The namespace which includes all objects (crystallographic and algorithmic) in ObjCryst++. More...

Classes
class	AsymmetricUnit
	The basic description of spacegroup asymmetric unit. More...

class	Atom
	The basic atom scatterer, in a crystal. More...

struct	BBox

class	CellExplorer
	Algorithm class to find the correct indexing from observed peak positions. More...

class	CIF
	Main CIF class - parses the stream and separates data blocks, comments, items, loops. More...

class	CIFData
	The CIFData class holds all the information from a single data_ block from a cif file. More...

class	Crystal
	Crystal class: Unit cell, spacegroup, scatterers. More...

struct	CrystalPOVRayOptions
	Class to store POV-Ray output options. More...

class	DiffractionDataSingleCrystal
	DiffractionData object for Single Crystal analysis. More...

class	GlobalScatteringPower
	Global Scattering Power. More...

class	LorentzCorr
	Lorentz Correction. More...

class	LSQNumObj
	(Quick & dirty) Least-Squares Refinement Object with Numerical derivatives More...

class	MainTracker
	A class to hold all trackers. More...

struct	MDAtomGroup
	Groups of atoms that can be moved using molecular dynamics principles, taking a list of restraints as ptential. More...

class	MolAtom
	MolAtom : atom inside a Molecule. More...

class	MolBond
	Bond between two atoms, also a restraint on the associated bond length. More...

class	MolBondAngle
	Bond angle restraint between 3 atoms. More...

class	MolDihedralAngle
	Dihedral angle restraint between 4 atoms. More...

class	Molecule
	Molecule : class for complex scatterer descriptions using cartesian coordinates with bond length/angle restraints, and moves either of individual atoms or using torsion bonds. More...

class	MolRing
	Ring class. More...

struct	MolZAtom
	Light-weight representation of an atom in the molecule, as a part of a Z-matrix. More...

class	MonteCarloObj
	Base object for Monte-Carlo Global Optimization methods. More...

class	NiftyStaticGlobalObjectsInitializer_Crystal

class	NiftyStaticGlobalObjectsInitializer_RefinableObj

class	NiftyStaticGlobalObjectsInitializer_Scatterer

class	NiftyStaticGlobalObjectsInitializer_ScatteringData

class	NiftyStaticGlobalObjectsInitializer_ScatteringPower

class	NiftyStaticGlobalObjectsInitializer_UnitCell

class	ObjCrystException
	Exception class for ObjCryst++ library. More...

class	ObjRegistry
	Object Registry. More...

class	OptimizationObj
	Base object for Optimization methods. More...

class	PeakList
	Class to store positions of observed reflections. More...

class	PolarizationCorr
	Polarization Correction. More...

class	PowderPattern
	Powder pattern class, with an observed pattern and several calculated components to modelize the pattern. More...

class	PowderPatternBackground
	Phase to compute a background contribution to a powder pattern using an interpolation. More...

class	PowderPatternBackgroundBayesianMinimiser
	This object is used to estimate the background in a powder pattern, using a Bayesian approach (David & Sivia, Acta Cryst A50 (1994), 703) More...

class	PowderPatternComponent
	Generic class to compute components (eg the contribution of a given phase, or background) of a powder pattern. More...

class	PowderPatternDiffraction
	Class to compute the contribution to a powder pattern from a crystalline phase. More...

class	PowderSlitApertureCorr
	Slit aperture correction (for powder) More...

class	Quaternion
	A quaternion class, used to represent the orientation of the molecule. More...

class	Radiation
	Class to define the radiation (type, monochromaticity, wavelength(s)) of an experiment. More...

class	RecUnitCell
	Lightweight class describing the reciprocal unit cell, for the fast computation of d*_hkl^2. More...

class	RefinableObj
	Generic Refinable Object. More...

class	RefinableObjClock
	We need to record exactly when refinable objects have been modified for the last time (to avoid re-computation), and to do that we need a precise time. More...

class	RefinablePar
	Generic class for parameters of refinable objects. More...

class	ReflectionProfile
	Abstract base class for reflection profiles. More...

class	ReflectionProfileDoubleExponentialPseudoVoigt
	Double-Exponential Pseudo-Voigt profile for TOF. More...

class	ReflectionProfilePseudoVoigt
	Pseudo-Voigt reflection profile. More...

class	ReflectionProfilePseudoVoigtAnisotropic
	Pseudo-Voigt reflection profile, with 6-parameters anisotropic Lorentzian broadening and Toraya asymmetric modelling. More...

class	RefObjOpt
	Base class for options. More...

class	RefObjOption
	Class for options of RefinableObj, templated so that we can warn the object that something has been changed. More...

class	RefParType
	class of refinable parameter types. More...

class	Restraint
	Restraint: generic class for a restraint of a given model. More...

class	RigidGroup
	Rigid groups of atoms inside a molecule. More...

class	Scatterer
	Generic type of scatterer: can be an atom, or a more complex assembly of atoms. More...

struct	ScatteringComponent
	A scattering position in a crystal, associated with the corresponding occupancy and a pointer to the ScatteringPower. More...

class	ScatteringComponentList
	list of scattering positions in a crystal, associated with the corresponding occupancy and a pointer to the ScatteringPower. More...

class	ScatteringCorr
	Base class to compute all kind of corrections to intensities: Lorentz, Polar, absorption, texcture, extinction, etc... More...

class	ScatteringData
	Class to compute structure factors for a set of reflections and a Crystal. More...

class	ScatteringPower
	Abstract Base Class to describe the scattering power of any Scatterer component in a crystal. More...

class	ScatteringPowerAtom
	The Scattering Power for an Atom. More...

class	ScatteringPowerSphere
	\ brief ScatteringPower for a spherical particule More...

class	SimplexObj
	Conjugate Gradient Algorithm object. More...

class	SpaceGroup
	The crystallographic space group, and the cell choice. More...

struct	SpeedTestReport
	Structure to hold the results of a speedtest (see ObjCryst::SpeedTest()) More...

struct	StretchMode
	Abstract base Stretch Mode for Molecule objects. More...

struct	StretchModeBondAngle
	Atoms moved when changing a bond angle. More...

struct	StretchModeBondLength
	Group of atoms for random moves changing a bond length. More...

struct	StretchModeTorsion
	Atoms moved when rotated around a bond at0-at1-at2-at3. More...

struct	StretchModeTwist
	Atoms moved between two other atoms, using a "twist" of their positions - only small twists of their positions are allowed to avoid breaking restraints too much. More...

class	SymmetricPairCompare
	Class to compare pairs of objects, with the two objects playing a symmetric role. More...

class	TextureEllipsoid
	Texture correction using the Ellipsoidal preferred orientation function. More...

class	TextureMarchDollase
	Texture correction using the March-Dollase model. More...

struct	TexturePhaseMarchDollase
	One texture phase for the March-Dollase model. More...

class	tmp_C_Numeric_locale
	This class only serves to temporarilly set the LC_NUMERIC C locale to "C", in order to use '. More...

class	TOFCorr
	Time-Of-Flight Correction. More...

