|
typedef int(* | ComparatorType) (const void *, const void *) |
|
typedef TContour< float > | Contour |
|
typedef TContourLine< float > | ContourLine |
|
typedef Index | FacetArray[256][12] |
|
typedef TContourSurface< float > | ContourSurface |
| Default type. More...
|
|
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, boost::property< boost::vertex_atom_ptr_t, const Atom * >, boost::property< boost::edge_bond_ptr_t, const Bond * > > | MolecularGraphBase |
|
typedef GRAPH::GraphTraits< MolecularGraph > | MolecularGraphTraits |
|
typedef MolecularGraph::EditableGraph | EditableMolecularGraph |
|
typedef TRegularData1D< float > | RegularData1D |
|
typedef TRegularData2D< float > | RegularData2D |
|
typedef TRegularData3D< float > | RegularData3D |
|
typedef HashSet< String > | StringHashSet |
|
typedef FlexibleMolecule | Ligand |
|
typedef std::list< EnergyProcessor * > | EnergyProcessorList |
|
typedef BidirectionalIterator< Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraits > | FragmentIterator |
|
typedef ConstBidirectionalIterator< Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraits > | FragmentConstIterator |
|
typedef std::reverse_iterator< FragmentIterator > | FragmentReverseIterator |
|
typedef std::reverse_iterator< FragmentConstIterator > | FragmentConstReverseIterator |
|
typedef BidirectionalIterator< Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraits > | MoleculeIterator |
|
typedef ConstBidirectionalIterator< Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraits > | MoleculeConstIterator |
|
typedef std::reverse_iterator< MoleculeIterator > | MoleculeReverseIterator |
|
typedef std::reverse_iterator< MoleculeConstIterator > | MoleculeConstReverseIterator |
|
typedef BidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits > | NucleicAcidIterator |
|
typedef ConstBidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits > | NucleicAcidConstIterator |
|
typedef std::reverse_iterator< NucleicAcidIterator > | NucleicAcidReverseIterator |
|
typedef std::reverse_iterator< NucleicAcidConstIterator > | NucleicAcidConstReverseIterator |
|
typedef BidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits > | NucleotideIterator |
|
typedef ConstBidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits > | NucleotideConstIterator |
|
typedef std::reverse_iterator< NucleotideIterator > | NucleotideReverseIterator |
|
typedef std::reverse_iterator< NucleotideConstIterator > | NucleotideConstReverseIterator |
|
typedef BidirectionalIterator< Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraits > | ProteinIterator |
|
typedef ConstBidirectionalIterator< Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraits > | ProteinConstIterator |
|
typedef std::reverse_iterator< ProteinIterator > | ProteinReverseIterator |
|
typedef std::reverse_iterator< ProteinConstIterator > | ProteinConstReverseIterator |
|
typedef BidirectionalIterator< Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits > | ResidueIterator |
|
typedef ConstBidirectionalIterator< Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits > | ResidueConstIterator |
|
typedef std::reverse_iterator< ResidueIterator > | ResidueReverseIterator |
|
typedef std::reverse_iterator< ResidueConstIterator > | ResidueConstReverseIterator |
|
typedef BidirectionalIterator< Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraits > | SecondaryStructureIterator |
|
typedef ConstBidirectionalIterator< Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraits > | SecondaryStructureConstIterator |
|
typedef std::reverse_iterator< SecondaryStructureIterator > | SecondaryStructureReverseIterator |
|
typedef std::reverse_iterator< SecondaryStructureConstIterator > | SecondaryStructureConstReverseIterator |
|
typedef TAngle< float > | Angle |
|
typedef TBox3< float > | Box3 |
|
typedef TCircle3< float > | Circle3 |
|
typedef std::complex< BALL_COMPLEX_PRECISION > | Complex |
|
typedef TFFT1D< BALL_FFTW_DEFAULT_TRAITS > | FFT1D |
|
typedef TFFT2D< BALL_FFTW_DEFAULT_TRAITS > | FFT2D |
|
typedef TFFT3D< BALL_FFTW_DEFAULT_TRAITS > | FFT3D |
|
typedef TLine3< float > | Line3 |
|
typedef TMatrix4x4< float > | Matrix4x4 |
|
typedef std::vector< double > | Coefficients |
|
typedef std::pair< double, double > | Interval |
|
typedef TPlane3< float > | Plane3 |
|
typedef TQuaternion< float > | Quaternion |
|
