BALL::SmilesParser::SPBond Class Reference

#include <BALL/STRUCTURE/smilesParser.h>

Inheritance diagram for BALL::SmilesParser::SPBond:

Public Member Functions
virtual	~SPBond ()
	SPBond (SPAtom *first, SPAtom *second, Index order=1)
ZEIsomerType	getZEType () const
void	setZEType (ZEIsomerType type)
Public Member Functions inherited from BALL::Bond
void	persistentWrite (PersistenceManager &pm, const char *name=0) const
void	persistentRead (PersistenceManager &pm)
void	finalize ()
bool	operator== (const Bond &bond) const
	Equality operator. Two bonds are equal, if they are identical instances.
bool	operator!= (const Bond &bond) const
	Inequality operator. Two bonds are not equal, if they are different instances.
bool	isBondOf (const Atom &atom) const
bool	isBound () const
bool	isInterBond () const
bool	isInterBondOf (const AtomContainer &atom_container) const
bool	isIntraBond () const
bool	isIntraBondOf (const AtomContainer &atom_container) const
Bond &	operator= (const Bond &bond)
void	swap (Bond &bond)
void	setFirstAtom (Atom *atom)
void	setSecondAtom (Atom *atom)
const Atom *	getFirstAtom () const
	Return a pointer to the first atom.
Atom *	getFirstAtom ()
	Return a pointer to the first atom.
const Atom *	getSecondAtom () const
	Return a pointer to the second atom.
Atom *	getSecondAtom ()
	Return a pointer to the second atom.
Atom *	getPartner (const Atom &atom) const
void	setName (const String &name)
	Assign the atom name.
const String &	getName () const
	Return the atom name.
void	setOrder (Order bond_order)
	Assign the bond order.
Order	getOrder () const
	Return the bond order.
bool	isAromatic () const
void	setType (Type bond_type)
	Set the bond type.
Type	getType () const
	Return the bond type.
float	getLength () const
const Atom *	getBoundAtom (const Atom &atom) const
Atom *	getBoundAtom (const Atom &atom)
virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Bond ()
	Bond (const Bond &bond, bool deep=true)
	Bond (const String &name, Atom &first, Atom &second, Order order=BALL_BOND_DEFAULT_ORDER, Type type=BALL_BOND_DEFAULT_TYPE)
virtual	~Bond ()
virtual void	clear ()
virtual void	destroy ()
Public Member Functions inherited from BALL::Composite
template<typename T>
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)
template<typename T>
BALL_INLINE bool	apply (ConstUnaryProcessor< T > &processor) const
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
virtual bool	isAtom () const
virtual bool	isMolecule () const
virtual bool	isProtein () const
virtual bool	isFragment () const
virtual bool	isResidue () const
virtual bool	isChain () const
void	host (Visitor< Composite > &visitor)
template<typename T>
bool	applyAncestor (UnaryProcessor< T > &processor)
template<typename T>
bool	applyAncestor (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyChild (UnaryProcessor< T > &processor)
template<typename T>
bool	applyChild (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyDescendant (UnaryProcessor< T > &processor)
template<typename T>
bool	applyDescendant (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyPreorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyPreorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyPostorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyPostorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	apply (UnaryProcessor< T > &processor)
template<typename T>
bool	apply (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyLevel (UnaryProcessor< T > &processor, long level)
template<typename T>
bool	applyLevel (ConstUnaryProcessor< T > &processor, long level) const
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)
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
Public Member Functions inherited from BALL::Object
	Object ()
	Default constructor.
	Object (const Object &object)
	Copy constructor.
virtual	~Object ()
	Destructor.
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.
BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor.
virtual	~PropertyManager ()
	Destructor.
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 std::string &name)
void	setProperty (const std::string &name, bool value)
void	setProperty (const std::string &name, int value)
void	setProperty (const std::string &name, unsigned int value)
void	setProperty (const std::string &name, float value)
void	setProperty (const std::string &name, double value)
void	setProperty (const std::string &name, const std::string &value)
void	setProperty (const std::string &name, const PersistentObject &value)
const NamedProperty &	getProperty (const std::string &name) const
NamedPropertyIterator	beginNamedProperty ()
NamedPropertyIterator	endNamedProperty ()
void	clearProperty (const std::string &name)
Size	countNamedProperties () const
bool	hasProperty (Property property) const
	Query for an unnamed property.
bool	hasProperty (const std::string &name) const
	Query for a named property.
bool	operator== (const PropertyManager &pm) const
bool	operator!= (const PropertyManager &pm) const
	Inequality operator.
void	write (PersistenceManager &pm) const
	Persistent stream writing.
bool	read (PersistenceManager &pm)
	Persistent stream reading.
bool	isValid () const
void	dump (std::ostream &s=std::cout, Size depth=0) const

