#include <BALL/STRUCTURE/smilesParser.h>

Inheritance diagram for BALL::SmilesParser::SPAtom:

Public Member Functions
	SPAtom (const String &symbol, bool in_brackets)

virtual	~SPAtom ()

Size	getDefaultValence () const

Size	countRealValences () const

Size	getIsotope () const

void	setIsotope (Size isotope)

Index	getFormalCharge () const

void	setFormalCharge (Index charge)

const ChiralDef &	getChirality () const

void	setChirality (const ChiralDef &chirality)

bool	isAromatic () const

void	setAromatic (bool is_aromatic)

bool	isInBrackets () const

void	setInBrackets (bool in_brackets)

Public Member Functions inherited from BALL::Atom
	Atom ()

	Atom (const Atom &atom, bool deep=true)

	Atom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE)

virtual	~Atom ()

virtual void	clear ()

virtual void	destroy ()

virtual void	persistentWrite (PersistenceManager &pm, const char *name=0) const

virtual void	persistentRead (PersistenceManager &pm)

void	set (const Atom &atom, bool deep=true)

void	get (Atom &atom, bool deep=true) const

Atom &	operator= (const Atom &atom)

void	swap (Atom &atom)

bool	operator== (const Atom &atom) const

bool	operator!= (const Atom &atom) const

void	setElement (const Element &element)
	Assign the atom's element. More...

const Element &	getElement () const
	Return the atom's element. More...

void	setCharge (float charge)

float	getCharge () const

void	setFormalCharge (Index formal_charge)
	Set the atom's formal charge. More...

Index	getFormalCharge () const
	Return the atom's formal charge. More...

const Molecule *	getMolecule () const

Molecule *	getMolecule ()
	Return the molecule the atom is contained in (mutable) More...

const Fragment *	getFragment () const

Fragment *	getFragment ()
	Return the fragment the atom is contained in (mutable) More...

const Residue *	getResidue () const

Residue *	getResidue ()
	Return the residue the atom is contained in (mutable) More...

const SecondaryStructure *	getSecondaryStructure () const

SecondaryStructure *	getSecondaryStructure ()
	Return the secondary structure the atom is contained in (mutable) More...

const Chain *	getChain () const

Chain *	getChain ()
	Return the chain the atom is contained in (mutable) More...

void	setName (const String &name)
	Set the atom name. More...

const String &	getName () const
	Return the atom name. More...

String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const

void	setPosition (const Vector3 &position)

Vector3 &	getPosition ()
	Return the atom coordinates (mutable) More...

const Vector3 &	getPosition () const
	Return the atom coordinates (const) More...

void	setRadius (float radius)

float	getRadius () const
	Return the atom radius. More...

void	setType (Type atom_type)
	Assign the numerical atom type. More...

Type	getType () const
	Return the (numerical) atom type. More...

String	getTypeName () const
	Return the atom type name. More...

void	setTypeName (const String &name)
	Assign the atom type name. More...

void	setVelocity (const Vector3 &velocity)

Vector3 &	getVelocity ()

const Vector3 &	getVelocity () const

void	setForce (const Vector3 &force)

const Vector3 &	getForce () const
	Return the atom's force vector (const) More...

Vector3 &	getForce ()
	Return the atom's force vector (mutable) More...

Size	countBonds () const
	Return the number of bonds. More...

Bond *	getBond (Position index)

const Bond *	getBond (Position index) const

Bond *	getBond (const Atom &atom)

const Bond *	getBond (const Atom &atom) const

Bond *	createBond (Atom &atom)

Bond *	createBond (Bond &bond, Atom &atom)

Bond *	cloneBond (Bond &bond, Atom &atom)

bool	destroyBond (const Atom &atom)

void	destroyBonds ()

Atom *	getPartnerAtom (Position i)

const Atom *	getPartnerAtom (Position i) const

float	getDistance (const Atom &a) const

bool	hasBond (const Bond &bond) const

bool	isBoundTo (const Atom &atom) const

bool	isBound () const

bool	isGeminal (const Atom &atom) const

bool	isVicinal (const Atom &atom) const

virtual bool	isValid () const

virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

bool	applyBonds (UnaryProcessor< Bond > &processor)

BondIterator	beginBond ()
	Return a bond iterator pointing to the first bond of the atom. More...

BondIterator	endBond ()
	Return a past-the-end bond iterator. More...

BondConstIterator	beginBond () const
	Return a constant bond iterator pointing to the first bond. More...

BondConstIterator	endBond () const
	Return a constant past-the-end bond iterator. More...