typedef TSphere3< float > | Sphere3 |
|
typedef TSurface< float > | Surface |
|
typedef TVector2< float > | Vector2 |
|
typedef TVector3< float > | Vector3 |
|
typedef TVector4< float > | Vector4 |
|
typedef std::list< RegularData3D * > | RegularData3DList |
|
using | AtomContainerProcessor = UnaryProcessor< AtomContainer > |
|
using | AtomProcessor = UnaryProcessor< Atom > |
|
using | BondProcessor = UnaryProcessor< Bond > |
|
using | ChainProcessor = UnaryProcessor< Chain > |
|
using | CompositeProcessor = UnaryProcessor< Composite > |
|
using | FragmentProcessor = UnaryProcessor< Fragment > |
|
using | ResidueProcessor = UnaryProcessor< Residue > |
|
using | ConstAtomProcessor = ConstUnaryProcessor< Atom > |
|
using | ConstCompositeProcessor = ConstUnaryProcessor< Composite > |
|
typedef std::vector< Eigen::MatrixXd, Eigen::aligned_allocator< Eigen::MatrixXd > > | MatrixVector |
|
typedef vector< vector< vector< double > > > | ScoreGrid |
|
typedef std::list< std::pair< Atom *, Atom * > > | AtomPairList |
|
typedef std::vector< std::pair< Atom *, Atom * > > | AtomPairVector |
|
typedef TSimpleMolecularGraph< Index, Index > | SimpleMolecularGraph |
|
typedef TMutex< BALL_DEFAULT_MUTEX_TYPE > | Mutex |
|
typedef TReadWriteLock< BALL_DEFAULT_READWRITELOCK_TYPE > | ReadWriteLock |
|
typedef TMutexLocker< BALL_DEFAULT_MUTEXLOCKER_TYPE, BALL_DEFAULT_MUTEX_TYPE > | MutexLocker |
|
typedef TReadLocker< BALL_DEFAULT_READLOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE > | ReadLocker |
|
typedef TWriteLocker< BALL_DEFAULT_WRITELOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE > | WriteLocker |
|
|
These predefined types are used in BALL for portability and comprehensibility.
|
typedef BALL_INDEX_TYPE | Distance |
|
typedef BALL_SIZE_TYPE | Handle |
|
typedef BALL_INDEX_TYPE | Index |
|
typedef BALL_SIZE_TYPE | Size |
|
typedef time_t | Time |
|
typedef BALL_SIZE_TYPE | HashIndex |
|
typedef BALL_SIZE_TYPE | Position |
|
typedef float | Real |
|
typedef double | DoubleReal |
|
typedef BALL_SIZE_TYPE | Property |
|
typedef BALL_INDEX_TYPE | ErrorCode |
|
typedef unsigned char | Byte |
|
typedef BALL_ULONG64_TYPE | LongSize |
|
typedef BALL_LONG64_TYPE | LongIndex |
|
typedef BALL_POINTERSIZEUINT_TYPE | PointerSizeUInt |
|
|
typedef std::vector< NamedProperty >::iterator | NamedPropertyIterator |
|
|
typedef BidirectionalIterator< Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraits > | AtomContainerIterator |
|
typedef ConstBidirectionalIterator< Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraits > | AtomContainerConstIterator |
|
typedef std::reverse_iterator< AtomContainerIterator > | AtomContainerReverseIterator |
| A mutable reverse bidirectional iterator for the AtomContainer class. More...
|
|
typedef std::reverse_iterator< AtomContainerConstIterator > | AtomContainerConstReverseIterator |
| A constant reverse bidirectional iterator for the AtomContainer class. More...
|
|
|
typedef BidirectionalIterator< Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits > | AtomIterator |
|
typedef ConstBidirectionalIterator< Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits > | AtomConstIterator |
|
typedef std::reverse_iterator< AtomIterator > | AtomReverseIterator |
| A mutable reverse bidirectional iterator for the Atom class. More...
|
|
typedef std::reverse_iterator< AtomConstIterator > | AtomConstReverseIterator |
| A constant reverse bidirectional iterator for the Atom class. More...
|
|
|
typedef Atom::BondIterator | AtomBondIterator |
|
typedef Atom::BondConstIterator | AtomBondConstIterator |
|
typedef Atom::BondReverseIterator | AtomBondReverseIterator |
|
typedef Atom::BondConstReverseIterator | AtomBondConstReverseIterator |
|
|
typedef BidirectionalIterator< Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits > | ChainIterator |
| A mutable bidirectional iterator for the Chain class. More...
|
|
typedef ConstBidirectionalIterator< Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits > | ChainConstIterator |
| A constant bidirectional iterator for the Chain class. More...
|
|
typedef std::reverse_iterator< ChainIterator > | ChainReverseIterator |
| A mutable reverse bidirectional iterator for the Chain class. More...
|
|
typedef std::reverse_iterator< ChainConstIterator > | ChainConstReverseIterator |
| A constant reverse bidirectional iterator for the Chain class. More...
