BALL::AtomContainer

BALL::AtomContainer Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/atomContainer.h>

Inheritance diagram for BALL::AtomContainer:
BALL::Composite BALL::PropertyManager BALL::PersistentObject BALL::Selectable BALL::Object BALL::AutoDeletable BALL::Chain BALL::Fragment BALL::Molecule BALL::SecondaryStructure BALL::System BALL::Nucleotide BALL::Residue BALL::NucleicAcid BALL::Protein

List of all members.


Public Types

Enums
enum  Property { NUMBER_OF_PROPERTIES = 0 }
 

The number of predefined properties for AtomContainer.

More...

Public Member Functions

Constructors and Destructors
 AtomContainer ()
 AtomContainer (const AtomContainer &atom_container, bool deep=true)
 AtomContainer (const String &name)
virtual ~AtomContainer ()
virtual void clear ()
virtual void destroy ()
Persistence
virtual void persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
virtual void persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment
void set (const AtomContainer &atom_container, bool deep=true)
AtomContainer & operator= (const AtomContainer &atom_container)
void get (AtomContainer &atom_container, bool deep=true) const
void swap (AtomContainer &atom_container)
Predicates
bool operator== (const AtomContainer &atom_container) const
bool operator!= (const AtomContainer &atom_container) const
Accessors
void setName (const String &name)
const String & getName () const
AtomContainer * getSuperAtomContainer ()
const AtomContainer * getSuperAtomContainer () const
AtomContainer * getAtomContainer (Position position)
const AtomContainer * getAtomContainer (Position position) const
Atom * getAtom (Position position)
const Atom * getAtom (Position position) const
Atom * getAtom (const String &name)
const Atom * getAtom (const String &name) const
Size countAtomContainers () const
Size countAtoms () const
Size countBonds () const
Size countInterBonds () const
Size countIntraBonds () const
void prepend (Atom &atom)
void append (Atom &atom)
void insert (Atom &atom)
void insertBefore (Atom &atom, Composite &before)
void insertAfter (Atom &atom, Composite &after)
bool remove (Atom &atom)
Size removeHavingProperty (BALL::Property p)
Size removeNotHavingProperty (BALL::Property p)
Size removeHavingProperty (const string &name)
Size removeNotHavingProperty (const string &name)
void prepend (AtomContainer &atom_container)
void append (AtomContainer &atom_container)
void insert (AtomContainer &atom_container)
void insertBefore (AtomContainer &atom_container, Composite &before)
void insertAfter (AtomContainer &atom_container, Composite &after)
void spliceBefore (AtomContainer &atom_container)
void spliceAfter (AtomContainer &atom_container)
void splice (AtomContainer &atom_container)
bool remove (AtomContainer &atom_container)
Miscellaneous
void destroyBonds ()
Predicates
bool isSubAtomContainerOf (const AtomContainer &atom_container) const
bool isSuperAtomContainerOf (const AtomContainer &atom_container) const
virtual bool isValid () const
virtual void dump (std::ostream &s=std::cout, Size depth=0) const
Internal Iteration
bool applyIntraBond (UnaryProcessor< Bond > &processor)
 

Apply to all bonds connecting two atoms inside this AtomContainer.


bool applyInterBond (UnaryProcessor< Bond > &processor)
 

Apply to all bonds connected to atoms outside this AtomContainer.



Private Attributes

String name_

Detailed Description

Atom Container Base Class. The AtomContainer class is the base class of all kernel classes containing atoms.

Member Enumeration Documentation

enum BALL::AtomContainer::Property

The number of predefined properties for AtomContainer.

Enumerator:
NUMBER_OF_PROPERTIES 

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, and BALL::Residue.

Constructor & Destructor Documentation

BALL::AtomContainer::AtomContainer (  ) 

Default constructor

BALL::AtomContainer::AtomContainer ( const AtomContainer &  atom_container,
bool  deep = true 
)

Copy constructor

Parameters:
atom_container the AtomContainer to construct from
deep a flag indicating cloning
BALL::AtomContainer::AtomContainer ( const String &  name  ) 

Detailed Constructor

Parameters:
name the name of the AtomContainer
virtual BALL::AtomContainer::~AtomContainer (  )  [virtual]

Destructor

Member Function Documentation

void BALL::AtomContainer::append ( AtomContainer &  atom_container  ) 

Append an AtomContainer at the last position.

Parameters:
atom_container the AtomContainer to prepend

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::append ( Atom &  atom  ) 

Append an atom to the last position.

Parameters:
atom the atom to append

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

bool BALL::AtomContainer::applyInterBond ( UnaryProcessor< Bond > &  processor  ) 

Apply to all bonds connected to atoms outside this AtomContainer.

bool BALL::AtomContainer::applyIntraBond ( UnaryProcessor< Bond > &  processor  ) 

Apply to all bonds connecting two atoms inside this AtomContainer.

virtual void BALL::AtomContainer::clear (  )  [virtual]

Clear the contents of this instance of AtomContainer. This methods clears the base fragment's name, destroys all its children (as in Composite::clear ), but does not remove it from its parent composite structures.