class	Tracker
	A class to track the variation of parameters as a function of a number of cycles/trials. More...

class	TrackerObject
	Tracker for objects (RefinableObj, Crystal, PowderPattern, RefPar,...) More...

struct	Triple

class	UnitCell
	Unit Cell class: Unit cell with spacegroup information. More...

class	WXAtom
	wxCryst class for Atoms More...

class	WXCRYST_ID
	Class to automatically assign a unique wxID to each window. More...

class	WXCrystal
	wxCryst class for Crystals More...

class	WXCrystalScrolledGridWindow

class	WXCrystMenuBar
	Our own local menu bar, using buttons and Popup menus. More...

class	WXCrystObj
	Base class for all displayed ObjCryst objects (with a title, and a sizer to stack objects). More...

class	WXCrystObjBasic
	Abstract base class for all objects in wxCryst. More...

class	WXCrystObjBasicList
	A List of WXCrystObjBasic. More...

class	WXDiffractionSingleCrystal
	WX Class for DiffractionDataSingleCrystal objects. More...

class	WXField
	This is the abstract base class for all fields, wether they contain a floating-point parameter, or a string,... More...

class	WXFieldChoice
	Class to pick one choice... More...

class	WXFieldName
	A field with the name of a WXCrystObj. More...

class	WXFieldOption
	WX representation of a RefObj option. This displays the names of the different choices. More...

class	WXFieldPar
	A field for a parameter. More...

class	WXFieldParBase
	A field for a parameter. More...

class	WXFieldRefPar
	A field for a RefinablePar. More...

class	WXFieldString
	A field which directly links to a string. More...

class	WXGlobalOptimRunThread
	Class for a GlobalOptimization thread. More...

class	WXLSQ

class	WXMolAtom
	wx class for MolAtom objects More...

class	WXMolBond
	wx class for MolBond objects More...

class	WXMolBondAngle
	wx class for MolBondAngle objects More...

class	WXMolDihedralAngle
	wx class for MolDihedralAngle objects More...

class	WXMolecule
	wxCryst class for Molecule objects More...

class	WXMolScrolledWindow

class	WXMonteCarloObj
	Class for Graphical interface to Monte-Carlo objects (Simulated Annealing, Parallel Tempering) More...

class	wxMultiChoiceDialog_ListBox
	Provides the same functionnality as wxMultiChoiceDialog, but always using a wxListBox, which is much easier when selecting a large number of successive choices (using shift-click). More...

class	WXMultiGraph

class	WXOptimizationObj
	WX Class for a Global Optimization objects. More...

class	WXPowderPattern
	WX Class for PowderPattern objects. More...

class	WXPowderPatternBackground
	Class to display a Powder Pattern Background. More...

class	WXPowderPatternDiffraction
	Class to display a Powder Pattern for a crystalline phase. More...

class	WXPowderPatternGraph
	Class to display a Powder Pattern (calc,obs) in a graphic window. More...

class	WXProfileDoubleExponentialPseudoVoigt
	Class to display a Powder Pattern Pseudo-Voigt Profile. More...

class	WXProfilePseudoVoigt
	Class to display a Powder Pattern Pseudo-Voigt Profile. More...

class	WXProfilePseudoVoigtAnisotropic
	Class to display a Powder Pattern Pseudo-Voigt Profile with Anisotropic broadening. More...

class	WXRadiation
	WX Class for Radiation. More...

class	WXRefinableObj
	The base wxCryst class for all RefinableObj objects. More...

class	WXRegistry
	This displays all components of a ObjCryst++ Registry. More...

class	WXScatterer
	base wxCryst class for Scatterers More...

class	WXScatteringPowerAtom
	wxCryst class for ScatteringPowerAtom More...

class	WXScatteringPowerSphere
	wxCryst class for ScatteringPowerSphere More...

class	WXTextureEllipsoid
	Class to display one Preferred Orientation phase using the Ellipsoid model. More...

class	WXTextureMarchDollase
	Class to display the Preferred Orientation Correction using the March-Dollase parametrization. More...

class	WXTexturePhaseMarchDollase
	Class to display one Preferred Orientation phase using the March-Dollase parametrization. More...

class	WXTrackerGraph

class	WXZAtom

class	WXZScatterer
	wxCryst class for ZScatterer objects More...

class	XMLCrystTag
	class to input or output a well-formatted xml beginning or ending tag. More...

struct	XYZ
	Structure holding 3 coordinates, or deriviatives with respect to each of these coordinates. More...

class	ZAtom
	Class for individual atoms in a ZScatterer Object. More...

class	ZMoveMinimizer
	Class to minimize conformation changes for random moves. More...

class	ZPolyhedron
	ZPolyhedron: a Scatterer to describe polyhedras such as octahedron, tetrahedron, square plane, etc... More...

class	ZScatterer
	ZScatterer: the basic type of complex scatterers, where atom positions are defined using a standard "Z-Matrix" description. More...

Enumerations
enum	RadiationType { RAD_NEUTRON, RAD_XRAY, RAD_ELECTRON }
	Type of radiation used. More...

enum	SampleType { SAMPLE_SINGLE_CRYSTAL, SAMPLE_POWDER }
	Sample type (not used yet)

enum	WavelengthType { WAVELENGTH_MONOCHROMATIC, WAVELENGTH_ALPHA12, WAVELENGTH_TOF, WAVELENGTH_MAD, WAVELENGTH_DAFS, WAVELENGTH_LAUE }
	Incident beam characteristics : monochromatic, X-Ray tube with Alpha1 and alpha2, MAD (a few wavelengths-UNUSED YET), DAFS (continuous wavelength range-UNUSED YET) LAUE (UNUSED YET), WAVELENGTH_TOF (neutron Time Of Flight)

enum	ReflectionProfileType { PROFILE_GAUSSIAN, PROFILE_LORENTZIAN, PROFILE_PSEUDO_VOIGT, PROFILE_PSEUDO_VOIGT_FINGER_COX_JEPHCOAT, PROFILE_PEARSON_VII }
	Profile type for powder (could it be used fopr single crystals on 2D detectors ?)

enum	PowderBackgroundInterpType { POWDER_BACKGROUND_LINEAR, POWDER_BACKGROUND_CUBIC_SPLINE }

enum	CrystalSystem { TRICLINIC, MONOCLINIC, ORTHOROMBIC, HEXAGONAL, RHOMBOEDRAL, TETRAGONAL, CUBIC }
	Different lattice types.

enum	CrystalCentering { LATTICE_P, LATTICE_I, LATTICE_A, LATTICE_B, LATTICE_C, LATTICE_F }

enum	RegularPolyhedraType { TETRAHEDRON, OCTAHEDRON, SQUARE_PLANE, CUBE, ANTIPRISM_TETRAGONAL, PRISM_TETRAGONAL_MONOCAP, PRISM_TETRAGONAL_DICAP, PRISM_TRIGONAL, PRISM_TRIGONAL_TRICAPPED, ICOSAHEDRON, TRIANGLE_PLANE }

enum	AnnealingSchedule { ANNEALING_CONSTANT, ANNEALING_BOLTZMANN, ANNEALING_CAUCHY, ANNEALING_EXPONENTIAL, ANNEALING_SMART, ANNEALING_GAMMA }
	Annealing schedule type. More...

enum	GlobalOptimType { GLOBAL_OPTIM_SIMULATED_ANNEALING, GLOBAL_OPTIM_PARALLEL_TEMPERING, GLOBAL_OPTIM_RANDOM_LSQ, GLOBAL_OPTIM_SIMULATED_ANNEALING_MULTI, GLOBAL_OPTIM_PARALLEL_TEMPERING_MULTI }
	Global optimization type. More...

enum	RefParDerivStepModel { REFPAR_DERIV_STEP_ABSOLUTE, REFPAR_DERIV_STEP_RELATIVE }
	How do we compute steps h for numerical derivative calculation : d=f(x+h)-f(x-h)/h/2 either h is fixed (absolute), or relative h=x*derivFactor.