BondReverseIterator	rbeginBond ()
	Return a reverse bond iterator pointing to the last bond. More...

BondReverseIterator	rendBond ()
	Return a past-the-end bond iterator for reverse traversal. More...

BondConstReverseIterator	rbeginBond () const
	Return a constant reverse bond iterator pointing to the first atom. More...

BondConstReverseIterator	rendBond () const
	Return a constant past-the-end bond iterator for reverse traversal. More...

Public Member Functions inherited from BALL::Composite
AncestorIterator	beginAncestor ()

AncestorIterator	endAncestor ()

AncestorConstIterator	beginAncestor () const

AncestorConstIterator	endAncestor () const

ChildCompositeIterator	beginChildComposite ()

ChildCompositeIterator	endChildComposite ()

ChildCompositeConstIterator	beginChildComposite () const

ChildCompositeConstIterator	endChildComposite () const

ChildCompositeReverseIterator	rbeginChildComposite ()

ChildCompositeReverseIterator	rendChildComposite ()

ChildCompositeConstReverseIterator	rbeginChildComposite () const

ChildCompositeConstReverseIterator	rendChildComposite () const

CompositeIterator	beginComposite ()

CompositeIterator	endComposite ()

CompositeConstIterator	beginComposite () const

CompositeConstIterator	endComposite () const

CompositeReverseIterator	rbeginComposite ()

CompositeReverseIterator	rendComposite ()

CompositeConstReverseIterator	rbeginComposite () const

CompositeConstReverseIterator	rendComposite () const

void	deleteChildrenList_ (std::list< Composite * > &composites)

template<typename T >
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)

template<typename T >
BALL_INLINE T *	getAncestor (const T &)

template<typename T >
BALL_INLINE const T *	getAncestor (const T &) const

template<typename T >
BALL_INLINE T *	getPrevious (const T &)

template<typename T >
BALL_INLINE const T *	getPrevious (const T &dummy) const

template<typename T >
BALL_INLINE T *	getNext (const T &)

template<typename T >
BALL_INLINE const T *	getNext (const T &dummy) const

template<typename T >
BALL_INLINE bool	hasAncestor (const T &dummy) const

	Composite ()

	Composite (const Composite &composite, bool deep=true)

virtual	~Composite ()

void	destroy (bool virtual_destroy)

void *	clone (Composite &root) const

bool	operator== (const Composite &composite) const

bool	operator!= (const Composite &composite) const

bool	isEmpty () const

bool	isRoot () const

bool	isRootOf (const Composite &composite) const

bool	isInterior () const

bool	hasChild () const

bool	isChildOf (const Composite &composite) const

bool	isFirstChild () const

bool	isFirstChildOf (const Composite &composite) const

bool	isLastChild () const

bool	isLastChildOf (const Composite &composite) const

bool	hasParent () const

bool	isParentOf (const Composite &composite) const

bool	hasSibling () const

bool	isSiblingOf (const Composite &composite) const

bool	hasPreviousSibling () const

bool	isPreviousSiblingOf (const Composite &composite) const

bool	hasNextSibling () const

bool	isNextSiblingOf (const Composite &composite) const

bool	isDescendantOf (const Composite &composite) const

template<typename T >
bool	hasAncestor (const T &dummy) const

bool	isAncestorOf (const Composite &composite) const

bool	isRelatedWith (const Composite &composite) const

bool	isHomomorph (const Composite &composite) const

bool	containsSelection () const

void	host (Visitor< Composite > &visitor)

template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)

template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	apply (UnaryProcessor< T > &processor)

template<typename T >
bool	applyLevel (UnaryProcessor< T > &processor, long level)

void	set (const Composite &composite, bool deep=true)

Composite &	operator= (const Composite &composite)

void	get (Composite &composite, bool deep=true) const

Size	getDegree () const

Size	count (const KernelPredicateType &predicate) const

Size	countDescendants () const

Size	getPathLength (const Composite &composite) const

Size	getDepth () const

Size	getHeight () const

Composite &	getRoot ()

const Composite &	getRoot () const

Composite *	getLowestCommonAncestor (const Composite &composite)

const Composite *	getLowestCommonAncestor (const Composite &composite) const

template<typename T >
T *	getAncestor (const T &)

template<typename T >
const T *	getAncestor (const T &) const

template<typename T >
T *	getPrevious (const T &)

template<typename T >
const T *	getPrevious (const T &dummy) const

template<typename T >
T *	getNext (const T &)

template<typename T >
const T *	getNext (const T &dummy) const

Composite *	getParent ()

