Clipper
|
Namespaces | |
data32 | |
data64 | |
datatypes | |
Classes | |
class | Array2d |
Simple 2-d array class. More... | |
class | Atom |
Atom class. More... | |
class | Atom_list |
Atom list class. More... | |
class | AtomSF |
Atomic scattering factor object. More... | |
class | AtomShapeFn |
Atomic shape function object. More... | |
class | BasisFn_aniso_gaussian |
simple anisotropic Gaussian basis function More... | |
class | BasisFn_base |
abstract base class for resolution function basis functions More... | |
class | BasisFn_binner |
simple binning basis function More... | |
class | BasisFn_expcubic |
simple Expcubic basis function More... | |
class | BasisFn_gaussian |
simple Gaussian basis function More... | |
class | BasisFn_linear |
simple linear basis function More... | |
class | BasisFn_log_aniso_gaussian |
simple anisotropic Gaussian basis function More... | |
class | BasisFn_log_gaussian |
simple log Gaussian basis function More... | |
class | BasisFn_spline |
simple smooth basis function More... | |
class | CCell |
CCell container. More... | |
class | Cell |
Cell object. More... | |
class | Cell_descr |
cell description (automatically converts to radians) More... | |
class | CGrid_sampling |
CGrid_sampling container. More... | |
class | CHKL_data |
Reflection data list container. More... | |
class | CHKL_info |
HKL list and indexing object container. More... | |
class | ClipperInstance |
class | ClipperInstantiator |
class | CNXmap |
Non-Crystallographic map container. More... | |
class | CNXmap_operator |
Non-Crystallographic map operator container. More... | |
struct | Compare_grid |
class | Container |
Definition for a generic container Object. More... | |
class | Coord_frac |
fractional (cell) coordinates More... | |
class | Coord_grid |
Grid coordinate. More... | |
class | Coord_map |
map coordinate: this is like Coord_grid, but non-integer More... | |
class | Coord_orth |
orthogonal (Angstrom) coordinates More... | |
class | Coord_reci_frac |
fractional reciprocal coordinate (i.e. non-integer hkl) More... | |
class | Coord_reci_orth |
orthogonal reciprocal coordinate (length of which is invresolsq) More... | |
class | CResolution |
Resolution container. More... | |
class | CSpacegroup |
Spacegroup container. More... | |
class | Curv_frac |
fractional (cell) curvatures, with respect to fractional u,v,w More... | |
class | Curv_map |
map coordinate curvatures, with respect to grid u,v,w More... | |
class | Curv_orth |
orthogonal (Angstom) curvatures, with respect to orthogonal x,y,z More... | |
class | CXmap |
Crystallographic map container. More... | |
class | Datatype_base |
Reflection data type objects. More... | |
class | Euler |
Euler angle class. More... | |
class | Euler_ccp4 |
Euler_ccp4 angle class. More... | |
class | FFTmap |
FFTmap: P1 map with symmetry used for calculating FFTs. More... | |
class | FFTmap_base |
class | FFTmap_p1 |
FFTmap_p1: low level P1 map used for calculating FFTs. More... | |
class | FFTmap_sparse_p1_base |
base type for sparse P1 fft maps More... | |
class | FFTmap_sparse_p1_hx |
FFTmap_sparse_p1_hx: low level sparse P1 map used for calculating FFTs. More... | |
class | FFTmap_sparse_p1_xh |
FFTmap_sparse_p1_xh: low level sparse P1 map used for calculating FFTs. More... | |
class | Generic_ordinal |
Generic ordinal gernerator. More... | |
class | Grad_frac |
fractional (cell) gradient, with respect to fractional u,v,w More... | |
class | Grad_map |
map coordinate gradient, with respect to grid u,v,w More... | |
class | Grad_orth |
orthogonal (Angstom) gradient, with respect to orthogonal x,y,z More... | |
class | Grid |
generic grid More... | |
class | Grid_range |
Grid range class: defines array limits for a grid. More... | |
class | Grid_sampling |
Grid sampling of a unit cell. More... | |
class | Histogram |
General histogram class. More... | |
class | HKL |
reflection 'Miller' index More... | |
class | HKL_class |
reflection class More... | |
class | HKL_data |
HKL_data<> More... | |
class | HKL_data_base |
HKL_data_base. More... | |
class | HKL_data_cacheobj |
class | HKL_info |
HKL list container and tree root. More... | |
class | HKL_lookup |
Fast reflection lookup object. More... | |
class | HKL_sampling |
HKL sampling of reciprocal space. More... | |
class | Interp_cubic |
Wrapper class for third-order (cubic) interpolation fns. More... | |
class | Interp_linear |
