#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.
const Element &	getElement () const
	Return the atom's element.
void	setCharge (float charge)
float	getCharge () const
void	setFormalCharge (Index formal_charge)
	Set the atom's formal charge.
Index	getFormalCharge () const
	Return the atom's formal charge.
const Molecule *	getMolecule () const
Molecule *	getMolecule ()
	Return the molecule the atom is contained in (mutable).
const Fragment *	getFragment () const
Fragment *	getFragment ()
	Return the fragment the atom is contained in (mutable).
const Residue *	getResidue () const
Residue *	getResidue ()
	Return the residue the atom is contained in (mutable).
const SecondaryStructure *	getSecondaryStructure () const
SecondaryStructure *	getSecondaryStructure ()
	Return the secondary structure the atom is contained in (mutable).
const Chain *	getChain () const
Chain *	getChain ()
	Return the chain the atom is contained in (mutable).
void	setName (const String &name)
	Set the atom name.
const String &	getName () const
	Return the atom name.
String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const
void	setPosition (const Vector3 &position)
Vector3 &	getPosition ()
	Return the atom coordinates (mutable).
const Vector3 &	getPosition () const
	Return the atom coordinates (const).
void	setRadius (float radius)
float	getRadius () const
	Return the atom radius.
void	setType (Type atom_type)
	Assign the numerical atom type.
Type	getType () const
	Return the (numerical) atom type.
String	getTypeName () const
	Return the atom type name.
void	setTypeName (const String &name)
	Assign the atom type name.
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).
Vector3 &	getForce ()
	Return the atom's force vector (mutable).
Size	countBonds () const
	Return the number of bonds.
Bond *	getBond (Position index)
const Bond *	getBond (Position index) const
Bond *	getBond (const Atom &atom)
const Bond *	getBond (const Atom &atom) 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	isAtom () 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.
BondIterator	endBond ()
	Return a past-the-end bond iterator.
BondConstIterator	beginBond () const
	Return a constant bond iterator pointing to the first bond.
BondConstIterator	endBond () const
	Return a constant past-the-end bond iterator.
BondReverseIterator	rbeginBond ()
	Return a reverse bond iterator pointing to the last bond.
BondReverseIterator	rendBond ()
	Return a past-the-end bond iterator for reverse traversal.
BondConstReverseIterator	rbeginBond () const
	Return a constant reverse bond iterator pointing to the first atom.
BondConstReverseIterator	rendBond () const
	Return a constant past-the-end bond iterator for reverse traversal.
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
void	addInteraction (const Atom *atom, String interaction_type, double energy)
void	addInteraction (String interaction_type, double energy)
void	disableStoreInteractions ()
void	enableStoreInteractions ()
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	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
virtual void	finalize ()
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
Size	isotope_
Index	formal_charge_
ChiralDef	chirality_
bool	is_aromatic_
bool	in_brackets_
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_
bool	selected_

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.
typedef std::reverse_iterator< BondIterator >	BondReverseIterator
	Reverse random access iterator for bonds.
typedef std::reverse_iterator< BondConstIterator >	BondConstReverseIterator
	Constant reverse random access iterator for bonds.
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 bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)
static Handle	getNextHandle ()
static Handle	getNewHandle ()
static void	clearLastPtr ()
MolecularInteractions *	interactions
bool	store_interactions_disabled_
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR
static KernelPredicateType	DEFAULT_UNARY_PREDICATE
	AutoDeletable ()
	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)
static AtomIndexList	free_list_

Detailed Description

Definition at line 79 of file smilesParser.h.

Constructor & Destructor Documentation

◆ SPAtom()

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

◆ ~SPAtom()

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

virtual

Member Function Documentation

◆ countRealValences()

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

◆ getChirality()

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

inline

Definition at line 96 of file smilesParser.h.

◆ getDefaultValence()

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

◆ getFormalCharge()

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

inline

Definition at line 93 of file smilesParser.h.

◆ getIsotope()

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

inline

Definition at line 90 of file smilesParser.h.

◆ isAromatic()

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

inline

Definition at line 99 of file smilesParser.h.

◆ isInBrackets()

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

inline

Definition at line 101 of file smilesParser.h.

◆ setAromatic()

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

inline

Definition at line 100 of file smilesParser.h.

◆ setChirality()

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

inline

Definition at line 97 of file smilesParser.h.

◆ setFormalCharge()

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

inline

Definition at line 94 of file smilesParser.h.

◆ setInBrackets()

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

inline

Definition at line 102 of file smilesParser.h.

◆ setIsotope()

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

inline

Definition at line 91 of file smilesParser.h.

Member Data Documentation

◆ chirality_

ChiralDef BALL::SmilesParser::SPAtom::chirality_

protected

Definition at line 107 of file smilesParser.h.

◆ formal_charge_

Index BALL::SmilesParser::SPAtom::formal_charge_

protected

Definition at line 106 of file smilesParser.h.

◆ in_brackets_

bool BALL::SmilesParser::SPAtom::in_brackets_

protected

Definition at line 109 of file smilesParser.h.

◆ is_aromatic_

bool BALL::SmilesParser::SPAtom::is_aromatic_

protected

Definition at line 108 of file smilesParser.h.

◆ isotope_

Size BALL::SmilesParser::SPAtom::isotope_

protected

Definition at line 105 of file smilesParser.h.

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SPAtom()

◆ ~SPAtom()

Member Function Documentation

◆ countRealValences()

◆ getChirality()

◆ getDefaultValence()

◆ getFormalCharge()

◆ getIsotope()

◆ isAromatic()

◆ isInBrackets()

◆ setAromatic()

◆ setChirality()

◆ setFormalCharge()

◆ setInBrackets()

◆ setIsotope()

Member Data Documentation

◆ chirality_

◆ formal_charge_

◆ in_brackets_

◆ is_aromatic_

◆ isotope_