Miscellaneous
[Kernel Classes]

Further classes and functions related to the kernel classes. More...

Collaboration diagram for Miscellaneous:


Classes
class	BALL::Bond
	Bond class. More...
class	BALL::ExpressionParser
	Expression Parser. More...
class	BALL::ExpressionTree
	Expression tree class. More...
class	BALL::Element
	Element class. More...
class	BALL::SecondaryStructure
	Secondary structure class. More...
Modules
	Periodic Table of Elements
	These classes represent elements and the periodic table of elements.
Functions
template<class AtomContainerType >
void	BALL::cloneBonds (const AtomContainerType &atom_container, AtomContainerType &cloned)
	Bond cloning method.
Variables
bool	BALL::clone_bonds
	Global static variable needed for the cloning of kernel objects containing bonds.
BALL_EXPORT PTE_	BALL::PTE
	Global static instance of the periodic table.
typedef std::list< Atom * >	BALL::AtomList
	Kernel object list classes.
typedef std::list< Bond * >	BALL::BondList
typedef std::list < AtomContainer * >	BALL::AtomContainerList
typedef std::list< PDBAtom * >	BALL::PDBAtomList
typedef std::list< Residue * >	BALL::ResidueList
typedef std::list< Fragment * >	BALL::FragmentList
typedef std::list< Molecule * >	BALL::MoleculeList
typedef std::list< Protein * >	BALL::ProteinList
typedef std::list < SecondaryStructure * >	BALL::SecondaryStructureList
typedef std::list< Chain * >	BALL::ChainList
typedef std::list< Nucleotide * >	BALL::NucleotideList
typedef std::list< NucleicAcid * >	BALL::NucleicAcidList
BALL_EXPORT AtomList	BALL::atoms (const AtomContainer &fragment, const String &expression=String())
	Extraction functions for external iteration.
BALL_EXPORT AtomList	BALL::atoms (const AtomList &atoms, const String &expression)
	Extract atoms matching an expression.
BALL_EXPORT PDBAtomList	BALL::PDBAtoms (const AtomContainer &fragment, const String &expression=String())
	Extract PDB atoms matching an expression.
BALL_EXPORT BondList	BALL::bonds (const AtomContainer &fragment, bool selected_only=false)
	Extract all bonds from a kernel data structure.
BALL_EXPORT BondList	BALL::bonds (const Atom &atom)
	Extract all bonds from an atom.
BALL_EXPORT AtomContainerList	BALL::atomContainers (const AtomContainer &fragment, bool selected_only=false)
	Extract all base fragments from a kernel data structure.
BALL_EXPORT ResidueList	BALL::residues (const AtomContainer &fragment, bool selected_only=false)
	Extract all residues from a kernel data structure.
BALL_EXPORT FragmentList	BALL::fragments (const AtomContainer &fragment, bool selected_only=false)
	Extract all fragments from a kernel data structure.
BALL_EXPORT MoleculeList	BALL::molecules (const AtomContainer &fragment, bool selected_only=false)
	Extract all molecules from a kernel data structure.
BALL_EXPORT ProteinList	BALL::proteins (const AtomContainer &fragment, bool selected_only=false)
	Extract all proteins from a kernel data structure.
BALL_EXPORT SecondaryStructureList	BALL::secondaryStructures (const AtomContainer &fragment, bool selected_only=false)
	Extract all secondary structures from a kernel data structure.
BALL_EXPORT ChainList	BALL::chains (const AtomContainer &fragment, bool selected_only=false)
	Extract all chains from a kernel data structure.
BALL_EXPORT NucleicAcidList	BALL::nucleicAcids (const AtomContainer &fragment, bool selected_only=false)
	Extract all nucleic acids from a kernel data structure.
BALL_EXPORT NucleotideList	BALL::nucleotides (const AtomContainer &fragment, bool selected_only=false)
	Extract all nucleotides from a kernel data structure.

Detailed Description

Further classes and functions related to the kernel classes.

