BALL::DNAMutator Member List

This is the complete list of members for BALL::DNAMutator, including all inherited members.

addMutation(Index i, const String &new_frag_name)	BALL::DNAMutator	virtual
alignBases_(AtomContainer *from, const Vector3 &from_connection, const Vector3 &to_connection, Atom *from_at) const	BALL::DNAMutator	private
bases_	BALL::DNAMutator	privatestatic
canonizeName_(const String &frag_name) const	BALL::DNAMutator	private
clearMutations()	BALL::DNAMutator	virtual
db_	BALL::Mutator	protected
default_num_steps_	BALL::DNAMutator	privatestatic
DNAMutator(EnergyMinimizer *mini=NULL, ForceField *ff=NULL, FragmentDB *frag=NULL)	BALL::DNAMutator
ff_	BALL::DNAMutator	private
first_strand_	BALL::DNAMutator	private
freeFF_()	BALL::DNAMutator	private
getAttachmentAtom(AtomContainer *res) const	BALL::DNAMutator	private
getComplement_(const String &s) const	BALL::DNAMutator	private
getConnectionAtom_(Atom *at) const	BALL::DNAMutator	private
getNormalVector_(const Atom *at) const	BALL::DNAMutator	private
getTorsionDefiningAtom_(Atom *atom) const	BALL::DNAMutator	private
getTorsionDefiningAtom_(const Atom *atom) const	BALL::DNAMutator	private
isPurine_(const Atom &baseNitrogen) const	BALL::DNAMutator	private
isPyrimidine_(const Atom &baseNitrogen) const	BALL::DNAMutator	private
keep_ff_	BALL::DNAMutator	private
mapping_	BALL::DNAMutator	private
mark_(AtomContainer *atoms) const	BALL::DNAMutator	private
markBaseAtoms_(AtomContainer *res) const	BALL::DNAMutator	private
MATCH_TORSION enum value	BALL::DNAMutator
matching_mode_	BALL::DNAMutator	private
MatchingMode enum name	BALL::DNAMutator
minimizer_	BALL::DNAMutator	private
MINIMUM_ANGLE enum value	BALL::DNAMutator
mutate(MutatorOptions opts=NONE)	BALL::Mutator
mutate_impl_(MutatorOptions opt)	BALL::DNAMutator	protectedvirtual
mutateSingleBase_(Residue *res, const String &basename) const	BALL::DNAMutator	private
Mutations typedef	BALL::DNAMutator	private
mutations_	BALL::DNAMutator	private
Mutator(FragmentDB *db=0)	BALL::Mutator
MutatorOptions enum name	BALL::Mutator
MutIterator typedef	BALL::DNAMutator	private
NONE enum value	BALL::Mutator
num_steps_	BALL::DNAMutator	private
optimize()	BALL::DNAMutator	virtual
OPTIMIZE enum value	BALL::Mutator
optimize_(Fragment *frag)	BALL::DNAMutator	private
prop_	BALL::DNAMutator	private
rotateBasesMatchTorsion_(AtomContainer *from, const Atom *to_connection_at, Atom *from_at, const Atom *to_at) const	BALL::DNAMutator	private
rotateBasesMinAngle_(AtomContainer *from, const Vector3 &to_connection, Atom *from_at, const Atom *to_at) const	BALL::DNAMutator	private
rotateSameBases_(AtomContainer *from, AtomContainer *to) const	BALL::DNAMutator	private
second_strand_	BALL::DNAMutator	private
setFirstStrand(Chain *s1)	BALL::DNAMutator
setForceField(ForceField *ff)	BALL::DNAMutator
setFragmentDB(FragmentDB *db)	BALL::Mutator
setMatchingMode(MatchingMode mmode)	BALL::DNAMutator
setMaxOptimizationSteps(Size steps)	BALL::DNAMutator
setMinimizer(EnergyMinimizer *mini)	BALL::DNAMutator
setNucleotideMapping(const NucleotideMapping &bij)	BALL::DNAMutator
setSecondStrand(Chain *s2)	BALL::DNAMutator
setStrands(Chain *s1, Chain *s2)	BALL::DNAMutator
setup()	BALL::DNAMutator	virtual
setUsedProperty(Property p)	BALL::DNAMutator
to_optimize_	BALL::DNAMutator	private
unmark_(AtomContainer *atoms) const	BALL::DNAMutator	private
~DNAMutator()	BALL::DNAMutator
~Mutator()	BALL::Mutator	virtual