BALL::DNAMutator Class Reference

#include <BALL/STRUCTURE/DNAMutator.h>


Public Types
enum	Base { ADENINE = 0, THYMINE = 1, GUANINE = 2, CYTOSINE = 3, URACILE = 4 }
Public Member Functions
	DNAMutator (EnergyMinimizer mini=NULL, ForceField ff=NULL, FragmentDB *frag=NULL)
	~DNAMutator ()
void	setup ()
void	mutate (Fragment *res, Base base) throw (Exception::InvalidOption)
void	setMinimizer (EnergyMinimizer *mini)
void	setFragmentDB (FragmentDB *frag)
void	setForceField (ForceField *ff)
void	setMaxOptimizationSteps (Size steps)
void	setUsedProperty (Property p)
Private Member Functions
void	freeDB_ ()
void	freeFF_ ()
void	mark_ (AtomContainer *atoms)
void	unmark_ (AtomContainer *atoms)
void	tryFlip_ (Fragment *res, const Vector3 &connect_atom, const Vector3 &axis) const
bool	optimize_ (Fragment *frag)
Atom *	getAttachmentAtom (AtomContainer *res)
Atom *	markBaseAtoms (AtomContainer *res)
void	rotateBases (AtomContainer from, const Atom from_at, const Atom *to_at, const Vector3 &from_connection, const Vector3 &to_connection)
void	rotateSameBases (AtomContainer from, AtomContainer to)
const Atom *	getSecondNitro (const std::vector< const Atom * > &ring_atoms, const Atom *base)
Vector3	getNormalVector (const Atom *at)
Atom *	getConnectionAtom (Atom *at)
Vector3	getOrthogonalVector (const Vector3 &n, const Atom base, const Atom at)
bool	isPurine (const Atom &baseNitrogen) const
bool	isPyrimidine (const Atom &baseNitrogen) const
Private Attributes
bool	keep_db_
bool	keep_ff_
FragmentDB *	db_
ForceField *	ff_
EnergyMinimizer *	minimizer_
Size	num_steps_
Property	prop_
Static Private Attributes
static const char *	bases_ []
static const Size	default_num_steps_

Member Enumeration Documentation

enum BALL::DNAMutator::Base

Entries of this enum are used for the selection of bases in the mutate function

Enumerator:

ADENINE
THYMINE
GUANINE
CYTOSINE
URACILE

Constructor & Destructor Documentation

BALL::DNAMutator::DNAMutator	(	EnergyMinimizer *	mini = `NULL`,
		ForceField *	ff = `NULL`,
		FragmentDB *	frag = `NULL`
	)

Constructs a DNAMutator

Parameters:

	frag	A FragmentDB instance that shall be used to obtain structure of the new bases. If nothing or NULL is passed a default FragmentDB is used. The FragmentDB is initialized as needed causing a short delay when mutating the first base. If you do not want this either pass a valid FragmentDB instance or call DNAMutator::setup() prior to using. You can set a new FragmentDB using DNAMutator::setFragmentDB()
	mini	The minimizer that shall be used for optimization of the mutated base. If nothing or NULL is passed optimization is disabled. You can pass a new minimizer anytime using DNAMutator::setMinimizer().
	ff	The forcefield that should be used in conjunction with the minimizer You can set a new forcefield anytime using DNAMutator::setForceField().

See also:: DNAMutator::setup(), DNAMutator::setFragmentDB(), DNAMutator::setMinimizer() DNAMutator::setForceField()

BALL::DNAMutator::~DNAMutator ( )

The destructor of the the DNAMutator must delete the FragmentDB instance iff it has been auto generated

Member Function Documentation

void BALL::DNAMutator::freeDB_ ( ) [private]

void BALL::DNAMutator::freeFF_ ( ) [private]

Atom* BALL::DNAMutator::getAttachmentAtom ( AtomContainer * res ) [private]

This function returns a pointer to the nitrogen atom that attaches a base to the sugar backbone

Atom* BALL::DNAMutator::getConnectionAtom ( Atom * at ) [private]

Vector3 BALL::DNAMutator::getNormalVector ( const Atom * at ) [private]

Vector3 BALL::DNAMutator::getOrthogonalVector	(	const Vector3 &	n,
		const Atom *	base,
		const Atom *	at
	)			`[private]`

const Atom* BALL::DNAMutator::getSecondNitro	(	const std::vector< const Atom * > &	ring_atoms,
		const Atom *	base
	)			`[private]`

bool BALL::DNAMutator::isPurine ( const Atom & baseNitrogen ) const [private]

The methods below decide whether a base is a Purine or a Pyrimidine. In an ideal distant future this should be stored in the fragment and thus be not necessary.

bool BALL::DNAMutator::isPyrimidine ( const Atom & baseNitrogen ) const [private]

void BALL::DNAMutator::mark_ ( AtomContainer * atoms ) [private]

Atom* BALL::DNAMutator::markBaseAtoms ( AtomContainer * res ) [private]

Selects the atoms in a base. If succesfull it returns the pointer to the attachment nitrogen.

void BALL::DNAMutator::mutate	(	Fragment *	res,
		Base	base
	)			throw (Exception::InvalidOption)

This method changes a given base to another one. Changing the base on the opposite strand is
not handled. Most likely you will need to localy reoptimize the structure after the insertion.

Parameters:

	res	A pointer to the Fragment that will be changed
	base	A string specifiying the base which will be used to replace the current one. Can be one of "A", "T", "G", "C" and "U".

bool BALL::DNAMutator::optimize_ ( Fragment * frag ) [private]

Reoptimize the given fragment using the minimizer stored in minimizer_.

Returns:: false on error.

void BALL::DNAMutator::rotateBases	(	AtomContainer *	from,
		const Atom *	from_at,
		const Atom *	to_at,
		const Vector3 &	from_connection,
		const Vector3 &	to_connection
	)			`[private]`

void BALL::DNAMutator::rotateSameBases	(	AtomContainer *	from,
		AtomContainer *	to
	)			`[private]`

void BALL::DNAMutator::setForceField ( ForceField * ff )

void BALL::DNAMutator::setFragmentDB ( FragmentDB * frag )

void BALL::DNAMutator::setMaxOptimizationSteps ( Size steps )

void BALL::DNAMutator::setMinimizer ( EnergyMinimizer * mini )

void BALL::DNAMutator::setup ( )

Calling this method explicitly circumvents lazy loading of the FragmentDB. This method has no effect if mutate has already been called or if valid instances of the fragmentDB has been passed via the constructor.

Warning:: If you called setup() and then set the FragmentDB to NULL via setFragmentDB() you will need to call setup() again in order to prevent lazy loading.

void BALL::DNAMutator::setUsedProperty ( Property p )