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BALL::PDBAtom Class Reference

#include <BALL/KERNEL/PDBAtom.h>

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

Public Types

Enums
enum  RemotenessIndicator {
  REMOTENESS_INDICATOR__UNKNOWN = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, REMOTENESS_INDICATOR__ALPHA = 'A', REMOTENESS_INDICATOR__alpha = 'a', REMOTENESS_INDICATOR__BETA = 'B',
  REMOTENESS_INDICATOR__beta = 'b', REMOTENESS_INDICATOR__GAMMA = 'G', REMOTENESS_INDICATOR__gamma = 'g', REMOTENESS_INDICATOR__DELTA = 'D',
  REMOTENESS_INDICATOR__delta = 'd', REMOTENESS_INDICATOR__EPSILON = 'E', REMOTENESS_INDICATOR__epsilon = 'e', REMOTENESS_INDICATOR__ZETA = 'Z',
  REMOTENESS_INDICATOR__zeta = 'z', REMOTENESS_INDICATOR__ETA = 'H', REMOTENESS_INDICATOR__eta = 'h', NUMBER_OF_REMOTENESS_INDICATORS
}
 
enum  Property { PROPERTY__HETATM = Atom::NUMBER_OF_PROPERTIES + 1, NUMBER_OF_PROPERTIES }
 
- 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. 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...
 
- Public Types inherited from BALL::Composite
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
 
enum  StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }
 
typedef UnaryPredicate< CompositeKernelPredicateType
 

Public Member Functions

Constructors and Destructors
 PDBAtom ()
 Default constructor. More...
 
 PDBAtom (const PDBAtom &pdb_atom, bool deep=true)
 Copy constructor. More...
 
 PDBAtom (const String &name)
 Constructor. More...
 
 PDBAtom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Atom::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, char branch_designator=BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator=BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator=BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy=BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor=BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR)
 Detailed constructor. More...
 
virtual ~PDBAtom ()
 Destructor. More...
 
virtual void destroy ()
 
Predicates
bool operator== (const PDBAtom &pdb_atom) const
 
bool operator!= (const PDBAtom &pdb_atom) const
 
Persistence
void persistentWrite (PersistenceManager &pm, const char *name=0) const
 
void persistentRead (PersistenceManager &pm)
 
Assignment
void set (const PDBAtom &pdb_atom, bool deep=true)
 
void get (PDBAtom &pdb_atom, bool deep=true) const
 
PDBAtomoperator= (const PDBAtom &pdb_atom)
 
void swap (PDBAtom &pdb_atom)
 
virtual void clear ()
 
Accessors
ProteingetProtein ()
 
const ProteingetProtein () const
 
ChaingetChain ()
 
const ChaingetChain () const
 
ResiduegetResidue ()
 
const ResiduegetResidue () const
 
void setBranchDesignator (char branch_designator)
 
char getBranchDesignator () const
 
void setRemotenessIndicator (char remoteness_indicator)
 
char getRemotenessIndicator () const
 
void setAlternateLocationIndicator (char alternate_location_indicator)
 
char getAlternateLocationIndicator () const
 
void setOccupancy (float occupancy)
 
float getOccupancy () const
 
void setTemperatureFactor (float temperature_factor)
 
float getTemperatureFactor () const
 
Debugging and Diagnostics
virtual void dump (std::ostream &s=std::cout, Size depth=0) const
 
- 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 ()
 
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. More...
 
const ElementgetElement () 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 MoleculegetMolecule () const
 
MoleculegetMolecule ()
 Return the molecule the atom is contained in (mutable) More...
 
const FragmentgetFragment () const
 
FragmentgetFragment ()
 Return the fragment the atom is contained in (mutable) More...
 
const ResiduegetResidue () const
 
ResiduegetResidue ()
 Return the residue the atom is contained in (mutable) More...
 
const SecondaryStructuregetSecondaryStructure () const
 
SecondaryStructuregetSecondaryStructure ()
 Return the secondary structure the atom is contained in (mutable) More...
 
const ChaingetChain () const
 
ChaingetChain ()
 Return the chain the atom is contained in (mutable) More...
 
void setName (const String &name)
 Set the atom name. More...
 
const StringgetName () const
 Return the atom name. More...
 
String getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const
 
void setPosition (const Vector3 &position)
 
Vector3getPosition ()
 Return the atom coordinates (mutable) More...
 
const Vector3getPosition () 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)
 
Vector3getVelocity ()
 
const Vector3getVelocity () const
 
void setForce (const Vector3 &force)
 
const Vector3getForce () const
 Return the atom's force vector (const) More...
 
