#include <BALL/STRUCTURE/DNAMutator.h>

Inheritance diagram for BALL::DNAMutator:

Public Types
enum	MatchingMode { MINIMUM_ANGLE, MATCH_TORSION }

Public Types inherited from BALL::Mutator
enum	MutatorOptions { NONE = 0, OPTIMIZE = 1 }

Public Member Functions
	DNAMutator (EnergyMinimizer mini=NULL, ForceField ff=NULL, FragmentDB *frag=NULL)

	~DNAMutator ()

virtual void	setup ()

void	setMinimizer (EnergyMinimizer *mini)

void	setForceField (ForceField *ff)

void	setMaxOptimizationSteps (Size steps)

void	setUsedProperty (Property p)

bool	optimize ()

void	setStrands (Chain s1, Chain s2)

void	setFirstStrand (Chain *s1)

void	setSecondStrand (Chain *s2)

void	setNucleotideMapping (const NucleotideMapping &bij)

void	addMutation (Index i, const String &new_frag_name)

void	clearMutations ()

void	setMatchingMode (MatchingMode mmode)

Public Member Functions inherited from BALL::Mutator
	Mutator (FragmentDB *db=0)

virtual	~Mutator ()

void	setFragmentDB (FragmentDB *db)

void	mutate (MutatorOptions opts=NONE)

Protected Member Functions
virtual void	mutate_impl_ (MutatorOptions opt)

Private Types
typedef std::map< Residue *, String >	Mutations

typedef Mutations::iterator	MutIterator

Private Member Functions
void	mutateSingleBase_ (Residue *res, const String &basename) const

void	freeFF_ ()

void	mark_ (AtomContainer *atoms) const

void	unmark_ (AtomContainer *atoms) const

bool	optimize_ (Fragment *frag)

Atom *	getAttachmentAtom (AtomContainer *res) const

Atom *	markBaseAtoms_ (AtomContainer *res) const

void	alignBases_ (AtomContainer from, const Vector3 &from_connection, const Vector3 &to_connection, Atom from_at) const

Atom *	getTorsionDefiningAtom_ (Atom *atom) const

const Atom *	getTorsionDefiningAtom_ (const Atom *atom) const

void	rotateBasesMatchTorsion_ (AtomContainer from, const Atom to_connection_at, Atom from_at, const Atom to_at) const

void	rotateBasesMinAngle_ (AtomContainer from, const Vector3 &to_connection, Atom from_at, const Atom *to_at) const

void	rotateSameBases_ (AtomContainer from, AtomContainer to) const

Vector3	getNormalVector_ (const Atom *at) const

Atom *	getConnectionAtom_ (Atom *at) const

String	canonizeName_ (const String &frag_name) const

bool	isPurine_ (const Atom &baseNitrogen) const

bool	isPyrimidine_ (const Atom &baseNitrogen) const

String	getComplement_ (const String &s) const

Private Attributes
bool	keep_ff_

ForceField *	ff_

EnergyMinimizer *	minimizer_

Size	num_steps_

Property	prop_

Chain *	first_strand_

Chain *	second_strand_

NucleotideMapping	mapping_

MatchingMode	matching_mode_

std::map< Residue *, String >	mutations_

std::deque< Atom * >	to_optimize_

Static Private Attributes
static const char *	bases_ []

static const Size	default_num_steps_

Additional Inherited Members
Protected Attributes inherited from BALL::Mutator
FragmentDB *	db_

Detailed Description

Definition at line 30 of file DNAMutator.h.

Member Typedef Documentation

typedef std::map<Residue*, String> BALL::DNAMutator::Mutations

private

Definition at line 173 of file DNAMutator.h.

typedef Mutations::iterator BALL::DNAMutator::MutIterator

private

Definition at line 174 of file DNAMutator.h.

Member Enumeration Documentation

enum BALL::DNAMutator::MatchingMode

This controls how a purine and pyrimidine base are matched onto each other

Enumerator
MINIMUM_ANGLE	Use a minimum angle criterion and try out which conformation fits best.
MATCH_TORSION	Set the torsion angle of the sugar-base connection in the new base to the torsion angle found in the second base

Definition at line 36 of file DNAMutator.h.

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 DNAMutator; Deletes the FragmentDB instance iff it has been auto generated

Member Function Documentation

void BALL::DNAMutator::addMutation	(	Index	i,
		const String &	new_frag_name
	)

virtual

Implements Mutator::addMutation.

See Also: Mutator::addMutation

Exceptions

Exception::NotInitialized	This exception is thrown when the first DNA strand has not been set.
Exception::IndexOverflow	If the specified index is larger than the number of bases in the first strand, an exception is raised.

Implements BALL::Mutator.

void BALL::DNAMutator::alignBases_	(	AtomContainer *	from,
		const Vector3 &	from_connection,
		const Vector3 &	to_connection,
		Atom *	from_at
	)		const

private

String BALL::DNAMutator::canonizeName_ ( const String & frag_name ) const

private

void BALL::DNAMutator::clearMutations ( )

virtual

Clears the already specified mutations.