Functions
bool	iseol (const char c)

std::string	trimString (const std::string &s)

string	CIFReadValue (stringstream &in, char &lastc)
	Read one value, whether it is numeric, string or text.

REAL	CIFNumeric2REAL (const string &s)

int	CIFNumeric2Int (const string &s)

Crystal *	CreateCrystalFromCIF (CIF &cif, const bool verbose=true, const bool checkSymAsXYZ=true)
	Extract Crystal object(s) from a CIF, if possible. More...

Crystal *	CreateCrystalFromCIF (CIF &cif, const bool verbose, const bool checkSymAsXYZ, const bool oneScatteringPowerPerElement, const bool connectAtoms)
	Extract Crystal object(s) from a CIF, if possible. More...

PowderPattern *	CreatePowderPatternFromCIF (CIF &cif)
	Create PowderPattern object(s) from a CIF, if possible. More...

DiffractionDataSingleCrystal *	CreateSingleCrystalDataFromCIF (CIF &cif, Crystal *pryst=0)
	Create DiffractionDataSingleCrystal object(s) from a CIF, if possible. More...

REAL	CIFNumeric2REAL (const std::string &s)
	Convert one CIF value to a floating-point value Return 0 if no value can be converted (e.g. More...

int	CIFNumeric2Int (const std::string &s)
	Convert one CIF value to a floating-point value Return 0 if no value can be converted (e.g. More...

bool	CompareBondDist (MolBond b1, MolBond b2)

void	ObjCrystInformUserStdOut (const string &)
	Print some information for the user during long processes.

float	string2floatC (const string &s)
	Function to convert a substring to a floating point value, imposing a C locale (using '. More...

void	RealGeomStructFactor (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

void	RealGeomStructFactor_1 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_2 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_67 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_67ba_c (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_67cab (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_67_cba (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_67bca (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_67a_cb (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_97 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	RealGeomStructFactor_230 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor_centro (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

void	ImagGeomStructFactor_1 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

void	ImagGeomStructFactor_2 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

void	ImagGeomStructFactor_67 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

void	ImagGeomStructFactor_67ba_c (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor_67cab (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor_67_cba (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor_67bca (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor_67a_cb (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &rsf)

void	ImagGeomStructFactor_97 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

void	ImagGeomStructFactor_230 (const REAL x, const REAL y, const REAL z, const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l, CrystVector_REAL &isf)

float	EstimateCellVolume (const float dmin, const float dmax, const float nbrefl, const CrystalSystem system, const CrystalCentering centering, const float kappa=1)
	Estimate volume from number of peaks at a given dmin See J. More...

bool	compareHKL_d (const PeakList::hkl &d1, const PeakList::hkl &d2)

template<class T , class U >
bool	comparePairFirst (std::pair< T, U > &p1, std::pair< T, U > &p2)

float	Score (const PeakList &dhkl, const RecUnitCell &ruc, const unsigned int nbSpurious=0, const bool verbose=false, const bool storehkl=false, const bool storePredictedHKL=false)
	Compute score for a candidate RecUnitCell and a PeakList.

bool	DichoIndexed (const PeakList &dhkl, const RecUnitCell &par, const RecUnitCell &dpar, const unsigned int nbUnindexed=0, const bool verbose=false, unsigned int useStoredHKL=0, const unsigned int maxNbMissingBelow5=0)
	Number of reflexions found in the intervals calculated between par+dpar and par-dpar. More...

vector< float >	linspace (float min, float max, unsigned int nb)

bool	SimilarRUC (const RecUnitCell &c0, const RecUnitCell &c1, const float delta=0.005)

bool	compareRUCScore (std::pair< RecUnitCell, float > &p1, std::pair< RecUnitCell, float > &p2)

float	InputFloat (istream &is, const char endchar=' ')
	Safely read a floating-point value from a stream. More...

bool	ISNAN_OR_INF (REAL r)
	Test if the value is a NaN.

void	XMLCrystFileSaveGlobal (const string &filename)
	Save all Objcryst++ objects. More...

void	XMLCrystFileSaveGlobal (ostream &out)

ObjRegistry< XMLCrystTag >	XMLCrystFileLoadObjectList (const string &filename)
	Get the list (tags) of ObjCryst objects in a file. More...

template<class T >
void	XMLCrystFileLoadObject (const string &file, const string &tagName, const string &name, T *obj)
	Load an object from a file, identifying it from its tag. More...

template void	XMLCrystFileLoadObject (const string &, const string &, const string &, Crystal *)

template void	XMLCrystFileLoadObject (const string &, const string &, const string &, PowderPattern *)

template void	XMLCrystFileLoadObject (const string &, const string &, const string &, DiffractionDataSingleCrystal *)

template void	XMLCrystFileLoadObject (const string &, const string &, const string &, PowderPatternBackground *)

template void	XMLCrystFileLoadObject (const string &, const string &, const string &, PowderPatternDiffraction *)

template void	XMLCrystFileLoadObject (const string &, const string &, const string &, MonteCarloObj *)

void	XMLCrystFileLoadAllObject (const string &file)
	Load all 'top' objects from a file (Crystal, PowderPattern, DiffDataSingleCrystal and GlobalOptimObj objects). More...

void	XMLCrystFileLoadAllObject (istream &is)

void	XMLCrystFileSaveGlobal (std::ostream &out)
	Save all Objcryst++ objects. More...

void	XMLCrystFileLoadAllObject (std::istream &is)
	Load all 'top' objects from a file (Crystal, PowderPattern, DiffDataSingleCrystal and GlobalOptimObj objects). More...

REAL	GetBondLength (const MolAtom &, const MolAtom &)
	Get The Bond Length between two atoms.

REAL	GetBondAngle (const MolAtom &, const MolAtom &, const MolAtom &)
	Get The Bond Angle of 3 atoms.

REAL	GetDihedralAngle (const MolAtom &, const MolAtom &, const MolAtom &, const MolAtom &)
	Get The dihedral angle defined by 4 atoms.

void	ExpandAtomGroupRecursive (MolAtom atom, const map< MolAtom , set< MolAtom * > > &connect, set< MolAtom * > &atomlist, const MolAtom *finalAtom=0)
	Build recursively a list of atoms, starting from a one atom, and given a connectivity table. More...

void	ExpandAtomGroupRecursive (MolAtom atom, const map< MolAtom , set< MolAtom * > > &connect, map< MolAtom *, unsigned long > &atomlist, const unsigned long maxdepth, unsigned long depth=0)
	Build recursively a list of atoms, starting from a one atom, and given a connectivity table, until a certain depth (number of bonds) is reached. More...