Reimplemented from BALL::Composite.

Reimplemented in BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

Size BALL::AtomContainer::countAtomContainers (  )  const

Count the child AtomContainers.

Returns:
Size the number of AtomContainers

Reimplemented in BALL::Nucleotide, and BALL::Residue.

Size BALL::AtomContainer::countAtoms (  )  const

Count the child atoms.

Returns:
Size the number of atoms

Reimplemented in BALL::System.

Size BALL::AtomContainer::countBonds (  )  const

Count the child bonds.

Returns:
Size the number of bonds
Size BALL::AtomContainer::countInterBonds (  )  const

Count all bonds which connect atoms in this instance with atoms outside.

Returns:
Size the number of inter bonds
Size BALL::AtomContainer::countIntraBonds (  )  const

Count all bonds which connect 2 atoms in this instance.

Returns:
Size the number of intra bonds
virtual void BALL::AtomContainer::destroy (  )  [virtual]

Clear the contents of this instance of AtomContainer and removes it from parent composite structures. This methods clears the base fragment's name, destroys all its children (as in Composite::destroy ), and removes it from its parent composite structures.

Reimplemented from BALL::Composite.

Reimplemented in BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::destroyBonds (  ) 

Destroy all bonds in this instance.

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

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

Parameters:
s - output stream where to output the internal state of this instance
depth - the dumping depth

Reimplemented from BALL::Composite.

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::get ( AtomContainer &  atom_container,
bool  deep = true 
) const

Copy to another instance of AtomContainer. The assignment is either deep or shallow (default is deep).

Parameters:
atom_container the AtomContainer to be assigned to
See also:
Composite::get
const Atom* BALL::AtomContainer::getAtom ( const String &  name  )  const

Get a pointer to a child atom with the name name . The pointer is 0 if this instance AtomContainer does not have an atom with this name.

Parameters:
name the name of the child atom
Returns:
Atom* - constant pointer to the child
Atom* BALL::AtomContainer::getAtom ( const String &  name  ) 

Get a pointer to a child atom with the name name . The pointer is 0 if this instance does not have an atom with this name.

Parameters:
name the name of the child atom
Returns:
Atom* - mutable pointer to the child
const Atom* BALL::AtomContainer::getAtom ( Position  position  )  const

Get a pointer to a child atom at a given position. The pointer is 0 if this instance does not have an atom at the given position.

Parameters:
position the position of the child atom
Returns:
Atom* - constant pointer to the child

Reimplemented in BALL::Chain, and BALL::SecondaryStructure.

Atom* BALL::AtomContainer::getAtom ( Position  position  ) 

Get a pointer to a child atom at a given position. The pointer is 0 if this instance does not have an atom at the given position.

Parameters:
position the position of the child atom
Returns:
Atom* - mutable pointer to the child

Reimplemented in BALL::Chain, and BALL::SecondaryStructure.

const AtomContainer* BALL::AtomContainer::getAtomContainer ( Position  position  )  const

Get a constant pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:
position of the child AtomContainer
Returns:
AtomContainer* - constant pointer to the child

Reimplemented in BALL::Chain, BALL::Nucleotide, and BALL::Residue.

AtomContainer* BALL::AtomContainer::getAtomContainer ( Position  position  ) 

Get a pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:
position of the child AtomContainer
Returns:
AtomContainer* - mutable pointer to the child

Reimplemented in BALL::Chain, BALL::Nucleotide, and BALL::Residue.

const String& BALL::AtomContainer::getName (  )  const

Return the name.

Returns:
String& - constant reference to the name of this instance

Referenced by BALL::PDB::Residue::set().

const AtomContainer* BALL::AtomContainer::getSuperAtomContainer (  )  const

Get a constant pointer to the parent AtomContainer. The pointer is 0 if this instance does not have a parent AtomContainer.

Returns:
AtomContainer* - constant pointer to the parent AtomContainer

Reimplemented in BALL::Molecule.

AtomContainer* BALL::AtomContainer::getSuperAtomContainer (  ) 

Get a mutable pointer to the parent AtomContainer. The pointer is 0 if this instance does not have a parent AtomContainer.

Returns:
AtomContainer* - mutable pointer to the parent AtomContainer

Reimplemented in BALL::Molecule.

void BALL::AtomContainer::insert ( AtomContainer &  atom_container  ) 

Insert an AtomContainer at the last position.

Parameters:
atom_container the AtomContainer to insert

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::insert ( Atom &  atom  ) 

Insert an atom to the last position.

Parameters:
atom the atom to insert

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

void BALL::AtomContainer::insertAfter ( AtomContainer &  atom_container,
Composite &  after 
)

Insert an AtomContainer after a given Composite object.