Vector3getForce ()
 Return the atom's force vector (mutable) More...
 
Size countBonds () const
 Return the number of bonds. More...
 
BondgetBond (Position index)
 
const BondgetBond (Position index) const
 
BondgetBond (const Atom &atom)
 
const BondgetBond (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
 
bool applyBonds (UnaryProcessor< Bond > &processor)
 
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
 
void addInteraction (const Atom *atom, String interaction_type, double energy)
 
void addInteraction (String interaction_type, double energy)
 
void disableStoreInteractions ()
 
void enableStoreInteractions ()
 
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
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)
 
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)
 
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. More...
 
 Object (const Object &object)
 Copy constructor. More...
 
virtual ~Object ()
 Destructor. More...
 
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. More...
 
BALL_INLINE PropertyManager (const PropertyManager &property_manager)
 Copy constructor. More...
 
virtual ~PropertyManager ()
 Destructor. More...
 
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 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 NamedPropertygetProperty (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. More...
 
bool hasProperty (const std::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
 

Friends

class Bond
 

Additional Inherited Members

- 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 ()
 
- Public Attributes inherited from BALL::Atom
MolecularInteractionsinteractions
 
bool store_interactions_disabled_
 
- 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)
 
- 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_
 
- Protected Attributes inherited from BALL::Selectable
bool selected_
 
- Static Protected Attributes inherited from BALL::Atom
static AtomIndexList free_list_
 

Detailed Description

Atom class with additional attributes. This class represents atoms read from PDB files. It contains additional attributes to hold the crystallographic properties of atoms from a PDB file (e.g., temperature factor, occupancy). For details on the PDB format and the detailed meaning of those fields, please refer to the PDB documentation at http://www.rcsb.org

See also
PDBFile

Definition at line 38 of file PDBAtom.h.

Member Enumeration Documentation

Properties of the PDBAtom.

Enumerator
PROPERTY__HETATM 

Property which indicates whether the current atom is a HETATM.

NUMBER_OF_PROPERTIES 

The number of properties in PDBAtom.

Definition at line 76 of file PDBAtom.h.

Possible values for the PDB remoteness indicator

Enumerator
REMOTENESS_INDICATOR__UNKNOWN 
REMOTENESS_INDICATOR__ALPHA 
REMOTENESS_INDICATOR__alpha 
REMOTENESS_INDICATOR__BETA 
REMOTENESS_INDICATOR__beta 
REMOTENESS_INDICATOR__GAMMA 
REMOTENESS_INDICATOR__gamma 
REMOTENESS_INDICATOR__DELTA 
REMOTENESS_INDICATOR__delta 
REMOTENESS_INDICATOR__EPSILON 
REMOTENESS_INDICATOR__epsilon 
REMOTENESS_INDICATOR__ZETA 
REMOTENESS_INDICATOR__zeta 
REMOTENESS_INDICATOR__ETA 
REMOTENESS_INDICATOR__eta 
NUMBER_OF_REMOTENESS_INDICATORS 

Definition at line 53 of file PDBAtom.h.

Constructor & Destructor Documentation

BALL::PDBAtom::PDBAtom ( )

Default constructor.

BALL::PDBAtom::PDBAtom ( const PDBAtom pdb_atom,
bool  deep = true 
)

Copy constructor.

BALL::PDBAtom::PDBAtom ( const String name)

Constructor.

BALL::PDBAtom::PDBAtom ( Element element,
const String name,
const String type_name = BALL_ATOM_DEFAULT_TYPE_NAME,
Atom::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,
char  branch_designator = BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR,
char  remoteness_indicator = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR,
char  alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR,
float  occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY,
float  temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR 
)

Detailed constructor.

virtual BALL::PDBAtom::~PDBAtom ( )
virtual

Destructor.

Member Function Documentation

virtual void BALL::PDBAtom::clear ( )
virtual

Clear the contents of the atom.

Reimplemented from BALL::Atom.

virtual void BALL::PDBAtom::destroy ( )
virtual

Clears the contents of the atom and removes it from all composite structures.

Reimplemented from BALL::Atom.

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

Internal state dump. Dump the current internal state of {*this} to the output ostream s with dumping depth depth .