Wrapper class for first-order (linear) interpolation fns. More... | |
class | Interp_nearest |
Wrapper class for zeroth-order (nearest neighbour) interpolation fns. More... | |
class | Isymop |
Integerised symmetry matrix. More... | |
class | LogPhaseProb |
Log phase probability distribution object. More... | |
class | Map_index_sort |
Generic map sorting class. More... | |
class | Map_stats |
Generic map statistics class. More... | |
class | Mat33 |
3x3-matrix class More... | |
class | Mat33sym |
Compressed form for 3x3 symmetric matrix class. More... | |
class | Matrix |
General matrix class: like Array2d but with numerical methods. More... | |
class | Message |
Message handler class. More... | |
class | Message_base |
Base type for messages. More... | |
class | Message_ctor |
Constructor message (level = 2) More... | |
class | Message_dtor |
Destructor message (level = 2) More... | |
class | Message_fatal |
Fatal message (level = 9) More... | |
class | Message_generic |
Generic message. More... | |
class | Message_info |
Info message (level = 1) More... | |
class | Message_warn |
Warning message (level = 5) More... | |
class | Metric_tensor |
Metric tensor. More... | |
class | Mutex |
Mutex class: used for locking and unlocking shared resources. More... | |
class | NX_operator |
NX_operator: non-crystal map operator. More... | |
class | NXmap |
NXmap<T>: actual non-crystallographic map class. More... | |
class | NXmap_base |
NXmap_base: base for non-crystallographic map class. More... | |
class | NXmap_operator |
NXmap_operator: non-crystal map operator referencing a particular NXmap. More... | |
class | ObjectCache |
Object Cache manager. More... | |
class | Polar_ccp4 |
Polar_ccp4 angle class. More... | |
class | Prob_phi_2d |
2-d angular probability distibution class More... | |
class | Property |
Template for a property holding an arbitrary type. More... | |
class | Property_base |
Base class for properties of arbitrary types. More... | |
class | PropertyManager |
Class for holding a list of labelled properties of arbitrary types. More... | |
class | Ramachandran |
Ramachandran plot class. More... | |
class | Range |
Range - upper and lower bounds of some type. More... | |
class | Range_sampling |
Range sampling: discrete sampling of a real range. More... | |
class | Resolution |
Resolution in angstroms. More... | |
class | Resolution_ordinal |
Resolution ordinal gernerator. More... | |
class | ResolutionFn |
2nd order resolution function evaluator More... | |
class | ResolutionFn_nonlinear |
2nd order resolution function evaluator More... | |
class | Rotation |
Rotation class. More... | |
class | RTop |
Rotation-translation operator. More... | |
class | RTop_frac |
Fractional operator class. More... | |
class | RTop_orth |
Orthogonal operator class. More... | |
class | Spacegroup |
Spacegroup object. More... | |
class | Spgr_cacheobj |
class | Spgr_descr |
spacegroup description More... | |
class | String |
String extension with simple parsing methods. More... | |
class | Symop |
Crystallographic symmetry operator. More... | |
class | Symop_code |
Compressed encoded symmetry operator. More... | |
class | TargetFn_base |
abstract base class for least-squares resolution function target functions More... | |
class | TargetFn_meanEnth |
simple mean |E|n target More... | |
class | TargetFn_meanFnth |
simple mean |F|n target More... | |
class | TargetFn_scaleEsq |
|E|2 scaling target More... | |
class | TargetFn_scaleF1F2 |
|F|2 scaling target More... | |
class | TargetFn_scaleI1I2 |
class | TargetFn_scaleLogF1F2 |
log |F|2 scaling target More... | |
class | TargetFn_scaleLogI1I2 |
log |I| scaling target More... | |
class | TargetFn_sigmaa |
class | TargetFn_sigmaa_omegaa |
class | Test_base |
Base class for clipper self-test classes. More... | |
class | Test_core |
class | Thread_base |
Thread base class: Override this to create new threads. More... | |
class | U_aniso_frac |
Anisotropic fractional atomic displacement parameters. More... | |
class | U_aniso_orth |
Anisotropic orthogonal atomic displacement parameters. More... | |
class | Util |
Utility class. More... | |
class | Vec3 |
3-vector class More... | |
class | Xmap |
Xmap<T>: actual crystallographic map class. More... | |
class | Xmap_base |
Xmap_base: base for crystallographic map class. More... | |
class | Xmap_cacheobj |
Typedefs | |
typedef ftype64 | ftype |