REAL	FlatLorentzianProba (const REAL x, const REAL sigma, const REAL delta)

REAL	FlatLorentzianIntegral (const REAL x1, const REAL x2, const REAL sigma, const REAL delta)

REAL	LorentzianBiasedRandomMove (const REAL x0, const REAL sigma, const REAL delta, const REAL amplitude)
	Random move respecting a gaussian probability distribution with a flat top. More...

void	TestLorentzianBiasedRandomMove ()

void	BuildZMatrixRecursive (long &z, const long curr, const vector< MolAtom * > &vpAtom, const map< MolAtom , set< MolAtom > > &connT, vector< MolZAtom > &zmatrix, const map< const MolAtom *, long > &vIndex, vector< long > &vZIndex, vector< long > &vrZIndex)

void	BuildRingRecursive (MolAtom currentAtom, MolAtom previousAtom, const map< MolAtom , set< MolAtom > > &connect, list< MolAtom * > &atomlist, map< set< MolAtom * >, list< MolAtom * > > &ringlist)
	Find rings, starting from a one atom, and given a connectivity table. More...

Molecule *	MakeTetrahedron (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL dist)

Molecule *	MakeOctahedron (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL dist)

Molecule *	MakeSquarePlane (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL d)

Molecule *	MakeCube (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL d)

Molecule *	MakeAntiPrismTetragonal (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL d)

Molecule *	MakePrismTrigonal (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL d)

Molecule *	MakeIcosahedron (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL d)

Molecule *	MakeTriangle (Crystal &cryst, const string &name, const ScatteringPower centralAtom, const ScatteringPower peripheralAtom, const REAL d)

	normalized (ie integral is equal to 1)

as a function of theta and of the FWHM The input is an array of the theta values The maximum of the function is in negative tth values must be first CrystVector_REAL	PowderProfileGauss (const CrystVector_REAL theta, const REAL fwhm, const REAL asymmetryPar=1.)

as a function of theta and of the FWHM The input is an array of the theta values The maximum of the function is in negative tth values must be first CrystVector_REAL	PowderProfileLorentz (const CrystVector_REAL theta, const REAL fwhm, const REAL asymmetryPar=1.)

CrystVector_REAL	PowderProfileGauss (const CrystVector_REAL theta, const REAL fwhm, const REAL center, const REAL asym=1.0)
	Gaussian, normalized (ie integral is equal to 1), as a function of theta and of the FWHM. More...

CrystVector_REAL	PowderProfileLorentz (const CrystVector_REAL theta, const REAL fwhm, const REAL center, const REAL asym=1.0)
	Lorentzian, normalized (ie integral is equal to 1), as a function of theta and of the FWHM. More...

CrystVector_REAL	AsymmetryBerarBaldinozzi (const CrystVector_REAL theta, const REAL fwhm, const REAL center, const REAL A0, const REAL A1, const REAL B0, const REAL B1)
	Asymmetry function [Ref J. Appl. Cryst 26 (1993), 128-129.

template<class T >
std::complex< T >	ExponentialIntegral1 (const complex< T > z)
	Complex exponential integral E1(z) (Abramowitz & Stegun, chap. More...

template<class T >
std::complex< T >	ExponentialIntegral1_ExpZ (const complex< T > z)
	E1(z)*exp(z) More...

void	InitLibCrystTabulCosine ()

void	DeleteLibCrystTabulCosine ()

void	InitLibCrystTabulExp ()

void	DeleteLibCrystTabulExp ()

CrystMatrix_REAL	Bij2Betaij (const CrystVector_REAL &Bij, const UnitCell &cell)

SpeedTestReport	SpeedTest (const unsigned int nbAtom, const int nbAtomType, const string spacegroup, const RadiationType radiation, const unsigned long nbReflections, const unsigned int dataType, const REAL time)

std::vector< std::string >	SplitString (const std::string &s)

void	ReadFHLine (const char *buf, const unsigned int nb, string &symbol, int &n1, float &v1, int &n2, float &v2, int &n3, float &v3)
	Function to parse one line from a Fenske-Hall zmatrix file. More...

void	CompareWorlds (const CrystVector_long &idx, const CrystVector_long &swap, const RefinableObj &obj)

ostream &	operator<< (ostream &, const XMLCrystTag &)
	Output an XMLCrystTag to a stream.

istream &	operator>> (istream &, XMLCrystTag &)
	Input an XMLCrystTag from a stream.

void	RecursiveMapFunc (RefinableObj &obj, map< RefinableObj *, unsigned int > &themap, const unsigned int value)

template<class T >
void	RefObjRegisterRecursive (T &obj, ObjRegistry< T > &reg)
	Register a new object in a registry, and recursively include all included (sub)objects. More...

void	GetSubRefObjListClockRecursive (ObjRegistry< RefinableObj > &reg, RefinableObjClock &clock)
	Get the last time any object was added in the recursive list of objects.

void	GetRefParListClockRecursive (ObjRegistry< RefinableObj > &reg, RefinableObjClock &clock)
	Get the last time any RefinablePar was added in a recursive list of objects.

template void	RefObjRegisterRecursive (RefinableObj &obj, ObjRegistry< RefinableObj > &reg)

void	WXCrystValidateAllUserInput ()
	This function validates all user input (in a WXField) not yet taken into account, if needs be. More...

GLvoid	crystGLPrint (const string &s)

Molecule *	ZScatterer2Molecule (ZScatterer *scatt)
	Conversion from ZScatterer to the newer Molecule object. (in WXZScatterer.cpp) More...

Molecule *	Atoms2Molecule (list< Atom * > &vAtom)

template<class T >
T const *	WXDialogChooseFromVector (const vector< T * > &reg, wxWindow *parent, const string &message, int &choice)

template<class T >
T *	WXDialogChooseFromVector (vector< T * > &reg, wxWindow *parent, const string &message, int &choice)

template<class T >
list< T * >	WXDialogChooseMultipleFromVector (vector< T * > &reg, wxWindow *parent, const string &message)

template<class T >
list< T const * >	WXDialogChooseMultipleFromVector (const vector< T * > &reg, wxWindow *parent, const string &message)

string	CompressString (const string &s, const string &c)

list< string >	SplitString (const string &str, const string &separator)

	EVT_MENU (ID_POWDERBACKGROUND_IMPORT, WXPowderPatternBackground::OnMenuImportUserBackground) EVT_MENU(ID_POWDERBACKGROUND_OPTIMIZEBAYESIAN

WXPowderPatternBackground::OnMenuOptimizeBayesianBackground	EVT_GRID_CMD_CELL_CHANGE (ID_POWDERBACKGROUND_GRID, WXPowderPatternBackground::OnEditGridBackgroundPoint) EVT_MENU(ID_POWDERBACKGROUND_NEWBAYESIAN