const Composite *	getParent () const

Composite *	getChild (Index index)

const Composite *	getChild (Index index) const

Composite *	getSibling (Index index)

const Composite *	getSibling (Index index) const

Composite *	getFirstChild ()

const Composite *	getFirstChild () const

Composite *	getLastChild ()

const Composite *	getLastChild () const

const PreciseTime &	getModificationTime () const

const PreciseTime &	getSelectionTime () const

void	stamp (StampType stamp=BOTH)

void	prependChild (Composite &composite)

void	appendChild (Composite &composite)

void	insertBefore (Composite &composite)

void	insertAfter (Composite &composite)

void	spliceBefore (Composite &composite)

void	spliceAfter (Composite &composite)

void	splice (Composite &composite)

bool	removeChild (Composite &child)

Size	removeSelected ()

Size	removeUnselected ()

void	replace (Composite &composite)

void	swap (Composite &composite)

virtual void	select ()

virtual void	deselect ()

Public Member Functions inherited from BALL::PersistentObject
	PersistentObject ()

virtual	~PersistentObject ()

PersistenceManager &	operator>> (PersistenceManager &pm) const

virtual void	finalize ()

Public Member Functions inherited from BALL::Object
	Object ()
	Default constructor. More...

	Object (const Object &object)
	Copy constructor. More...

virtual	~Object ()
	Destructor. More...

const Object &	operator= (const Object &)

bool	operator== (const Object &object) const

bool	operator!= (const Object &object) const

bool	operator< (const Object &object) const

bool	operator<= (const Object &object) const

bool	operator>= (const Object &object) const

bool	operator> (const Object &object) const

int	compare (const Object &object) const

virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const

Handle	getHandle () const

Public Member Functions inherited from BALL::AutoDeletable
virtual	~AutoDeletable ()

void *	operator new (size_t size)

void	operator delete (void *ptr)

void *	operator new (size_t size, void *ptr)

void	operator delete (void ptr, void )

bool	isAutoDeletable () const

void	setAutoDeletable (bool enable)

Public Member Functions inherited from BALL::Selectable
	Selectable ()

	Selectable (const Selectable &selectable, bool deep=true)

virtual	~Selectable ()

void	set (const Selectable &selectable, bool deep=true)

const Selectable &	operator= (const Selectable &selectable)

void	get (Selectable &selectable, bool deep=true) const

void	swap (Selectable &selectable)

virtual void	setSelected (bool selected)

bool	isSelected () const

bool	operator== (const Selectable &selectable) const

bool	operator!= (const Selectable &selectable) const

void	write (PersistenceManager &pm) const

bool	read (PersistenceManager &pm)

virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const

Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor. More...

BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor. More...

virtual	~PropertyManager ()
	Destructor. More...

void	set (const PropertyManager &property_manager)

const PropertyManager &	operator= (const PropertyManager &property_manager)

void	get (PropertyManager &property_manager) const

void	swap (PropertyManager &property_manager)

BitVector &	getBitVector ()

const BitVector &	getBitVector () const

	operator BitVector & ()

void	setProperty (Property property)

void	clearProperty (Property property)

void	toggleProperty (Property property)

Size	countProperties () const

const NamedProperty &	getNamedProperty (Position index) const

NamedProperty &	getNamedProperty (Position index)

void	setProperty (const NamedProperty &property)

void	setProperty (const string &name)

void	setProperty (const string &name, bool value)

void	setProperty (const string &name, int value)

void	setProperty (const string &name, unsigned int value)

void	setProperty (const string &name, float value)

void	setProperty (const string &name, double value)

void	setProperty (const string &name, const string &value)

void	setProperty (const string &name, const PersistentObject &value)

const NamedProperty &	getProperty (const string &name) const

NamedPropertyIterator	beginNamedProperty ()

NamedPropertyIterator	endNamedProperty ()

void	clearProperty (const string &name)

Size	countNamedProperties () const

bool	hasProperty (Property property) const
	Query for an unnamed property. More...

bool	hasProperty (const string &name) const
	Query for a named property. More...

bool	operator== (const PropertyManager &pm) const

bool	operator!= (const PropertyManager &pm) const
	Inequality operator. More...

void	write (PersistenceManager &pm) const
	Persistent stream writing. More...

bool	read (PersistenceManager &pm)
	Persistent stream reading. More...