Parameters
soutput stream where to output the internal state of the instance
depththe dumping depth

Reimplemented from BALL::Atom.

void BALL::PDBAtom::get ( PDBAtom pdb_atom,
bool  deep = true 
) const

Copy this instance to {pdb_atom}. The assignment is either deep or shallow (default).

Parameters
pdb_atomthe PDBAtom to be assigned to
char BALL::PDBAtom::getAlternateLocationIndicator ( ) const

Get the alternate location indicator.

Returns
char the alternate location indicator
char BALL::PDBAtom::getBranchDesignator ( ) const

Get the branch designator.

Returns
char the branch designator
Chain* BALL::PDBAtom::getChain ( )

Get a pointer to the parent chain. The pointer is 0 if the instance does not have a parent chain.

Returns
Chain* - mutable pointer to the parent chain
const Chain* BALL::PDBAtom::getChain ( ) const

Get a pointer to the parent chain. The pointer is 0 if the instance does not have a parent chain.

Returns
Chain* - constant pointer to the parent chain
float BALL::PDBAtom::getOccupancy ( ) const

Get the occupancy.

Returns
float occupancy the occupancy
Protein* BALL::PDBAtom::getProtein ( )

Get a pointer to the parent protein. The pointer is 0 if the instance does not have a parent protein.

Returns
Protein* - mutable pointer to the parent protein
const Protein* BALL::PDBAtom::getProtein ( ) const

Get a pointer to the parent protein. The pointer is 0 if the instance does not have a parent protein.

Returns
Protein* - constant pointer to the parent protein
char BALL::PDBAtom::getRemotenessIndicator ( ) const

Get the remoteness indicator.

Returns
char the remoteness indicator
Residue* BALL::PDBAtom::getResidue ( )

Get a pointer to the parent residue. The pointer is 0 if the instance does not have a parent residue.

Returns
Residue* - mutable pointer to the parent residue
const Residue* BALL::PDBAtom::getResidue ( ) const

Get a pointer to the parent residue. The pointer is 0 if the instance does not have a parent residue.

Returns
Residue* - constant pointer to the parent residue
float BALL::PDBAtom::getTemperatureFactor ( ) const

Get the temperature factor.

Returns
float the temperature factor
bool BALL::PDBAtom::operator!= ( const PDBAtom pdb_atom) const

Inequality operator

See also
operator ==
PDBAtom& BALL::PDBAtom::operator= ( const PDBAtom pdb_atom)

Assignment operator. The assignment is deep.

Parameters
pdb_atomthe PDBAtom to be copied (cloned)
Returns
pdb_atom& - the instance
bool BALL::PDBAtom::operator== ( const PDBAtom pdb_atom) const

Equality operator.

See also
Object::operator ==
void BALL::PDBAtom::persistentRead ( PersistenceManager pm)
virtual

Reads a PDBAtom object from a persistent stream.

Parameters
pmthe persistence manager

Reimplemented from BALL::Atom.

void BALL::PDBAtom::persistentWrite ( PersistenceManager pm,
const char *  name = 0 
) const
virtual

Writes a PDBAtom object to a persistent stream.

Parameters
pmthe persistence manager
namethe instance name

Reimplemented from BALL::Atom.

void BALL::PDBAtom::set ( const PDBAtom pdb_atom,
bool  deep = true 
)

Assignment with cloning facility. The assignment is either deep or shallow (default).

Parameters
pdb_atomthe PDBAtom to be copied (cloned)
deepmake a deep (=true) or shallow (=false) copy
void BALL::PDBAtom::setAlternateLocationIndicator ( char  alternate_location_indicator)

Set the alternate location indicator.

Parameters
alternate_location_indicatorthe alternate location indicator
void BALL::PDBAtom::setBranchDesignator ( char  branch_designator)

Set the branch designator.

Parameters
branch_designatorthe branch designator
void BALL::PDBAtom::setOccupancy ( float  occupancy)

Set the occupancy.

Parameters
occupancythe occupancy
void BALL::PDBAtom::setRemotenessIndicator ( char  remoteness_indicator)

Set the remoteness indicator.

Parameters
remoteness_indicatorthe remoteness indicator
void BALL::PDBAtom::setTemperatureFactor ( float  temperature_factor)

Set the temperature factor.

Parameters
temperature_factorthe temperature factor
void BALL::PDBAtom::swap ( PDBAtom pdb_atom)

Swapping of PDBAtoms.

Parameters
pdb_atomthe PDBAtom {*this} is being swapped with

Friends And Related Function Documentation

friend class Bond
friend

Definition at line 43 of file PDBAtom.h.