	EVT_MENU (ID_POWDERDIFF_SAVEHKLFCALC, WXPowderPatternDiffraction::OnMenuSaveHKLFcalc) WXPowderPatternDiffraction

bool	compareSPGScore (const SPGScore &s1, const SPGScore &s2)

std::vector< bool >	spgExtinctionFingerprint (Crystal &c, cctbx::sgtbx::space_group &spg)

template<class T >
T *	WXDialogChooseFromRegistry (ObjRegistry< T > &reg, wxWindow *parent, const string &message, int &)
	This function allows to pick up one object in a registry. More...

template RefinableObj *	WXDialogChooseFromRegistry (ObjRegistry< RefinableObj > &, wxWindow *, const string &, int &)

template Crystal *	WXDialogChooseFromRegistry (ObjRegistry< Crystal > &, wxWindow *, const string &, int &)

template Scatterer *	WXDialogChooseFromRegistry (ObjRegistry< Scatterer > &, wxWindow *, const string &, int &)

template ScatteringPower *	WXDialogChooseFromRegistry (ObjRegistry< ScatteringPower > &, wxWindow *, const string &, int &)

template ScatteringPowerAtom *	WXDialogChooseFromRegistry (ObjRegistry< ScatteringPowerAtom > &, wxWindow *, const string &, int &)

template ZAtom *	WXDialogChooseFromRegistry (ObjRegistry< ZAtom > &, wxWindow *, const string &, int &)

template PowderPattern *	WXDialogChooseFromRegistry (ObjRegistry< PowderPattern > &, wxWindow *, const string &, int &)

template PowderPatternComponent *	WXDialogChooseFromRegistry (ObjRegistry< PowderPatternComponent > &, wxWindow *, const string &, int &)

template DiffractionDataSingleCrystal *	WXDialogChooseFromRegistry (ObjRegistry< DiffractionDataSingleCrystal > &, wxWindow *, const string &, int &)

template OptimizationObj *	WXDialogChooseFromRegistry (ObjRegistry< OptimizationObj > &, wxWindow *, const string &, int &)

template XMLCrystTag *	WXDialogChooseFromRegistry (ObjRegistry< XMLCrystTag > &, wxWindow *, const string &, int &)

template<class T >
const T *	WXDialogChooseFromRegistry (const ObjRegistry< T > &reg, wxWindow *parent, const string &message, int &)
	This function allows to pick up one object in a registry. More...

template const RefinableObj *	WXDialogChooseFromRegistry (const ObjRegistry< RefinableObj > &, wxWindow *, const string &, int &)

template const Crystal *	WXDialogChooseFromRegistry (const ObjRegistry< Crystal > &, wxWindow *, const string &, int &)

template const Scatterer *	WXDialogChooseFromRegistry (const ObjRegistry< Scatterer > &, wxWindow *, const string &, int &)

template const ScatteringPower *	WXDialogChooseFromRegistry (const ObjRegistry< ScatteringPower > &, wxWindow *, const string &, int &)

template const ScatteringPowerAtom *	WXDialogChooseFromRegistry (const ObjRegistry< ScatteringPowerAtom > &, wxWindow *, const string &, int &)

template const ZAtom *	WXDialogChooseFromRegistry (const ObjRegistry< ZAtom > &, wxWindow *, const string &, int &)

template const PowderPattern *	WXDialogChooseFromRegistry (const ObjRegistry< PowderPattern > &, wxWindow *, const string &, int &)

template const PowderPatternComponent *	WXDialogChooseFromRegistry (const ObjRegistry< PowderPatternComponent > &, wxWindow *, const string &, int &)

template const DiffractionDataSingleCrystal *	WXDialogChooseFromRegistry (const ObjRegistry< DiffractionDataSingleCrystal > &, wxWindow *, const string &, int &)

template const OptimizationObj *	WXDialogChooseFromRegistry (const ObjRegistry< OptimizationObj > &, wxWindow *, const string &, int &)

template const XMLCrystTag *	WXDialogChooseFromRegistry (const ObjRegistry< XMLCrystTag > &, wxWindow *, const string &, int &)

Variables
static REAL	defaultWavelength =1.0
	This is the default wavelength - whenever a "_diffrn_radiation_wavelength" or "_pd_proc_wavelength"entry is found, it is used as a new value for the default wavelength. More...

const RefParType *	gpRefParTypeCrystal =0

ObjRegistry< Crystal >	gCrystalRegistry ("List of all Crystals")
	Global registry for all Crystal objects.

static NiftyStaticGlobalObjectsInitializer_Crystal	NiftyStaticGlobalObjectsInitializer_Crystal_counter

ObjRegistry < DiffractionDataSingleCrystal >	gDiffractionDataSingleCrystalRegistry ("Global DiffractionDataSingleCrystal Registry")
	Global registry for all PowderPattern objects.

void(*	fpObjCrystInformUser )(const string &) =ObjCrystInformUserStdOut
	Pointer to a function for passing info to the user during or after long/important processes (use scarcely!) More...

ofstream	f

ObjRegistry < PowderPatternComponent >	gPowderPatternComponentRegistry ("List of all PowderPattern Components")
	Global registry for all PowderPatternComponent objects.

ObjRegistry< PowderPattern >	gPowderPatternRegistry ("List of all PowderPattern objects")

	Gaussian

as a function of theta and of the FWHM The input is an array of the theta values The maximum of the function is in	theta =0. If asymmetry is used

	Lorentzian

const RefParType *	gpRefParTypeScattDataProfile =0
	Type for reflection profile.

const RefParType *	gpRefParTypeScattDataProfileType =0
	Type for reflection profiles type (e.g. gaussian/lorentzian mix)

const RefParType *	gpRefParTypeScattDataProfileWidth =0
	Type for reflection profile width.

const RefParType *	gpRefParTypeScattDataProfileAsym =0
	Type for reflection profile asymmetry.

ObjRegistry< ReflectionProfile >	gReflectionProfileRegistry ("List of all ReflectionProfile types")
	Global registry for all ReflectionProfile objects.

const RefParType *	gpRefParTypeScatt =0

const RefParType *	gpRefParTypeScattTransl =0

const RefParType *	gpRefParTypeScattTranslX =0

const RefParType *	gpRefParTypeScattTranslY =0

const RefParType *	gpRefParTypeScattTranslZ =0

const RefParType *	gpRefParTypeScattOrient =0

const RefParType *	gpRefParTypeScattConform =0

const RefParType *	gpRefParTypeScattConformBondLength =0

const RefParType *	gpRefParTypeScattConformBondAngle =0

const RefParType *	gpRefParTypeScattConformDihedAngle =0

const RefParType *	gpRefParTypeScattConformX =0

const RefParType *	gpRefParTypeScattConformY =0

const RefParType *	gpRefParTypeScattConformZ =0

const RefParType *	gpRefParTypeScattOccup =0

ObjRegistry< Scatterer >	gScattererRegistry ("Global Scatterer Registry")
	Global registry for all Scatterer objects.

