BALL
1.5.0
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include
BALL
KERNEL
KERNEL/system.h
Go to the documentation of this file.
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// -*- Mode: C++; tab-width: 2; -*-
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// vi: set ts=2:
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//
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#ifndef BALL_KERNEL_SYSTEM_H
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#define BALL_KERNEL_SYSTEM_H
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#ifndef BALL_KERNEL_ATOM_H
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# include <
BALL/KERNEL/atomIterator.h
>
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#endif
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#ifndef BALL_KERNEL_MOLECULEITERATOR_H
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# include <
BALL/KERNEL/moleculeIterator.h
>
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#endif
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#ifndef BALL_KERNEL_PROTEINITERATOR_H
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# include <
BALL/KERNEL/proteinIterator.h
>
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#endif
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#ifndef BALL_KERNEL_NUCLEICACIDITERATOR_H
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# include <
BALL/KERNEL/nucleicAcidIterator.h
>
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#endif
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#ifndef BALL_KERNEL_NUCLEOTIDEIDITERATOR_H
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# include <
BALL/KERNEL/nucleotideIterator.h
>
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#endif
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#define BALL_SYSTEM_DEFAULT_NAME ""
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namespace
BALL
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{
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class
BALL_EXPORT
System
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:
public
AtomContainer
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{
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public
:
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BALL_CREATE_DEEP
(
System
)
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System
();
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System
(const
System
& system,
bool
deep = true);
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System
(const
String
& name);
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virtual ~
System
();
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void
persistentWrite(
PersistenceManager
& pm, const
char
* name = 0) const;
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void
persistentRead(
PersistenceManager
& pm);
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void
set(const
System
& system,
bool
deep = true);
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System
& operator = (const
System
& system);
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void
get(
System
& system,
bool
deep = true) const;
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bool
operator == (const
System
& system) const;
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bool
operator != (const
System
& system) const;
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Molecule
* getMolecule(
Position
position);
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const
Molecule
* getMolecule(
Position
position) const;
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Protein
* getProtein(
Position
position);
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const
Protein
* getProtein(
Position
position) const;
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Size
countMolecules() const;
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Size
countFragments() const;
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Size
countAtoms() const;
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Size
countProteins() const;
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Size
countChains() const;
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Size
countSecondaryStructures() const;
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Size
countResidues() const;
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Size
countNucleicAcids() const;
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Size
countNucleotides() const;
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void
prepend(
Molecule
& molecule);
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void
append(
Molecule
& molecule);
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void
insert(
Molecule
& molecule);
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void
insertBefore(
Molecule
& molecule,
Composite
& before);
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void
insertAfter(
Molecule
& molecule,
Composite
& after);
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bool
remove(
Molecule
& molecule);
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void
spliceBefore(
System
& system);
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void
spliceAfter(
System
& system);
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void
splice(
System
& system);
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// --- EXTERNAL ITERATORS ---
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Atom
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
AtomContainer
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Fragment
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Molecule
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Protein
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Residue
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Chain
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
SecondaryStructure
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
Nucleotide
)
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BALL_KERNEL_DEFINE_ITERATOR_CREATORS
(
NucleicAcid
)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Atom
, atoms)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
AtomContainer
, atomContainers)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Fragment
, fragments)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Molecule
, molecules)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Protein
, proteins)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Residue
, residues)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Chain
, chains)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
SecondaryStructure
, secondaryStructures)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
Nucleotide
, nucleotides)
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BALL_DECLARE_STD_ITERATOR_WRAPPER
(
System
,
NucleicAcid
, nucleicAcids)
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};
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}
// namespace BALL
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#endif
// BALL_KERNEL_SYSTEM_H
proteinIterator.h
atomIterator.h
nucleotideIterator.h
nucleicAcidIterator.h
moleculeIterator.h
BALL_KERNEL_DEFINE_ITERATOR_CREATORS
#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
Definition
iterator.h:25
BALL_DECLARE_STD_ITERATOR_WRAPPER
#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
Definition
stdIteratorWrapper.h:30
BALL_CREATE_DEEP
#define BALL_CREATE_DEEP(name)
Definition
create.h:26
BALL
Definition
constants.h:13
BALL::Composite
Definition
composite.h:74
BALL::PersistenceManager
Definition
persistenceManager.h:73
BALL::String
Definition
string.h:57
BALL::Atom
Definition
atom.h:90
BALL::AtomContainer
Definition
atomContainer.h:32
BALL::Chain
Definition
chain.h:32
BALL::Fragment
Definition
fragment.h:22
BALL::Molecule
Definition
molecule.h:31
BALL::NucleicAcid
Definition
nucleicAcid.h:29
BALL::Nucleotide
Definition
nucleotide.h:37
BALL::Protein
Definition
protein.h:30
BALL::Residue
Definition
residue.h:38
BALL::SecondaryStructure
Definition
secondaryStructure.h:31
BALL::System
Definition
KERNEL/system.h:40
BALL_SIZE_TYPE
BALL_EXPORT
#define BALL_EXPORT
Definition
COMMON/global.h:50
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