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massXpert::PolChemDef Class Reference

#include <polChemDef.hpp>

List of all members.


Detailed Description

The PolChemDef class provides a polymer chemistry definition.

A polymer chemistry definition allows to characterize in a fine manner the chemistry of a polymer. That means that it should contain:

and a number of chemical data, like the left and right cap formulas, the code length(that is the maximum number of characters that might be used to construct a monomer code).

Because monomers have to be graphically rendered at some point, in the form of monomer vignettes in the sequence editor, the polymer chemistry definition also contains:

Definition at line 103 of file polChemDef.hpp.


Public Member Functions

const QList< Atom * > & atomList () const
 Returns the list of atoms.
QList< Atom * > * atomListPtr ()
 Returns the list of atoms.
bool calculateDelimitedCodes ()
 Constructs a string with all the known monomer codes.
ChemEntVignetteRenderer * chemEntVignetteRenderer (const QString &)
 Searches a chemical entity vignette renderer associated to key.
QHash< QString,
ChemEntVignetteRenderer * > * 
chemEntVignetteRendererHash ()
 Returns the hash of vignette renderers.
const QList< CleaveSpec * > & cleaveSpecList () const
 Returns the list of cleavage specifications.
QList< CleaveSpec * > * cleaveSpecListPtr ()
 Returns the list of cleavage specifications.
int codeLength () const
 Returns the code length.
bool crossLinker (const QString &, CrossLinker *=0) const
const QList< CrossLinker * > & crossLinkerList () const
 Returns the list of cross-linkers.
QList< CrossLinker * > * crossLinkerListPtr ()
 Returns the list of cross-linkers.
QList< CrossLinkerSpec * > * crossLinkerSpecList ()
 Returns the list of cross-link specifications.
void decrementRefCount ()
 Decrements the reference count by one unit.
const QString & delimitedCodes ()
 Returns the delimited codes string.
QString dirPath () const
 Computes the directory path.
QString filePath () const
 Returns the file path.
QString * formatXmlDtd ()
 Creates the XML DTD for a polymer chemistry definition file.
const QList< FragSpec * > & fragSpecList () const
 Returns the list of fragmentation specifications.
QList< FragSpec * > * fragSpecListPtr ()
 Returns the list of fragmentation specifications.
void incrementRefCount ()
 Increments the reference count by one unit.
const IonizeRuleionizeRule () const
 Returns the ionization rule.
IonizeRuleionizeRulePtr ()
 Returns the ionization rule.
const FormulaleftCap () const
 Returns the left cap formula.
bool modif (const QString &, Modif *=0) const
 Returns the modification object corresponding to name.
const QList< Modif * > & modifList () const
 Returns the list of modifications.
QList< Modif * > * modifListPtr ()
 Returns the list of modifications.
QList< ModifSpec * > * modifSpecList ()
 Returns the list of modification specifications.
const QList< Monomer * > & monomerList () const
 Returns the list of monomers.
QList< Monomer * > * monomerListPtr ()
 Returns the list of monomers.
QList< MonomerSpec * > * monomerSpecList ()
 Returns the list of monomer specifications.
QString name () const
 Returns the name.
ChemEntVignetteRenderer * newChemEntVignetteRenderer (const QString &, QObject *=0)
 Creates a chemical entity vignette renderer.
ChemEntVignetteRenderer * newCrossLinkerVignetteRenderer (const QString &, QObject *=0)
ChemEntVignetteRenderer * newModifVignetteRenderer (const QString &, QObject *=0)
 Creates a modification vignette renderer.
ChemEntVignetteRenderer * newMonomerVignetteRenderer (const QString &, QObject *=0)
 Creates a monomer vignette renderer.
 PolChemDef (const PolChemDefSpec &)
 Constructs a polymer chemistry definition.
 PolChemDef ()
 Constructs a polymer chemistry definition.
int refCount ()
 Returns the reference count.
bool renderXmlPolChemDefFile ()
 Parses a polymer chemistry definition file.
const FormularightCap () const
 Returns the right cap formula.
void setCodeLength (int)
 Sets the code length.
void setFilePath (const QString &)
 Sets the file path.
void setIonizeRule (const IonizeRule &)
 Sets the ionization rule.
void setLeftCap (const Formula &)
 Sets the left cap formula.
void setName (const QString &)
 Sets the name.
void setRefCount (int)
 Sets the reference count.
void setRepositoryList (QList< PolChemDef * > *)
void setRightCap (const Formula &)
 Sets the right cap formula.
void setVersion (const QString &)
QString version () const
bool writeXmlFile ()
 Write the polymer chemistry definition to file.
 ~PolChemDef ()
 Destroys the polymer chemistry definition.

Private Attributes

QList< Atom * > m_atomList
 List of atoms.
QHash< QString,
ChemEntVignetteRenderer * > 
m_chemEntVignetteRendererHash
 Hash of graphical vignettes.
QList< CleaveSpec * > m_cleaveSpecList
 List of cleavage specifications.
int m_codeLength
 Code length.
QList< CrossLinker * > m_crossLinkerList
 List of cross-linkers.
QList< CrossLinkerSpec * > m_crossLinkerSpecList
 List of cross-link specifications.
QString m_delimitedCodes
 Delimited codes string.
QString m_filePath
 File path.
QList< FragSpec * > m_fragSpecList
 List of fragmentation specifications.
IonizeRule m_ionizeRule
 Ionization rule.
Formula m_leftCap
 Left cap formula.
QList< Modif * > m_modifList
 List of modifications.
QList< ModifSpec * > m_modifSpecList
 List of modification specifications.
QList< Monomer * > m_monomerList
 List of monomers.
QList< MonomerSpec * > m_monomerSpecList
 List of monomer specifications.
QString m_name
 Name.
int m_refCount
 Reference count.
Formula m_rightCap
 Right cap formula.
QList< PolChemDef * > * mp_repositoryList

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

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