static NiftyStaticGlobalObjectsInitializer_Scatterer	NiftyStaticGlobalObjectsInitializer_Scatterer_counter

const RefParType *	gpRefParTypeScattData = 0
	Generic type for scattering data.

const RefParType *	gpRefParTypeScattDataScale =0
	Type for scattering data scale factors.

const RefParType *	gpRefParTypeScattDataCorr =0
	Generic type for scattering data correction parameter.

const RefParType *	gpRefParTypeScattDataCorrInt =0
	Generic type for correction to calculated intensities.

const RefParType *	gpRefParTypeScattDataCorrIntPO_Direction =0
	Parameter type for preferred orientation direction.

const RefParType *	gpRefParTypeScattDataCorrIntPO_Fraction =0
	Parameter type for fraction of preferred orientation.

const RefParType *	gpRefParTypeScattDataCorrIntPO_Amplitude =0
	Parameter type for the amplitude of preferred orientation.

const RefParType *	gpRefParTypeScattDataCorrInt_Ellipsoid =0
	Parameter type for the ellipsoid coefficient.

const RefParType *	gpRefParTypeScattDataCorrIntAbsorp =0
	Parameter type for absorption correction.

const RefParType *	gpRefParTypeScattDataCorrIntPolar =0
	Parameter type for polarization correction.

const RefParType *	gpRefParTypeScattDataCorrIntExtinc =0
	Parameter type for extinction correction.

const RefParType *	gpRefParTypeScattDataCorrPos =0
	Parameter type for correction to peak positions.

const RefParType *	gpRefParTypeScattDataBackground =0
	Parameter type for background intensity.

const RefParType *	gpRefParTypeRadiation =0

const RefParType *	gpRefParTypeRadiationWavelength =0

static REAL	sLibCrystTabulCosineRatio

static REAL *	spLibCrystTabulCosine

static REAL *	spLibCrystTabulCosineSine

static bool	sLibCrystTabulExpIsInit =false

static const long	sLibCrystNbTabulExp =10000

static const REAL	sLibCrystMinTabulExp =-5.

static const REAL	sLibCrystMaxTabulExp =10.

static REAL *	spLibCrystTabulExp

static NiftyStaticGlobalObjectsInitializer_ScatteringData	NiftyStaticGlobalObjectsInitializer_ScatteringData_counter

const RefParType *	gpRefParTypeScattPow =0

const RefParType *	gpRefParTypeScattPowResonant =0

const RefParType *	gpRefParTypeScattPowTemperature =0

const RefParType *	gpRefParTypeScattPowTemperatureIso =0

const RefParType *	gpRefParTypeScattPowTemperatureAniso =0

ObjRegistry< ScatteringPower >	gScatteringPowerRegistry ("Global ScatteringPower Registry")
	Global registry for all ScatteringPower objects.

ObjRegistry< ScatteringPowerAtom >	gScatteringPowerAtomRegistry ("Global ScatteringPowerAtom Registry")
	Global registry for all ScatteringPowerAtom objects.

static bool	warnADP =true

static NiftyStaticGlobalObjectsInitializer_ScatteringPower	NiftyStaticGlobalObjectsInitializer_ScatteringPower_counter

const RefParType *	gpRefParTypeUnitCell =0

const RefParType *	gpRefParTypeUnitCellLength =0

const RefParType *	gpRefParTypeUnitCellAngle =0

static NiftyStaticGlobalObjectsInitializer_UnitCell	NiftyStaticGlobalObjectsInitializer_UnitCell_counter

ObjRegistry< OptimizationObj >	gOptimizationObjRegistry ("List of all Optimization objects")
	Global Registry for all OptimizationObj.

const RefParType *	gpRefParTypeObjCryst =0
	Top RefParType for the ObjCryst++ library.

ObjRegistry< RefinableObj >	gRefinableObjRegistry ("Global RefinableObj registry")
	Global Registry for all RefinableObj.

ObjRegistry< RefinableObj >	gTopRefinableObjRegistry ("Global Top RefinableObj registry")
	This is a special registry for 'top' object for an optimization. More...

const long	ID_WXOBJ_ENABLE =WXCRYST_ID()

const long	ID_WXOBJ_DISABLE =WXCRYST_ID()

static NiftyStaticGlobalObjectsInitializer_RefinableObj	NiftyStaticGlobalObjectsInitializer_RefinableObj_counter

static const long	ID_ATOM_SCATTPOW =WXCRYST_ID()

std::map< wxWindowID, std::pair< wxPoint, wxSize > >	gvWindowPosition
	Used to remember window positions. More...

WXField *	spLastWXFieldInputNotValidated =0
	This pointer records the last wxField in which something was enetered, so that it can be validated when inpu is finished (either when another input has begun in another field, or when an action requires to purge all input.

WXCRYST_ID	ID_CRYST_MENU1

WXCRYST_ID	ID_CRYST_MENU2

WXCRYST_ID	ID_CRYST_MENU3

WXCRYST_ID	ID_CRYST_MENU4

WXCRYST_ID	ID_CRYST_MENU5

WXCRYST_ID	ID_CRYST_MENU6

WXCRYST_ID	ID_CRYST_MENU7

WXCRYST_ID	ID_CRYST_MENU8

WXCRYST_ID	ID_CRYST_MENU9

WXCRYST_ID	ID_CRYST_MENU10

WXCRYST_ID	ID_CRYST_MENU11

WXCRYST_ID	ID_CRYST_MENU12

WXCRYST_ID	ID_CRYST_MENU13

WXCRYST_ID	ID_CRYST_MENU14

WXCRYST_ID	ID_CRYST_MENU15

WXCRYST_ID	ID_CRYST_MENU16

static int	sFontDisplayListBase =0

static const long	ID_CRYSTAL_MENU_SAVECIF =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SAVETEXT =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_DISPLAY =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_DISPLAY_3DVIEW =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_PAR_SETRELATIVEXYZLIMITS =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_PAR_TEST_RANDOM_MOVES =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_REMOVESCATTPOW =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDSCATTPOWATOM =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDSCATTPOWSPHERE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDATOM =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_IMPORTATOMLIST =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDZSCATTERER =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDMOLECULE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ATOMS2MOLECULE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_IMPORTFENSKEHALLZMATRIX =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_IMPORTNAMEDZMATRIX =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDTETRAHEDRON =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDOCTAHEDRON =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDTRIANGLE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDSQUAREPLANE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDCUBE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDANTIPRISMTETRAGONAL =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDPRISMTRIGONAL =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_ADDICOSAHEDRON =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_REMOVESCATTERER =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SCATT_DUPLICSCATTERER =WXCRYST_ID()

static const long	ID_CRYSTAL_SPACEGROUP =WXCRYST_ID()

static const long	ID_GLCRYSTAL_MENU_UPDATE =WXCRYST_ID()

static const long	ID_GLCRYSTAL_WINDOW =WXCRYST_ID()

static const long	ID_CRYSTAL_WIN_SCATTPOW =WXCRYST_ID()

static const long	ID_CRYSTAL_WIN_ANTIBUMP =WXCRYST_ID()