bool	isValid () const

void	dump (std::ostream &s=std::cout, Size depth=0) const

Protected Attributes
Size	isotope_

Index	formal_charge_

ChiralDef	chirality_

bool	is_aromatic_

bool	in_brackets_

Protected Attributes inherited from BALL::Atom
String	name_

String	type_name_

const Element *	element_

float	radius_

Type	type_

unsigned char	number_of_bonds_

Bond *	bond_ [MAX_NUMBER_OF_BONDS]

Index	formal_charge_

Vector3	position_

float	charge_

Vector3	velocity_

Vector3	force_

Additional Inherited Members
Public Types inherited from BALL::Atom
enum	{ UNKNOWN_TYPE = -1, ANY_TYPE = 0, MAX_NUMBER_OF_BONDS = 12 }

enum	Property { NUMBER_OF_PROPERTIES = 0 }

enum	FullNameType { NO_VARIANT_EXTENSIONS, ADD_VARIANT_EXTENSIONS, ADD_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_ID, ADD_CHAIN_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID }

typedef std::list< Atom * >	AtomPtrList

typedef std::list< Position >	AtomIndexList

typedef short	Type

typedef Index	BondIteratorPosition

typedef RandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondIterator

typedef ConstRandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondConstIterator
	Constant random access iterator for bonds. More...

typedef std::reverse_iterator < BondIterator >	BondReverseIterator
	Reverse random access iterator for bonds. More...

typedef std::reverse_iterator < BondConstIterator >	BondConstReverseIterator
	Constant reverse random access iterator for bonds. More...

Static Public Member Functions inherited from BALL::Composite
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)

Static Public Member Functions inherited from BALL::Object
static Handle	getNextHandle ()

static Handle	getNewHandle ()

Static Public Member Functions inherited from BALL::AutoDeletable
static void	clearLastPtr ()

Static Public Attributes inherited from BALL::Composite
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR

static KernelPredicateType	DEFAULT_UNARY_PREDICATE

Protected Member Functions inherited from BALL::AutoDeletable
	AutoDeletable ()

	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Static Protected Attributes inherited from BALL::Atom
static AtomIndexList	free_list_

Friends inherited from BALL::Atom

Detailed Description

Definition at line 79 of file smilesParser.h.

Constructor & Destructor Documentation

BALL::SmilesParser::SPAtom::SPAtom	(	const String &	symbol,
		bool	in_brackets
	)

virtual BALL::SmilesParser::SPAtom::~SPAtom ( )

virtual

Member Function Documentation

Size BALL::SmilesParser::SPAtom::countRealValences ( ) const

const ChiralDef& BALL::SmilesParser::SPAtom::getChirality ( ) const

inline

Definition at line 96 of file smilesParser.h.

Size BALL::SmilesParser::SPAtom::getDefaultValence ( ) const

Index BALL::SmilesParser::SPAtom::getFormalCharge ( ) const

inline

Definition at line 93 of file smilesParser.h.

Size BALL::SmilesParser::SPAtom::getIsotope ( ) const

inline

Definition at line 90 of file smilesParser.h.

bool BALL::SmilesParser::SPAtom::isAromatic ( ) const

inline

Definition at line 99 of file smilesParser.h.

bool BALL::SmilesParser::SPAtom::isInBrackets ( ) const

inline

Definition at line 101 of file smilesParser.h.

void BALL::SmilesParser::SPAtom::setAromatic ( bool is_aromatic )

inline

Definition at line 100 of file smilesParser.h.

void BALL::SmilesParser::SPAtom::setChirality ( const ChiralDef & chirality )

inline

Definition at line 97 of file smilesParser.h.

void BALL::SmilesParser::SPAtom::setFormalCharge ( Index charge )

inline

Definition at line 94 of file smilesParser.h.

void BALL::SmilesParser::SPAtom::setInBrackets ( bool in_brackets )

inline

Definition at line 102 of file smilesParser.h.

void BALL::SmilesParser::SPAtom::setIsotope ( Size isotope )

inline

Definition at line 91 of file smilesParser.h.

Member Data Documentation

ChiralDef BALL::SmilesParser::SPAtom::chirality_

protected

Definition at line 107 of file smilesParser.h.

Index BALL::SmilesParser::SPAtom::formal_charge_

protected

Definition at line 106 of file smilesParser.h.

bool BALL::SmilesParser::SPAtom::in_brackets_

protected

Definition at line 109 of file smilesParser.h.

bool BALL::SmilesParser::SPAtom::is_aromatic_

protected

Definition at line 108 of file smilesParser.h.

Size BALL::SmilesParser::SPAtom::isotope_

protected

Definition at line 102 of file smilesParser.h.

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation