &)
 Parses a formula XML element and sets the data to the formula.
bool renderXmlMdfElement (const QDomElement &)
bool renderXmlMdfElement (const QDomElement &, int)
 Renders a modification XML element specifically for version.
bool renderXmlMdfElementV2 (const QDomElement &)
bool renderXmlMdfElementV3 (const QDomElement &)
void reset ()
 Reset the modification to an empty object.
double & rmono ()
 Returns a reference to the monoisotopic mass.
bool setAvg (const QString &, const QLocale &)
 Sets the average mass to mass.
void setAvg (double)
 Sets the average mass to mass.
void setFormula (const Formula &)
 Sets the formula.
void setFormula (const QString &)
 Sets the formula.
void setMass (double, MassType)
void setMasses (double, double)
 Sets the monoisotopic and average masses.
void setMaxCount (int)
bool setMono (const QString &, const QLocale &)
 Sets the monoisotopic mass to mass.
void setMono (double)
 Sets the monoisotopic mass to mass.
void setName (const QString &)
 Sets the name.
void setPolChemDef (PolChemDef *)
QString & setTargets (QString)
int targets (QStringList &) const
QString targets () const
int totalAtoms () const
 Computes the total number of atoms.
bool totalEntities (const QList< Atom * > &refList, int *=0, int *=0) const
 Computes the number of entities(atoms and isotopes).
int totalIsotopes (const QList< Atom * > &refList) const
 Computes the total number of isotopes.
virtual bool validate (const QList< Atom * > &, bool=false, bool=false)
 Validates the formula.
virtual bool validate () const
bool validate ()
bool validateTargets (bool=true)

Static Public Member Functions

static bool checkSyntax (QString &)
 Checks the syntax of the formula.
static int isNameInList (const QString &, const QList< Modif * > &, Modif *=0)
 Searches a modification in a modification list.

Protected Member Functions

const QString & minusFormula () const
 Returns the minus-formula.
bool parse (const QList< Atom * > &, const QString &, int=1, bool=false, bool=false)
 Parses the formula using the reference atom list.
const QString & plusFormula () const
 Returns the plus-formula.
void setMinusFormula (const QString &)
 Sets the minus-formula.
void setPlusFormula (const QString &)
 Sets the plus-formula.
int splitParts (const QList< Atom * > &, int=1, bool=false, bool=false)
 Splits the formula according to its plus-/minus- actions.

Protected Attributes

QList< AtomCount * > m_atomCountList
 List of dynamically allocated AtomCount objects.
double m_avg
 Average mass.
QString m_formula
 Formula or action-formula.
QString m_minusFormula
 Minus-formula(or '-'-associated formula).
double m_mono
 Monoisotopic mass.
QString m_name
 Name.
QString m_plusFormula
 Plus-formula(or '+'-associated formula).
QList< Prop * > m_propList
const PolChemDefmp_polChemDef
 Pointer to the reference polymer chemistry definition.

Private Attributes

int m_maxCount
QString m_targets

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

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