Implements BALL::Mutator.

void BALL::DNAMutator::freeFF_ ( )

private

Atom* BALL::DNAMutator::getAttachmentAtom ( AtomContainer * res ) const

private

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

String BALL::DNAMutator::getComplement_ ( const String & s ) const

private

Atom* BALL::DNAMutator::getConnectionAtom_ ( Atom * at ) const

private

Vector3 BALL::DNAMutator::getNormalVector_ ( const Atom * at ) const

private

Atom* BALL::DNAMutator::getTorsionDefiningAtom_ ( Atom * atom ) const

private

const Atom* BALL::DNAMutator::getTorsionDefiningAtom_ ( const Atom * atom ) const

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 ) const

private

Atom* BALL::DNAMutator::markBaseAtoms_ ( AtomContainer * res ) const

private

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

virtual void BALL::DNAMutator::mutate_impl_ ( MutatorOptions opt )

protectedvirtual

Implements BALL::Mutator.

void BALL::DNAMutator::mutateSingleBase_	(	Residue *	res,
		const String &	basename
	)		const

private

bool BALL::DNAMutator::optimize ( )

virtual

This function optimizes the new bases. Inherited from Mutator. Calling it before mutate will have no effect.

Returns: true if the optimization was successful false otherwise.

Implements BALL::Mutator.

bool BALL::DNAMutator::optimize_ ( Fragment * frag )

private

Reoptimize the given fragment using the minimizer stored in minimizer_.

Returns: false on error.

void BALL::DNAMutator::rotateBasesMatchTorsion_	(	AtomContainer *	from,
		const Atom *	to_connection_at,
		Atom *	from_at,
		const Atom *	to_at
	)		const

private

void BALL::DNAMutator::rotateBasesMinAngle_	(	AtomContainer *	from,
		const Vector3 &	to_connection,
		Atom *	from_at,
		const Atom *	to_at
	)		const

private

void BALL::DNAMutator::rotateSameBases_	(	AtomContainer *	from,
		AtomContainer *	to
	)		const

private

void BALL::DNAMutator::setFirstStrand ( Chain * s1 )

Sets the first strand. If the second strand is already specified, this will lead to the computation of a NucleotideMapping using NucleotideMapping::assignNaively

See Also: NucleotideMapping::assignNaively

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

Set a new ForceField instance that is used in conjunction with the minimizer to refine the structure. Even if no minimizer has been passed this force field will be used to calculate the most favourable rotation of the base using a simple heuristic. If you do not want this behaviour pass NULL.

void BALL::DNAMutator::setMatchingMode ( MatchingMode mmode )

Sets the matching heuristic used for aligning a pyrimidine to a purine base. Default is MATCH_TORSION.

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

Controlls maximum number of steps to be used when refining the generated structure via a minimizer.

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

Set the current minimizer to mini. Passing NULL will disable minimization.

void BALL::DNAMutator::setNucleotideMapping ( const NucleotideMapping & bij )

Assign a custom NucleotideMapping.

void BALL::DNAMutator::setSecondStrand ( Chain * s2 )

Sets the second strand. If the first strand is already specified, this will lead to the computation of a NucleotideMapping using NucleotideMapping::assignNaively

See Also: NucleotideMapping::assignNaively

void BALL::DNAMutator::setStrands	(	Chain *	s1,
		Chain *	s2
	)

Sets the first and the second strand. This will lead to the computation of a NucleotideMapping using NucleotideMapping::assignNaively

See Also: NucleotideMapping::assignNaively

virtual void BALL::DNAMutator::setup ( )

virtual

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.

Reimplemented from BALL::Mutator.

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

The DNAMutator internally uses the unnamed property mechanism of the Atoms. This defaults to property Atom::NUMBER_OF_PROPERTIES. If you already use this property in your code you can set another property by passing it to this function.

void BALL::DNAMutator::unmark_ ( AtomContainer * atoms ) const

private

Member Data Documentation

const char* BALL::DNAMutator::bases_[]

staticprivate

Definition at line 238 of file DNAMutator.h.

const Size BALL::DNAMutator::default_num_steps_

staticprivate

Definition at line 239 of file DNAMutator.h.

ForceField* BALL::DNAMutator::ff_

private

Definition at line 178 of file DNAMutator.h.

Chain* BALL::DNAMutator::first_strand_

private

Definition at line 184 of file DNAMutator.h.

bool BALL::DNAMutator::keep_ff_

private

Definition at line 176 of file DNAMutator.h.

NucleotideMapping BALL::DNAMutator::mapping_

private

Definition at line 187 of file DNAMutator.h.

MatchingMode BALL::DNAMutator::matching_mode_

private

Definition at line 188 of file DNAMutator.h.

EnergyMinimizer* BALL::DNAMutator::minimizer_

private

Definition at line 179 of file DNAMutator.h.

std::map<Residue*, String> BALL::DNAMutator::mutations_

private

Definition at line 243 of file DNAMutator.h.

Size BALL::DNAMutator::num_steps_

private

Definition at line 181 of file DNAMutator.h.

Property BALL::DNAMutator::prop_

private

Definition at line 182 of file DNAMutator.h.

Chain* BALL::DNAMutator::second_strand_

private

Definition at line 185 of file DNAMutator.h.

std::deque<Atom*> BALL::DNAMutator::to_optimize_

private

Definition at line 244 of file DNAMutator.h.

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation