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

#include <BALL/STRUCTURE/smilesParser.h>

Inheritance diagram for BALL::SmilesParser::SPAtom:
BALL::Atom BALL::Composite BALL::PropertyManager BALL::PersistentObject BALL::Selectable BALL::Object BALL::AutoDeletable

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
 Return the atom's formal charge.
void setFormalCharge (Index charge)
 Set the atom's formal charge.
const ChiralDefgetChirality () 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
Atomoperator= (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 ElementgetElement () const
 Return the atom's element.
void setCharge (float charge)
float getCharge () const
const MoleculegetMolecule () const
MoleculegetMolecule ()
 Return the molecule the atom is contained in (mutable)
const FragmentgetFragment () const
FragmentgetFragment ()
 Return the fragment the atom is contained in (mutable)
const ResiduegetResidue () const
ResiduegetResidue ()
 Return the residue the atom is contained in (mutable)
const SecondaryStructuregetSecondaryStructure () const
SecondaryStructuregetSecondaryStructure ()
 Return the secondary structure the atom is contained in (mutable)
const ChaingetChain () const
ChaingetChain ()
 Return the chain the atom is contained in (mutable)
void setName (const String &name)
 Set the atom name.
const StringgetName () const
 Return the atom name.
String getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const
void setPosition (const Vector3 &position)
Vector3getPosition ()
 Return the atom coordinates (mutable)
const Vector3getPosition () 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)
Vector3getVelocity ()
const Vector3getVelocity () const
void setForce (const Vector3 &force)
const Vector3getForce () const
 Return the atom's force vector (const)
Vector3getForce ()
 Return the atom's force vector (mutable)
Size countBonds () const
 Return the number of bonds.
BondgetBond (Position index)
const BondgetBond (Position index) const
BondgetBond (const Atom &atom)
const BondgetBond (const Atom &atom) const
BondcreateBond (Atom &atom)
BondcreateBond (Bond &bond, Atom &atom)
BondcloneBond (Bond &bond, Atom &atom)
bool destroyBond (const Atom &atom)
void destroyBonds ()
AtomgetPartnerAtom (Position i)
const AtomgetPartnerAtom (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.
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.
- 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
virtual void finalize ()
- 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

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 Elementelement_
float radius_
Type type_
unsigned char number_of_bonds_
Bondbond_ [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< PositionAtomIndexList
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.
- 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)
- 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

Return the atom's formal charge.

Reimplemented from BALL::Atom.

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  formal_charge)
inline

Set the atom's formal charge.

Reimplemented from BALL::Atom.

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.