Typedef Documentation

typedef std::list<Atom*> BALL::AtomList

Kernel object list classes.

These classes can be used to hold pointers to kernel objects. They are returned by kernel extractors. These lists are a convenient way to execute operations on subsets of kernel structures and an often convenient, albeit slower, alternative to iterators. They are just convenient tyepdefs, so they will behave exactly as any STL list. In order to create these lists from kernel objects, use extractors .

Function Documentation

BALL_EXPORT AtomList BALL::atoms	(	const AtomList &	atoms,
		const String &	expression
	)

Extract atoms matching an expression.

This method extracts all atoms from an atom list that match the Expression expression.

Parameters:

	atoms	the AtomContainer containing the atoms
	expression	the expression that selects the atoms

BALL_EXPORT AtomList BALL::atoms	(	const AtomContainer &	fragment,
		const String &	expression = `String()`
	)

Extraction functions for external iteration.

The following set of functions can by used from python to compile lists of objects from BALL kernel data structures. Extract atoms matching an expression. This method extracts all atoms of a kernel data structure into a list that match the Expression expression. If no expression is given, all atoms will be extracted.

Parameters:

	fragment	the AtomContainer containing the atoms.
	expression	the expression that selects the atoms (default: no expression)

BALL_EXPORT BondList BALL::bonds ( const Atom & atom )

Extract all bonds from an atom.

This function returns all bonds of an atom.

BALL_EXPORT BondList BALL::bonds	(	const AtomContainer &	fragment,
		bool	selected_only = `false`
	)

Extract all bonds from a kernel data structure.

This function extracts all bonds from the atoms contained in the base fragment. If selected_only is set to true, only bonds are extracted where both atoms are selected.

template<class AtomContainerType >

void BALL::cloneBonds	(	const AtomContainerType &	atom_container,
		AtomContainerType &	cloned
	)

Bond cloning method.

This template function implements the cloning of Bond s in AtomContainers. As Bonds are not integrated in the Composite tree structure of kernel objects, a simple deep cloning of a composite only copies all composites down to atoms. Bonds are not included because they are not children of the atoms but stored in a bond array. However, cloning of any kernel objects should naturally clone bonds, too. The implementation of this {cloning-with-bonds} is divided in two parts: first, a deep (recursive) cloning of all composites is performed. Second, the root composite (which is always an AtomContainer) calls cloneBonds for the cloned system to copy the bonds.

The trouble with this implementation is that each clone method must have the possibility to call cloneBonds, but only the first clone method in the recursive call tree is allowed to call it. This is guaranteed by the use of a global static variable clone_bonds . The first clone method called sets clone_bonds to false thereby forbidding the use of cloneBonds to all subsequently called clone methods. Then, it calls cloneBonds and resets clone_bonds to true.

This method assumes that the second argument (the composite without bonds) is a deep copy of the first argument (the composite containing the atoms). If the tree structures of both composites are not isomorphous, bonds are created in an unpredictable way.

Namespace: BALL

Parameters:

	atom_container	the atom_container containing the bonds
	cloned	a deep copy of atom_container

References BALL::Bond::createBond(), BALL::Bond::finalize(), BALL::Bond::setFirstAtom(), and BALL::Bond::setSecondAtom().

BALL_EXPORT PDBAtomList BALL::PDBAtoms	(	const AtomContainer &	fragment,
		const String &	expression = `String()`
	)

Extract PDB atoms matching an expression.

This method extracts all PDB atoms of a kernel data structure into a list that match the Expression expression. If no expression is given, all PDB atoms will be returned.

Parameters:

	fragment	the AtomContainer containing the atoms
	expression	the expression that selects the atoms (default: no expression)

Variable Documentation

bool BALL::clone_bonds

Global static variable needed for the cloning of kernel objects containing bonds.

Namespace: BALL

See also:: cloneBonds

Miscellaneous [Kernel Classes]

Classes

Modules

Functions

Variables

Detailed Description

Typedef Documentation

Function Documentation

Variable Documentation

Miscellaneous
[Kernel Classes]