|
|
|
typedef std::list< Atom * > | AtomList |
|
typedef std::list< Bond * > | BondList |
|
typedef std::list< AtomContainer * > | AtomContainerList |
|
typedef std::list< PDBAtom * > | PDBAtomList |
|
typedef std::list< Residue * > | ResidueList |
|
typedef std::list< Fragment * > | FragmentList |
|
typedef std::list< Molecule * > | MoleculeList |
|
typedef std::list< Protein * > | ProteinList |
|
typedef std::list< SecondaryStructure * > | SecondaryStructureList |
|
typedef std::list< Chain * > | ChainList |
|
typedef std::list< Nucleotide * > | NucleotideList |
|
typedef std::list< NucleicAcid * > | NucleicAcidList |
|
|
typedef BidirectionalIterator< Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits > | PDBAtomIterator |
| A mutable bidirectional iterator for the PDBAtom class. More...
|
|
typedef ConstBidirectionalIterator< Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits > | PDBAtomConstIterator |
| A constant bidirectional iterator for the PDBAtom class. More...
|
|
typedef std::reverse_iterator< PDBAtomIterator > | PDBAtomReverseIterator |
| A mutable reverse bidirectional iterator for the PDBAtom class. More...
|
|
typedef std::reverse_iterator< PDBAtomConstIterator > | PDBAtomConstReverseIterator |
| A constant reverse bidirectional iterator for the PDBAtom class. More...
|
|
|
This chapter describes a set of unary predicates acting on Composite instances, that can be used to identify the class type of a composite at runtime. - This predicates are functionally similar to the RTTI:isKindOf function. They decide whether a given composite is an instance of a certain class (or of a class derived thereof). For instance, the application of a MoleculePredicate to a composite will yield true, if the given composite was an instance of Molecule (or Protein , as Protein is derived from Molecule). Otherwise false is returned.
- Each KernelPredicate possesses three methods:
-operator (const Composite&) -operator (const Composite&) const
The two operators are functionally identical (two methods are needed, because the class is derived from TUnaryPredicate and we want to make sure both methods are overwritten). operator() returns true, if the given composite is a kind of the class corresponding to the respective predicate, false otherwise.
- See also
- UnaryPredicate
-
RTTI
|
typedef UnaryPredicate< Composite > | KernelPredicateType |
|
|
typedef Experiment< PeakList1D > | Experiment1D |
|
typedef Experiment< PeakList3D > | Experiment3D |
|
typedef Peak< float > | Peak1D |
|
typedef Peak< Vector2 > | Peak2D |
|
typedef Peak< Vector3 > | Peak3D |
|
|
typedef PeakList< Peak< float > > | PeakList1D |
| 1D peak list More...
|
|
typedef PeakList< Peak< Vector2 > > | PeakList2D |
| 2D peak list More...
|
|
typedef PeakList< Peak< Vector3 > > | PeakList3D |
| 3D peak list More...
|
|
|
typedef Spectrum< RegularData1D, Peak1D > | Spectrum1D |
| One-dimensional spectrum. More...
|
|
typedef Spectrum< RegularData2D, Peak2D > | Spectrum2D |
| Two-dimensional spectrum. More...
|
|
typedef Spectrum< RegularData3D, Peak3D > | Spectrum3D |
| Three-dimensional spectrum. More...
|
|
|
BALL_EXPORT std::ostream & | operator<< (std::ostream &os, const Exception::GeneralException &e) |
|
template<class T > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_sleepfor (T ms) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_max (T a, T b) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_max3 (T a, T b, T c) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_min (T a, T b) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_min3 (T a, T b, T c) |
|
template<class X > |
int BALL_DEPRECATED BALL_INLINE | ball_macro_abs (X x) |
|
template<class X > |
int BALL_DEPRECATED BALL_INLINE | ball_macro_sgn (X x) |
|
template<class X > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_odd (X x) |
|
template<class X > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_int_odd (X x) |
|
template<class X > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_int_even (X x) |
|
template<class X > |
X BALL_DEPRECATED BALL_INLINE | ball_macro_real_round (X x) |
|
template<class X , class Y , class E > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_equal (X x, Y y, E e) |
|
template<class X , class Y , class E > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_not_equal (X x, Y y, E e) |
|
template<class X , class Y , class E > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_less (X x, Y y, E e) |
|
template<class X , class Y , class E > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_less_or_equal (X x, Y y, E e) |
|
template<class X , class Y , class E > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_greater (X x, Y y, E e) |
|
template<class X , class Y , class E > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_greater_or_equal (X x, Y y, E e) |
|
template<class X > |
X BALL_DEPRECATED BALL_INLINE | ball_macro_real_abs (X x) |
|
template<class X > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_odd (X x) |
|
template<class X > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_real_even (X x) |
|
template<class X > |
long BALL_DEPRECATED BALL_INLINE | ball_macro_real_floor (X x) |
|
template<class X > |
long BALL_DEPRECATED BALL_INLINE | ball_macro_real_ceiling (X x) |
|
template<class X > |
int BALL_DEPRECATED BALL_INLINE | ball_macro_real_round_int (X x) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_char_bits () |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_char_mask () |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_char_shift () |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_all_bits_set () |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_all_bits_cleared () |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_number_of_bytes (T x) |
|
template<class T , std::size_t N> |
std::size_t BALL_DEPRECATED BALL_INLINE | ball_macro_sizeof_array (T(&)[N]) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_bitarray_size (T x) |
|
template<class BitArray , class X > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bitarray_clear_bit (BitArray *a, X x) |
|
template<class BitArray , class X > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bitarray_set_bit (BitArray *a, X x) |
|
template<class BitArray , class X > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bitarray_toggle_bit (BitArray *a, X x) |
|
template<class BitArray , class X > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_bitarray_is_bit_set (BitArray *a, X x) |
|
template<class Bit > |
unsigned BALL_DEPRECATED BALL_INLINE | ball_macro_bit (Bit bit) |
|
template<class Bitset , class Bit > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_set (Bitset &bitset, Bit bit) |
|
template<class Bitset > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_set_all (Bitset &bitset) |
|
template<class Bitset , class Bit > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_set_all_to (Bitset &bitset, Bit bit) |
|
template<class Bitset , class Bit > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_set_all_from (Bitset &bitset, Bit bit) |
|
template<class Bitset , class Bit > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_clear (Bitset &bitset, Bit bit) |
|
template<class Bitset > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_clear_all (Bitset &bitset) |
|
template<class Bitset , class Bit > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_clear_all_to (Bitset &bitset, Bit bit) |
|
template<class Bitset , class Bit > |
void BALL_DEPRECATED BALL_INLINE | ball_macro_bit_clear_all_from (Bitset &bitset, Bit bit) |
|
template<class Bitset , class Bit > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_bit_is_set (Bitset &bitset, Bit bit) |
|
template<class Bitset , class Bit > |
bool BALL_DEPRECATED BALL_INLINE | ball_macro_bit_is_cleared (Bitset &bitset, Bit bit) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_angle_radians_to_degree (T rad_angle) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_angle_degree_to_radian (T deg_angle) |
|
template<class T > |
T BALL_DEPRECATED BALL_INLINE | ball_macro_generic_echo (T value) |
|
BALL_EXPORT string | streamClassName (const std::type_info &t) |
|
template<typename Container , typename DataType , typename Position , typename Traits > |
ConstRandomAccessIterator< Container, DataType, Position, Traits > | operator+ (Distance distance, const ConstRandomAccessIterator< Container, DataType, Position, Traits > &iterator) |
|
template<> |
BALL_EXPORT HashIndex | Hash (const std::pair< Position, Position > &p) |
|
BALL_EXPORT const FacetArray & | getContourSurfaceFacetData (double threshold) |
|
BALL_EXPORT bool | operator== (const String &s1, const String &s2) |
|
BALL_EXPORT bool | operator!= (const String &s1, const String &s2) |
|
BALL_EXPORT bool | operator< (const String &s1, const String &s2) |
|
BALL_EXPORT bool | operator<= (const String &s1, const String &s2) |
|
BALL_EXPORT bool | operator> (const String &s1, const String &s2) |
|
BALL_EXPORT bool | operator>= (const String &s1, const String &s2) |
|
BALL_EXPORT String | operator+ (const String &s1, const string &s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (const string &s1, const String &s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (const String &s1, const String &s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (const String &s1, const char *char_ptr) |
| Concatenates a string and a C type string. More...
|
|
BALL_EXPORT String | operator+ (const char *char_ptr, const String &s) |
| Concatenates a C type string and a string. More...
|
|
BALL_EXPORT String | operator+ (const String &s, char c) |
| Concatenates a string and a character. More...
|
|
BALL_EXPORT String | operator+ (char c, const String &s) |
| Concatenates a character and a string. More...
|
|
BALL_EXPORT String | operator+ (String &&s1, const string &s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (String &&s1, const String &s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (String &&s1, String &&s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (const String &s1, string &&s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (string &&s1, const String &s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (const string &s1, String &&s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (const String &s1, String &&s2) |
| Concatenates two strings. More...
|
|
BALL_EXPORT String | operator+ (String &&s1, const char *char_ptr) |
| Concatenates a string and a C type string. More...
|
|
BALL_EXPORT String | operator+ (const char *char_ptr, String &&s) |
| Concatenates a C type string and a string. More...
|
|
BALL_EXPORT String | operator+ (String &&s, char c) |
| Concatenates a string and a character. More...
|
|
BALL_EXPORT String | operator+ (char c, String &&s) |
| Concatenates a character and a string. More...
|
|
std::ostream & | operator<< (std::ostream &out, const DockResult &dock_res) throw () |
|
std::istream & | operator>> (std::istream &in, DockResult &dock_res) throw () |
|
BALL_EXPORT double | calculateACE (const AtomContainer &atom_container, const string &type_filename="energy/ACE_types.dat", const string ¶meter_filename="energy/ACE_parameters.dat") |
|
BALL_EXPORT double | calculateCoulomb (const AtomContainer &atoms) |
|
BALL_EXPORT double | calculateDistanceCoulomb (const AtomContainer &fragment) |
|
BALL_EXPORT HashIndex | Hash (const PDBFile::ResidueQuadruple &quadruple) |
|
BALL_EXPORT std::ostream & | operator<< (std::ostream &s, const Quadruple< String, PDB::Character, PDB::Integer, PDB::AChar > &) |
|
template<class AtomContainerType > |
void | cloneBonds (const AtomContainerType &atom_container, AtomContainerType &cloned) |
|
template<class NucleotideContainerType > |
const Nucleotide * | get5Prime (const NucleotideContainerType &nucleotide_container) |
|
template<class NucleotideContainerType > |
const Nucleotide * | get3Prime (const NucleotideContainerType &nucleotide_container) |
|
BALL_EXPORT std::ostream & | operator<< (std::ostream &s, const Element &element) |
|
template<class ResidueContainerType > |
const Residue * | getNTerminal (const ResidueContainerType &residue_container) |
|
template<class ResidueContainerType > |
const Residue * | getCTerminal (const ResidueContainerType &residue_container) |
|
template<typename T > |
BALL_INLINE T | getDeterminant_ (const T *m, Size dim) |
|
template<typename T > |
T | getDeterminant (const T *m, Size dim) |
|
template<typename T > |
BALL_INLINE T | getDeterminant2 (const T *m) |
|
template<typename T > |
BALL_INLINE T | getDeterminant2 (const T &m00, const T &m01, const T &m10, const T &m11) |
|
template<typename T > |
BALL_INLINE T | getDeterminant3 (const T *m) |
|
template<typename T > |
BALL_INLINE T | getDeterminant3 (const T &m00, const T &m01, const T &m02, const T &m10, const T &m11, const T &m12, const T &m20, const T &m21, const T &m22) |
|
template<typename T > |
bool | SolveSystem (const T *m, T *x, const Size dim) |
|
template<typename T > |
BALL_INLINE bool | SolveSystem2 (const T &a1, const T &b1, const T &c1, const T &a2, const T &b2, const T &c2, T &x1, T &x2) |
|
template<typename T > |
short | SolveQuadraticEquation (const T &a, const T &b, const T &c, T &x1, T &x2) |
|
template<typename T > |
BALL_INLINE TVector3< T > | GetPartition (const TVector3< T > &a, const TVector3< T > &b) |
|
template<typename T > |
BALL_INLINE TVector3< T > | GetPartition (const TVector3< T > &a, const TVector3< T > &b, const T &r, const T &s) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TVector3< T > &a, const TVector3< T > &b) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TLine3< T > &line, const TVector3< T > &point) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TVector3< T > &point, const TLine3< T > &line) |
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template<typename T > |
T | GetDistance (const TLine3< T > &a, const TLine3< T > &b) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TVector3< T > &point, const TPlane3< T > &plane) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TPlane3< T > &plane, const TVector3< T > &point) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TLine3< T > &line, const TPlane3< T > &plane) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TPlane3< T > &plane, const TLine3< T > &line) |
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template<typename T > |
BALL_INLINE T | GetDistance (const TPlane3< T > &a, const TPlane3< T > &b) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TVector3< T > &a, const TVector3< T > &b, TAngle< T > &intersection_angle) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TLine3< T > &a, const TLine3< T > &b, TAngle< T > &intersection_angle) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TPlane3< T > &plane, const TVector3< T > &vector, TAngle< T > &intersection_angle) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TVector3< T > &vector, const TPlane3< T > &plane, TAngle< T > &intersection_angle) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TPlane3< T > &plane, const TLine3< T > &line, TAngle< T > &intersection_angle) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TLine3< T > &line, const TPlane3< T > &plane, TAngle< T > &intersection_angle) |
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template<typename T > |
BALL_INLINE bool | GetAngle (const TPlane3< T > &a, const TPlane3< T > &b, TAngle< T > &intersection_angle) |
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template<typename T > |
bool | GetIntersection (const TLine3< T > &a, const TLine3< T > &b, TVector3< T > &point) |
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template<typename T > |
BALL_INLINE bool | GetIntersection (const TPlane3< T > &plane, const TLine3< T > &line, TVector3< T > &intersection_point) |
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template<typename T > |
BALL_INLINE bool | GetIntersection (const TLine3< T > &line, const TPlane3< T > &plane, TVector3< T > &intersection_point) |
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template<typename T > |
bool | GetIntersection (const TPlane3< T > &plane1, const TPlane3< T > &plane2, TLine3< T > &line) |
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template<typename T > |
bool | GetIntersection (const TSphere3< T > &sphere, const TLine3< T > &line, TVector3< T > &intersection_point1, TVector3< T > &intersection_point2) |
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template<typename T > |
BALL_INLINE bool | GetIntersection (const TLine3< T > &line, const TSphere3< T > &sphere, TVector3< T > &intersection_point1, TVector3< T > &intersection_point2) |
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template<typename T > |
bool | GetIntersection (const TSphere3< T > &sphere, const TPlane3< T > &plane, TCircle3< T > &intersection_circle) |
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template<typename T > |
BALL_INLINE bool | GetIntersection (const TPlane3< T > &plane, const TSphere3< T > &sphere, TCircle3< T > &intersection_circle) |
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template<typename T > |
bool | GetIntersection (const TSphere3< T > &a, const TSphere3< T > &b, TCircle3< T > &intersection_circle) |
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template<class T > |
bool | GetIntersection (const TSphere3< T > &s1, const TSphere3< T > &s2, const TSphere3< T > &s3, TVector3< T > &p1, TVector3< T > &p2, bool test=true) |
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template<typename T > |
BALL_INLINE bool | isCollinear (const TVector3< T > &a, const TVector3< T > &b) |
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template<typename T > |
BALL_INLINE bool | isComplanar (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &c) |
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template<typename T > |
BALL_INLINE bool | isComplanar (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &c, const TVector3< T > &d) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TVector3< T > &a, const TVector3< T > &b) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TVector3< T > &vector, const TLine3< T > &line) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TLine3< T > &line, const TVector3< T > &vector) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TLine3< T > &a, const TLine3< T > &b) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TVector3< T > &vector, const TPlane3< T > &plane) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TPlane3< T > &plane, const TVector3< T > &vector) |
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template<typename T > |
BALL_INLINE bool | isOrthogonal (const TPlane3< T > &a, const TPlane3< T > &b) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TVector3< T > &point, const TLine3< T > &line) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TLine3< T > &line, const TVector3< T > &point) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TLine3< T > &a, const TLine3< T > &b) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TVector3< T > &point, const TPlane3< T > &plane) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TPlane3< T > &plane, const TVector3< T > &point) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TLine3< T > &line, const TPlane3< T > &plane) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TPlane3< T > &plane, const TLine3< T > &line) |
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template<typename T > |
BALL_INLINE bool | isIntersecting (const TPlane3< T > &a, const TPlane3< T > &b) |
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template<typename T > |
BALL_INLINE bool | isParallel (const TLine3< T > &line, const TPlane3< T > &plane) |
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template<typename T > |
BALL_INLINE bool | isParallel (const TPlane3< T > &plane, const TLine3< T > &line) |
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template<typename T > |
BALL_INLINE bool | isParallel (const TPlane3< T > &a, const TPlane3< T > &b) |
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template<typename T > |
TAngle< T > | getOrientedAngle (const T &ax, const T &ay, const T &az, const T &bx, const T &by, const T &bz, const T &nx, const T &ny, const T &nz) |
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template<typename T > |
BALL_INLINE TAngle< T > | getOrientedAngle (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &normal) |
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template<typename T > |
TAngle< T > | getTorsionAngle (const T &ax, const T &ay, const T &az, const T &bx, const T &by, const T &bz, const T &cx, const T &cy, const T &cz, const T &dx, const T &dy, const T &dz) |
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template<typename T > |
BALL_INLINE TAngle< T > | operator* (const T &val, const TAngle< T > &angle) |
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template<typename T > |
BALL_INLINE TAngle< T > | operator+ (const T &val, const TAngle< T > &angle) |
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template<typename T > |
BALL_INLINE TAngle< T > | operator- (const T &val, const TAngle< T > &angle) |
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template<typename T > |
std::istream & | operator>> (std::istream &s, TAngle< T > &angle) |
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template<typename T > |
std::ostream & | operator<< (std::ostream &s, const TAngle< T > &angle) |
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template<typename ComplexTraits > |
const RegularData1D & | operator<< (RegularData1D &to, const TFFT1D< ComplexTraits > &from) |
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template<typename ComplexTraits > |
const TRegularData2D< typename TFFT2D< ComplexTraits >::Complex > & | operator<< (TRegularData2D< typename TFFT2D< ComplexTraits >::Complex > &to, const TFFT2D< ComplexTraits > &from) |
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template<typename ComplexTraits > |
const RegularData2D & | operator<< (RegularData2D &to, const TFFT2D< ComplexTraits > &from) |
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template<typename ComplexTraits > |
const TRegularData3D< typename TFFT3D< ComplexTraits >::Complex > & | operator<< (TRegularData3D< typename TFFT3D< ComplexTraits >::Complex > &to, const TFFT3D< ComplexTraits > &from) |
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template<typename ComplexTraits > |
const RegularData3D & | operator<< (RegularData3D &to, const TFFT3D< ComplexTraits > &from) |
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template<typename T > |
TMatrix4x4< T > | operator* (const T &scalar, const TMatrix4x4< T > &m) |
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template<typename T > |
TVector3< T > | operator* (const TMatrix4x4< T > &matrix, const TVector3< T > &vector) |
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template<typename T > |
std::istream & | operator>> (std::istream &s, TQuaternion< T > &q) |
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template<typename T > |
std::ostream & | operator<< (std::ostream &s, const TQuaternion< T > &q) |
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template<typename T > |
BALL_INLINE TVector4< T > | operator* (const T &scalar, const TVector4< T > &v) |
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template<typename T > |
BALL_INLINE TVector4< T > | operator* (const TVector4< T > &v, const T &scalar) |
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::std::ostream & | operator<< (::std::ostream &os, const SnapShot &ss) |
| Output stream operator for SnapShots. More...
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::std::istream & | operator>> (::std::istream &is, SnapShot &ss) |
| Input stream operator for SnapShots. More...
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Position | getMMFF94Index (Position atom_type1, Position atom_type2) |
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BALL_EXPORT const RegularData1D & | operator<< (RegularData1D &data, const PeakList1D &peak_list) |
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template<typename PositionType > |
std::ostream & | operator<< (std::ostream &os, const Peak< PositionType > &peak) |
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std::ostream & | operator<< (std::ostream &os, const BALL::ShiftModel2D &shiftmodel) |
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template<typename DataT , typename PeakT , typename PositionT > |
double | operator- (const Spectrum< DataT, PeakT, PositionT > &s1, const Spectrum< DataT, PeakT, PositionT > &s2) |
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template<typename DataT , typename PeakT , typename PositionT > |
std::ostream & | operator<< (std::ostream &os, const Spectrum< DataT, PeakT, PositionT > &spectrum) |
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template<typename DataT , typename PeakT , typename PositionT > |
std::istream & | operator>> (std::istream &is, Spectrum< DataT, PeakT, PositionT > &spectrum) |
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PyObject * | pyMapBALLObjectToSip (Composite &object) |
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BALL_EXPORT void | calculateResidueChiAngles (const Protein &protein, HashMap< const Residue *, float > &residue_angles) |
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BALL_EXPORT void | calculateResidueChiAngles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles) |
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BALL_EXPORT float | calculateResidueChiAngles (const Residue &residue) |
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BALL_EXPORT void | calculateResidueChi2Angles (const Protein &protein, HashMap< const Residue *, float > &residue_angles) |
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BALL_EXPORT void | calculateResidueChi2Angles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles) |
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BALL_EXPORT float | calculateResidueChi2Angles (const Residue &residue) |
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BALL_EXPORT TRegularData3D< char > * | calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius) |
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BALL_EXPORT TRegularData3D< char > * | calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius) |
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BALL_EXPORT double | calculateOoiEnergy (AtomContainer &atoms) |
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BALL_EXPORT float | calculateSESAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5) |
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BALL_EXPORT float | calculateSESArea (const AtomContainer &fragment, float probe_radius=1.5) |
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BALL_EXPORT float | calculateSESVolume (const AtomContainer &fragment, float probe_radius=1.5) |
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template<typename Node , typename Edge > |
std::ostream & | operator<< (std::ostream &os, const TSimpleMolecularGraph< Node, Edge > &G) |
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template<typename T > |
void | swapBytes (T &t) |
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template<> |
BALL_EXPORT void | swapBytes (unsigned short &) |
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template<> |
BALL_EXPORT void | swapBytes (short &) |
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template<> |
BALL_EXPORT void | swapBytes (unsigned int &) |
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template<> |
BALL_EXPORT void | swapBytes (int &) |
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template<> |
BALL_EXPORT void | swapBytes (unsigned long &) |
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template<> |
BALL_EXPORT void | swapBytes (long &) |
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template<> |
BALL_EXPORT void | swapBytes (float &) |
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template<> |
BALL_EXPORT void | swapBytes (double &) |
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template<typename T > |
std::ostream & | operator<< (std::ostream &os, const BinaryFileAdaptor< T > &data) |
| Output stream for BinaryFileAdaptors. More...
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template<typename T > |
std::istream & | operator>> (std::istream &is, BinaryFileAdaptor< T > &data) |
| Input stream for BinaryFileAdaptors. More...
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BALL_EXPORT HashIndex | hashPointer (void *const ptr) |
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BALL_EXPORT HashIndex | hashString (const char *str) |
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BALL_EXPORT HashIndex | hashPJWString (const char *str) |
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BALL_EXPORT HashIndex | hashElfString (const char *str) |
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template<typename T > |
HashIndex | Hash (const T &key) |
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BALL_EXPORT HashIndex | Hash (const string &s) |
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BALL_EXPORT HashIndex | Hash (const String &s) |
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BALL_EXPORT HashIndex | Hash (void *const &ptr) |
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BALL_EXPORT HashIndex | getNextPrime (HashIndex l) |
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BALL_EXPORT std::ostream & | operator<< (std::ostream &os, const PreciseTime &time) |
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BALL_EXPORT std::ostream & | operator<< (std::ostream &os, const TimeStamp &stamp) |
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template<typename ValueType > |
std::ostream & | operator<< (std::ostream &os, const TRegularData1D< ValueType > &data) |
| Output operator. More...
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template<typename ValueType > |
std::istream & | operator>> (std::istream &is, TRegularData1D< ValueType > &grid) |
| Input operator. More...
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template<typename ValueType > |
std::ostream & | operator<< (std::ostream &os, const TRegularData2D< ValueType > &data) |
| Output operator. More...
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template<typename ValueType > |
std::istream & | operator>> (std::istream &is, TRegularData2D< ValueType > &grid) |
| Input operator. More...
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template<typename ValueType > |
std::ostream & | operator<< (std::ostream &os, const TRegularData3D< ValueType > &grid) |
| Output operator. More...
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template<typename ValueType > |
std::istream & | operator>> (std::istream &is, TRegularData3D< ValueType > &grid) |
| Input operator. More...
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BALL_EXPORT AtomList | atoms (const AtomContainer &fragment, const String &expression=String()) |
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BALL_EXPORT AtomList | atoms (const AtomList &atoms, const String &expression) |
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BALL_EXPORT PDBAtomList | PDBAtoms (const AtomContainer &fragment, const String &expression=String()) |
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BALL_EXPORT BondList | bonds (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT BondList | bonds (const Atom &atom) |
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BALL_EXPORT AtomContainerList | atomContainers (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT ResidueList | residues (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT FragmentList | fragments (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT MoleculeList | molecules (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT ProteinList | proteins (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT SecondaryStructureList | secondaryStructures (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT ChainList | chains (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT NucleicAcidList | nucleicAcids (const AtomContainer &fragment, bool selected_only=false) |
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BALL_EXPORT NucleotideList | nucleotides (const AtomContainer &fragment, bool selected_only=false) |
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template<typename T > |
BALL_INLINE TVector2< T > | operator* (const T &scalar, const TVector2< T > &vector) |
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template<typename T > |
std::istream & | operator>> (std::istream &s, TVector2< T > &vector) |
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template<typename T > |
std::ostream & | operator<< (std::ostream &s, const TVector2< T > &vector) |
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template<typename T > |
BALL_INLINE TVector3< T > | operator* (const T &a, const TVector3< T > &b) |
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template<typename T > |
std::istream & | operator>> (std::istream &s, TVector3< T > &vector) |
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template<typename T > |
std::ostream & | operator<< (std::ostream &s, const TVector3< T > &vector) |
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template<typename T > |
BALL_INLINE TVector4< T > | operator+ (const TVector4< T > &a, const TVector4< T > &b) |
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template<typename T > |
BALL_INLINE TVector4< T > | operator- (const TVector4< T > &a, const TVector4< T > &b) |
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template<typename T > |
std::istream & | operator>> (std::istream &s, TVector4< T > &vector) |
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template<typename T > |
std::ostream & | operator<< (std::ostream &s, const TVector4< T > &vector) |
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BALL_EXPORT Angle | calculateTorsionAngle (const Atom &a1, const Atom &a2, const Atom &a3, const Atom &a4) |
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BALL_EXPORT bool | setTorsionAngle (const Atom &a1, const Atom &a2, Atom &a3, const Atom &a4, Angle angle) |
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BALL_EXPORT Angle | calculateBondAngle (const Atom &a1, const Atom &a2, const Atom &a3) |
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