Parameters:
atom_container the AtomContainer to insert
after the Composite object to insert after

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::insertAfter ( Atom &  atom,
Composite &  after 
)

Insert an atom after a given Composite object.

Parameters:
atom the atom to insert
after the Composite object to insert after

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

void BALL::AtomContainer::insertBefore ( AtomContainer &  atom_container,
Composite &  before 
)

Insert an AtomContainer before a given Composite object.

Parameters:
atom_container the AtomContainer to insert
before the Composite object to insert before

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::insertBefore ( Atom &  atom,
Composite &  before 
)

Insert an atom before a given Composite object.

Parameters:
atom the atom to insert
before the Composite object to insert before

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

bool BALL::AtomContainer::isSubAtomContainerOf ( const AtomContainer &  atom_container  )  const

Test if an AtomContainer is a child.

Parameters:
atom_container the AtomContainer to test

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::isSuperAtomContainerOf ( const AtomContainer &  atom_container  )  const

Test if an AtomContainer is the parent.

Parameters:
atom_container the AtomContainer to test

Reimplemented in BALL::Nucleotide, and BALL::Residue.

virtual bool BALL::AtomContainer::isValid (  )  const [virtual]

Debugging and Diagnostics Internal state and consistency self-validation. If the internal state of this instance is correct (self-validated) and consistent true is returned, false otherwise.

Returns:
bool

Reimplemented from BALL::Composite.

Reimplemented in BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

bool BALL::AtomContainer::operator!= ( const AtomContainer &  atom_container  )  const

Inequality operator.

See also:
operator ==
AtomContainer& BALL::AtomContainer::operator= ( const AtomContainer &  atom_container  ) 

Assignment operator. The assignment is deep.

Parameters:
atom_container the AtomContainer to be copied (cloned)
Returns:
AtomContainer& - this instance AtomContainer
See also:
AtomContainer::set
bool BALL::AtomContainer::operator== ( const AtomContainer &  atom_container  )  const

Equality operator. Two instances of AtomContainer are equal if they have the same handle.

virtual void BALL::AtomContainer::persistentRead ( PersistenceManager &  pm  )  throw (Exception::GeneralException) [virtual]

Read an AtomContainer object from a persistent stream.

Parameters:
pm the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, and BALL::System.

virtual void BALL::AtomContainer::persistentWrite ( PersistenceManager &  pm,
const char *  name = 0 
) const throw (Exception::GeneralException) [virtual]

Write an AtomContainer object to a persistent stream.

Parameters:
pm the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, and BALL::System.

void BALL::AtomContainer::prepend ( AtomContainer &  atom_container  ) 

Prepend an AtomContainer at position 0.

Parameters:
atom_container the AtomContainer to prepend

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::prepend ( Atom &  atom  ) 

Prepend an atom at position 0.

Parameters:
atom the atom to prepend

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

bool BALL::AtomContainer::remove ( AtomContainer &  atom_container  ) 

Remove an AtomContainer

Parameters:
atom_container the AtomContainer to remove
Returns:
false if {atom_container} could not be removed

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

bool BALL::AtomContainer::remove ( Atom &  atom  ) 

Remove an atom

Parameters:
atom the atom to remove

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

Size BALL::AtomContainer::removeHavingProperty ( const string &  name  ) 
Size BALL::AtomContainer::removeHavingProperty ( BALL::Property  p  ) 
Size BALL::AtomContainer::removeNotHavingProperty ( const string &  name  ) 
Size BALL::AtomContainer::removeNotHavingProperty ( BALL::Property  p  ) 
void BALL::AtomContainer::set ( const AtomContainer &  atom_container,
bool  deep = true 
)

Assign the contents of an AtomContainer The assignment is either deep or shallow (default is deep).

Parameters:
atom_container the atom_container to be copied (cloned)
deep make a deep (=true) or shallow (=false) copy
See also:
Composite::set
void BALL::AtomContainer::setName ( const String &  name  ) 

Set the name.

Parameters:
name the new name
void BALL::AtomContainer::splice ( AtomContainer &  atom_container  ) 

Move the children of {atom_container} into this instance. The children of atom_container are inserted at its position if it is is a child of this. Otherwise the children are inserted using spliceBefore .

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::spliceAfter ( AtomContainer &  atom_container  ) 

Cut all children of atom_container and append them after the children of this instance.

Parameters:
atom_container the AtomContainer to access

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::spliceBefore ( AtomContainer &  atom_container  ) 

Cut all children of atom_container and prepend them before the children of this instance.

Parameters:
atom_container the AtomContainer to access

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::swap ( AtomContainer &  atom_container  ) 

Swap the contents of two AtomContainers.

Parameters:
atom_container the AtomContainer this instance is being swapped with.

Member Data Documentation

String BALL::AtomContainer::name_ [private]