static const long	ID_CRYSTAL_WIN_BONDVALENCE =WXCRYST_ID()

static const long	ID_CRYSTAL_MENU_SHOW_SCATTPOW_WIN =WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_ADD = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_REMOVE = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_UPDATE = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_WIREFRAME = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_SHOW = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_SHARPEN = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_LISTMAP = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_LISTGLMAP = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_CONTOUR = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_NEWCONTOUR = WXCRYST_ID()

static const long	ID_GLCRYSTAL_FOURIER_COLOURPICKER = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_SAVEHKLIOBSICALC = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_SAVEHKLFCALC = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_SIMULATE = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_IMPORT_HKLIOBS = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_IMPORT_HKLIOBSSIGMA = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_IMPORT_SHELXHKLF4 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_IMPORT_CIF = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_IMPORT_JANAM91 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_IMPORT_HKLIOBSGROUP = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_FITSCALE_R = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_FITSCALE_RW = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_XRAY = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_NEUTRON = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_ELECTRON = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_AG = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_MO = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_CU = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_FE = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_CO = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_CR = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_AGA1 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_MOA1 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_CUA1 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_FEA1 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_COA1 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_WAVELENGTH_SET_CRA1 = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_CRYSTAL = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_DATA = WXCRYST_ID()

static long	ID_DIFFSINGLECRYST_MENU_DATA_GRAPH = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OBJECTS = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OBJECTS_ADDOBJ = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OBJECTS_REMOVEOBJ = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OBJECTS_ADDCOSTFUNC = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OBJECTS_REMOVECOSTFUNC =WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OPT = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OPT_RUN = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OPT_RUN_MULTIPLE = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OPT_STOP = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_OPT_LSQ = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_SOLUTIONS = WXCRYST_ID()

static long	ID_GLOBALOPT_MENU_SOLUTIONS_BROWSE = WXCRYST_ID()

static long	ID_BROWSE_WIN = WXCRYST_ID()

static const long	ID_MOLATOM_SCATTPOW =WXCRYST_ID()

static const long	ID_MOLATOM_NAME =WXCRYST_ID()

WXCRYST_ID	ID_MOLBOND_ATOM1

WXCRYST_ID	ID_MOLBOND_ATOM2

WXCRYST_ID	ID_MOLBOND_FREEBUTTON

WXCRYST_ID	ID_MOLBONDANGLE_ATOM1

WXCRYST_ID	ID_MOLBONDANGLE_ATOM2

WXCRYST_ID	ID_MOLBONDANGLE_ATOM3

WXCRYST_ID	ID_MOLDIHEDRALANGLE_ATOM1

WXCRYST_ID	ID_MOLDIHEDRALANGLE_ATOM2

WXCRYST_ID	ID_MOLDIHEDRALANGLE_ATOM3

WXCRYST_ID	ID_MOLDIHEDRALANGLE_ATOM4

WXCRYST_ID	ID_MENU_OPTIMIZECONFORMATION

WXCRYST_ID	ID_MENU_SETLIMITS

WXCRYST_ID	ID_MOLECULE_MENU_FILE

WXCRYST_ID	ID_MOLECULE_MENU_FILE_2ZMATRIX

WXCRYST_ID	ID_MOLECULE_MENU_FILE_2ZMATRIXNAMED

WXCRYST_ID	ID_MOLECULE_MENU_PAR_MDTEST

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_OPTIMIZECONFORMATION

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_STATUS

WXCRYST_ID	ID_MOLECULE_MENU_EXPORT_RESTRAINTS

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_ADD_ATOM

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_ADD_BOND

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_ADD_ANGLE

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_ADD_DIHEDRAL

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_ADD_RIGID_GROUP

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_ADD_NONFLIP_ATOM

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_RIGIDIFY_WITH_DIHEDRALANGLES

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_TEST

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_REMOVE_ATOM

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_REMOVE_BOND

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_REMOVE_ANGLE

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_REMOVE_DIHEDRAL

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_REMOVE_RIGID_GROUP

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_REMOVE_NONFLIPATOM

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_SHOW_RESTRAINT

WXCRYST_ID	ID_MOLECULE_MENU_FORMULA_SET_DELTA_SIGMA

WXCRYST_ID	ID_MOLECULE_MENU_GEOMETRY

WXCRYST_ID	ID_MOLECULE_MENU_GEOMETRY_ROTATE_BOND

WXCRYST_ID	ID_MOLECULE_MENU_GEOMETRY_ROTATE_DIHED

WXCRYST_ID	ID_MOLECULE_CHANGE_CENTER_ATOM

WXCRYST_ID	ID_WINDOW_ATOM

WXCRYST_ID	ID_WINDOW_BONDLENGTH

WXCRYST_ID	ID_WINDOW_BONDANGLE

WXCRYST_ID	ID_WINDOW_DIHEDRALANGLE

WXCRYST_ID	ID_WINDOW_RIGIDGROUP

WXCRYST_ID	ID_WINDOW_NONFLIPATOM

static const long	ID_MOLECULE_ROTATE_BOND_GO =WXCRYST_ID()

static const long	ID_MOLECULE_ROTATE_BOND_ATOMS =WXCRYST_ID()

static const long	ID_MOLECULE_ROTATE_DIHED_GO =WXCRYST_ID()

static const long	ID_MOLECULE_ROTATE_DIHED_ATOMS =WXCRYST_ID()

static const char *	swxColourNameList []

static const long	ID_UPDATEUI = WXCRYST_ID()

static const long	ID_MENU_AUTOSCALE = WXCRYST_ID()

static const long	ID_POWDER_MENU_COMP_ADDBACKGD_BAYESIAN =WXCRYST_ID()

static const long	ID_POWDER_MENU_COMP_ADDBACKGD = WXCRYST_ID()

static const long	ID_POWDER_MENU_COMP_ADDCRYST = WXCRYST_ID()

static const long	ID_POWDER_MENU_GRAPH = WXCRYST_ID()

static const long	ID_POWDER_MENU_SAVETEXT = WXCRYST_ID()

static const long	ID_POWDER_MENU_SIMULATE = WXCRYST_ID()

static const long	ID_POWDER_MENU_EXPORT = WXCRYST_ID()

static const long	ID_POWDER_MENU_EXPORT_FULLPROF = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_FULLPROF = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_PSI_DMC = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_ILL_D1A5 = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_XDD = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_CPI = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_FULLPROF4 = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_MULTIDETECTORLLBG42 =WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_2THETAOBSSIGMA = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_2THETAOBS = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_TOFISISXYSIGMA = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_GSAS = WXCRYST_ID()

static const long	ID_POWDER_MENU_IMPORT_CIF = WXCRYST_ID()

static const long	ID_POWDER_MENU_FITSCALE_R = WXCRYST_ID()

static const long	ID_POWDER_MENU_FITSCALE_RW = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_XRAY = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_NEUTRON = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_NEUTRON_TOF = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_AG = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_MO = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_CU = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_FE = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_CO = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_CR = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_AGA1 = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_MOA1 = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_CUA1 = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_FEA1 = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_COA1 = WXCRYST_ID()