Protected Attributes
ZEIsomerType	ze_type_
Atom *	first_
Atom *	second_
String	name_
Order	bond_order_
Type	bond_type_
bool	selected_

Additional Inherited Members
Public Types inherited from BALL::Bond
enum	BondOrder {   ORDER__UNKNOWN = 0 , ORDER__SINGLE = 1 , ORDER__DOUBLE = 2 , ORDER__TRIPLE = 3 ,   ORDER__QUADRUPLE = 4 , ORDER__AROMATIC = 5 , ORDER__ANY = 6 , NUMBER_OF_BOND_ORDERS }
enum	BondType {   TYPE__UNKNOWN = 0 , TYPE__COVALENT = 1 , TYPE__HYDROGEN = 2 , TYPE__DISULPHIDE_BRIDGE = 3 ,   TYPE__SALT_BRIDGE = 4 , TYPE__PEPTIDE = 5 , NUMBER_OF_BOND_TYPES }
enum	Property { IS_AROMATIC = 0 , NUMBER_OF_PROPERTIES }
typedef short	Order
typedef short	Type
Public Types inherited from BALL::Composite
enum	StampType { MODIFICATION = 1 , SELECTION = 2 , BOTH = 3 }
typedef UnaryPredicate< Composite >	KernelPredicateType
typedef ForwardIterator< Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorIterator
typedef ConstForwardIterator< Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorConstIterator
typedef BidirectionalIterator< Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeIterator
typedef ConstBidirectionalIterator< Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeConstIterator
typedef std::reverse_iterator< ChildCompositeIterator >	ChildCompositeReverseIterator
typedef std::reverse_iterator< ChildCompositeConstIterator >	ChildCompositeConstReverseIterator
typedef BidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeIterator
typedef ConstBidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeConstIterator
typedef std::reverse_iterator< CompositeIterator >	CompositeReverseIterator
typedef std::reverse_iterator< CompositeConstIterator >	CompositeConstReverseIterator
static Bond *	createBond (Bond &bond, Atom &first, Atom &second)
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)
static Handle	getNextHandle ()
static Handle	getNewHandle ()
static void	clearLastPtr ()
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR
static KernelPredicateType	DEFAULT_UNARY_PREDICATE
	AutoDeletable ()
	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Detailed Description

Definition at line 64 of file smilesParser.h.

Constructor & Destructor Documentation

~SPBond()

virtual BALL::SmilesParser::SPBond::~SPBond ( )

virtual

SPBond()

BALL::SmilesParser::SPBond::SPBond	(	SPAtom *	first,
		SPAtom *	second,
		Index	order = 1 )

Member Function Documentation

getZEType()

ZEIsomerType BALL::SmilesParser::SPBond::getZEType

(

)

const

setZEType()

void BALL::SmilesParser::SPBond::setZEType

(

ZEIsomerType

type

)

Member Data Documentation

ze_type_

ZEIsomerType BALL::SmilesParser::SPBond::ze_type_

protected

Definition at line 76 of file smilesParser.h.