BALL  1.4.1
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Public Member Functions | Protected Attributes | List of all members
BALL::SmilesParser::SPBond Class Reference

#include <BALL/STRUCTURE/smilesParser.h>

Inheritance diagram for BALL::SmilesParser::SPBond:
BALL::Bond BALL::Composite BALL::PropertyManager BALL::PersistentObject BALL::Selectable BALL::Object BALL::AutoDeletable

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
Bondoperator= (const Bond &bond)
void swap (Bond &bond)
void setFirstAtom (Atom *atom)
void setSecondAtom (Atom *atom)
const AtomgetFirstAtom () const
 Return a pointer to the first atom.
AtomgetFirstAtom ()
 Return a pointer to the first atom.
const AtomgetSecondAtom () const
 Return a pointer to the second atom.
AtomgetSecondAtom ()
 Return a pointer to the second atom.
AtomgetPartner (const Atom &atom) const
void setName (const String &name)
 Assign the atom name.
const StringgetName () 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 AtomgetBoundAtom (const Atom &atom) const
AtomgetBoundAtom (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
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)
 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)
Compositeoperator= (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
CompositegetRoot ()
const CompositegetRoot () const
CompositegetLowestCommonAncestor (const Composite &composite)
const CompositegetLowestCommonAncestor (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
CompositegetParent ()
const CompositegetParent () const
CompositegetChild (Index index)
const CompositegetChild (Index index) const
CompositegetSibling (Index index)
const CompositegetSibling (Index index) const
CompositegetFirstChild ()
const CompositegetFirstChild () const
CompositegetLastChild ()
const CompositegetLastChild () const
const PreciseTimegetModificationTime () const
const PreciseTimegetSelectionTime () 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 ()
PersistenceManageroperator>> (PersistenceManager &pm) const
- Public Member Functions inherited from BALL::Object
 Object ()
 Default constructor.
 Object (const Object &object)
 Copy constructor.
virtual ~Object ()
 Destructor.
const Objectoperator= (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 Selectableoperator= (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 PropertyManageroperator= (const PropertyManager &property_manager)
void get (PropertyManager &property_manager) const
void swap (PropertyManager &property_manager)
BitVectorgetBitVector ()
const BitVectorgetBitVector () const
 operator BitVector & ()
void setProperty (Property property)
void clearProperty (Property property)
void toggleProperty (Property property)
Size countProperties () const
const NamedPropertygetNamedProperty (Position index) const
NamedPropertygetNamedProperty (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 NamedPropertygetProperty (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.
bool hasProperty (const 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.

Protected Attributes

ZEIsomerType ze_type_
- Protected Attributes inherited from BALL::Bond
Atomfirst_
Atomsecond_
String name_
Order bond_order_
Type bond_type_

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
- Static Public Member Functions inherited from BALL::Bond
static BondcreateBond (Bond &bond, Atom &first, Atom &second)
- 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< CompositeDEFAULT_PROCESSOR
static KernelPredicateType DEFAULT_UNARY_PREDICATE
- Protected Member Functions inherited from BALL::AutoDeletable
 AutoDeletable ()
 AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Detailed Description

Definition at line 64 of file smilesParser.h.

Constructor & Destructor Documentation

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

Member Function Documentation

ZEIsomerType BALL::SmilesParser::SPBond::getZEType ( ) const
void BALL::SmilesParser::SPBond::setZEType ( ZEIsomerType  type)

Member Data Documentation

ZEIsomerType BALL::SmilesParser::SPBond::ze_type_
protected

Definition at line 76 of file smilesParser.h.