ftype definition for floating point representation More... | |
typedef ftype64 | xtype |
xtype definition for import/export of data | |
typedef float | ftype32 |
typedef double | ftype64 |
typedef int | itype32 |
typedef unsigned int | uitype32 |
typedef long long | itype64 |
typedef unsigned long long | uitype64 |
typedef Grid_range | Grid_map |
Obsolete form for Grid_range. | |
typedef float | ffttype |
Functions | |
template<class T > | |
int | operator== (const Vec3< T > &v1, const Vec3< T > &v2) |
template<class T > | |
int | operator!= (const Vec3< T > &v1, const Vec3< T > &v2) |
template<class T > | |
Vec3< T > | operator- (const Vec3< T > &v) |
template<class T > | |
Vec3< T > | operator+ (const Vec3< T > &v1, const Vec3< T > &v2) |
template<class T > | |
Vec3< T > | operator- (const Vec3< T > &v1, const Vec3< T > &v2) |
template<class T > | |
Vec3< T > | operator* (const T &s, const Vec3< T > &v1) |
template<class T > | |
Vec3< T > | operator* (const Vec3< T > &v1, const T &s) |
template<class T > | |
T | operator* (const Vec3< T > &v1, const Vec3< T > &v2) |
template<class T > | |
Vec3< T > | operator* (const Mat33< T > &m, const Vec3< T > &v) |
template<class T > | |
Vec3< T > | operator* (const Vec3< T > &v, const Mat33< T > &m) |
template<class T > | |
Mat33< T > | operator* (const Mat33< T > &m1, const Mat33< T > &m2) |
template<class T > | |
Mat33< T > | operator+ (const Mat33< T > &m1, const Mat33< T > &m2) |
template<class T > | |
Mat33< T > | operator- (const Mat33< T > &m) |
template<class T > | |
Vec3< T > | operator* (const Mat33sym< T > &m, const Vec3< T > &v) |
template<class T > | |
Mat33sym< T > | operator+ (const Mat33sym< T > &m1, const Mat33sym< T > &m2) |
template<class T > | |
Mat33sym< T > | operator- (const Mat33sym< T > &m) |
template<class T > | |
Vec3< T > | operator* (const RTop< T > &r, const Vec3< T > &v) |
template<class T > | |
RTop< T > | operator* (const RTop< T > &r1, const RTop< T > &r2) |
template<class T > | |
std::vector< T > | operator* (const Matrix< T > &m, const std::vector< T > &v) |
Rotation | operator* (const Rotation &r1, const Rotation &r2) |
bool | reci_asu (const Spgr_descr::Symop_codes &ops, data::ASUfn asufn) |
Vec3 | real_asu (const Spgr_descr::Symop_codes &ops) |
Variables | |
Message | message |
Message_fatal | message_parent_of_root ("Container: attempt to access parent of root") |
Message_fatal | message_child_out_of_range ("Container: child index out of range") |
Message_fatal | message_duplicate_path ("Container: attempt to create duplicate path") |
const HKL_info | NullHKL_info |
const Resolution | NullResolution |
const Spacegroup | NullSpacegroup |
const Cell | NullCell |
const Grid_sampling | NullGrid_sampling |
Message_fatal | message_fftmap_get_real_space_error ("FFTmap: get_real_data in reciprocal space") |
Message_fatal | message_fftmap_set_real_space_error ("FFTmap: set_real_data in reciprocal space") |
Message_fatal | message_fftmap_get_reci_space_error ("FFTmap: get_recip_data in real space") |
Message_fatal | message_fftmap_set_reci_space_error ("FFTmap: set_recip_data in real space") |
Message_ctor | message_ctor_fftmap (" [FFTmap: constructed]") |
Message_ctor | message_ctor_hkl_data (" [HKL_data: constructed]") |
Message_fatal | message_recip_asu_error ("HKL_info: find_sym reciprocal space ASU error") |
Message_ctor | message_ctor_hkl_info (" [HKL_info: constructed]") |
Message_ctor | message_ctor_nxmap (" [NXmap: constructed]") |
Message_ctor | message_ctor_xmap (" [Xmap: constructed]") |
All normal clipper objects except data objects are defined in this namespace.
typedef ftype64 clipper::ftype |
ftype definition for floating point representation
This type is used for all floating point values except data. The whole package could be templatised on ftype. However for now it is typedef'ed
Assumes a column vector
Assumes a row vector, i.e. equivalent to the matrix-vector product with the matrix trasposed
std::vector<T> clipper::operator* | ( | const Matrix< T > & | m, |
const std::vector< T > & | v | ||
) |
Assumes a column vector
Note: This multiplication operator combines rotations in left-to-right order, rather than the right-to-left order used for matrices. Thus, the rotation which arises from applying rotation r1 followed by rotation r2 is given by r1*r2. Similarly, the rotation which arises from applying rotation r1 followed by rotation r2 and rotation r3 is given by (r1*r2)*r3.