static const long	ID_POWDER_MENU_WAVELENGTH_SET_CRA1 = WXCRYST_ID()

static const long	ID_POWDER_MENU_ADD_2THETA_EXCLUDE = WXCRYST_ID()

static const long	ID_POWDER_MENU_LEBAIL = WXCRYST_ID()

static const long	ID_POWDERBACKGROUND_IMPORT = WXCRYST_ID()

static const long	ID_POWDERBACKGROUND_OPTIMIZEBAYESIAN = WXCRYST_ID()

static const long	ID_POWDERDIFF_CRYSTAL = WXCRYST_ID()

static const long	ID_POWDERDIFF_SAVEHKLFCALC = WXCRYST_ID()

static const long	ID_POWDER_GRAPH_NEW_PATTERN = WXCRYST_ID()

static const long	ID_POWDERTEXTURE_MENU_ADDPHASE = WXCRYST_ID()

static const long	ID_POWDERTEXTURE_MENU_DELETEPHASE = WXCRYST_ID()

static const long	ID_POWDERPATTERN_MENU_COMPONENTS = WXCRYST_ID()

static const long	ID_POWDERPATTERN_MENU_PATTERN = WXCRYST_ID()

static const long	ID_POWDERDIFF_PROFILE_DEPV = WXCRYST_ID()

static const long	ID_POWDER_GRAPH_WIN = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_UPDATE = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_TOGGLELABEL = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_TOGGPEAK = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_FINDPEAKS = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_LOADPEAKS = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_SAVEPEAKS = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_ADDPEAK = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_REMOVEPEAK = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_INDEX = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_XSCALE_DATA = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_XSCALE_D = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_XSCALE_2PID = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_YSCALE_LINEAR = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_YSCALE_SQRT = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_YSCALE_LOG10 = WXCRYST_ID()

static const long	ID_POWDERGRAPH_MENU_LEBAIL = WXCRYST_ID()

static const long	ID_CELLEXPLORER_INDEX = WXCRYST_ID()

static const long	ID_CELLEXPLORER_INDEX_QUICK = WXCRYST_ID()

static const long	ID_CELLEXPLORER_WEAK = WXCRYST_ID()

static const long	ID_CELLEXPLORER_SELECTCELL = WXCRYST_ID()

static const long	ID_CELLEXPLORER_APPLYCELL = WXCRYST_ID()

static const long	ID_CELLEXPLORER_CHOOSECRYSTAL = WXCRYST_ID()

static const long	ID_CELLEXPLORER_LEBAIL = WXCRYST_ID()

static const long	ID_CELLEXPLORER_CENTERED = WXCRYST_ID()

static const long	ID_POWDERBACKGROUND_GRID = WXCRYST_ID()

static const long	ID_POWDERBACKGROUND_NEWBAYESIAN = WXCRYST_ID()

static const long	ID_POWDERDIFF_PROFILE = WXCRYST_ID()

static const long	ID_POWDERDIFF_PROFILE_PV = WXCRYST_ID()

static const long	ID_POWDERDIFF_PROFILE_PV_ANISO = WXCRYST_ID()

static const long	ID_POWDERDIFF_LEBAIL = WXCRYST_ID()

static const long	ID_POWDERDIFF_PROFILEFITTINGMODE = WXCRYST_ID()

static const long	ID_POWDERDIFF_USELOCALLATTICEPAR = WXCRYST_ID()

static const long	ID_PROFILEFITTING_RUN = WXCRYST_ID()

static const long	ID_PROFILEFITTING_RUN_MANUAL = WXCRYST_ID()

static const long	ID_PROFILEFITTING_EXPLORE_SPG = WXCRYST_ID()

static const long	ID_PROFILEFITTING_EXPLORE_SPG_QUICK = WXCRYST_ID()

static const long	ID_WXFIELD_REFPAR =WXCRYST_ID()

static const long	ID_WXFIELD_REFPAR_FIXBUTTON =WXCRYST_ID()

static const long	ID_WXFIELD_REFPAR_LIMITEDBUTTON =WXCRYST_ID()

static const long	ID_REFPAR_POPUP_SET_LIMITS =WXCRYST_ID()

static const long	ID_WXSCATTPOWATOM_SYMBOL =WXCRYST_ID()

static const long	ID_SCATTPOWATOM_MENU_COLOUR =WXCRYST_ID()

static const long	ID_SCATTPOWATOM_MENU_COLOUR_SETRGB =WXCRYST_ID()

static const long	ID_SCATTPOWATOM_MENU_COLOUR =WXCRYST_ID()

static const long	ID_SCATTPOWATOM_MENU_COLOUR_SETRGB =WXCRYST_ID()

static const long	ID_ZATOM_NAME = WXCRYST_ID()

static const long	ID_ZATOM_SCATTPOW =WXCRYST_ID()

static const long	ID_ZATOM_BOND = WXCRYST_ID()

static const long	ID_ZATOM_ANGLE = WXCRYST_ID()

static const long	ID_ZATOM_DIHED = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_ATOM = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_ATOM_ADD = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_ATOM_CHANGE_PIVOT = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_PAR_LIMITS_RELAT_BOND = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_PAR_LIMITS_RELAT_ANGLE =WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_PAR_LIMITS_RELAT_DIHED =WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_FILE = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_IMPORT_FHZ = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_EXPORT_FHZ = WXCRYST_ID()

static const long	ID_ZSCATTERER_MENU_CONVERT2MOLECULE = WXCRYST_ID()

Detailed Description

The namespace which includes all objects (crystallographic and algorithmic) in ObjCryst++.

Note: It may be a good idea to separate in 3 namespaces for ObjCryst, WXObjCryst, and RefinableObj

Enumeration Type Documentation

enum ObjCryst::AnnealingSchedule

Annealing schedule type.

Used to determine the variation of the temperature and the mutation amplitude

With A=Temperature or A=MutationAMplitude, and the corresponding , min and max values supplied (the latter is ignored for constant, Cauchy and Boltzmann), with 'step' being the current step, and NbStep the total number of steps. (In the Parallel Tempering algorithm, a 'step' denotes one of the parallel refinement).

$A_{constant} = A_{min}$

$A_{Boltzmann} = A_{min} \frac{\ln(NbStep)}{\ln(step)}$

$A_{Cauchy} = A_{min} \frac{NbStep}{step}$

$A_{exponential} = A_{max} (\frac{T_{min}}{T_{max}})^{\frac{step}{NbStep}}$

$A_{\gamma} = A_{max} +(A_{min}-A_{max}*(\frac{step}{NbStep})^{\gamma}$

For the 'smart' schedule, it is only supported so far for the mutation amplitude: it is modulated so that for each temperature between 30 and 70% of trial configurations are accepted, within the limits for the mutation.

Definition at line 66 of file GlobalOptimObj.h.

enum ObjCryst::GlobalOptimType

Global optimization type.

Eventually it would be better to build a base Global Optimization (or even Optimization) object, and to derive it in different classes for Simulated Annealing, Parallel Tempering, Genetic Algorithm,...

Definition at line 82 of file GlobalOptimObj.h.

enum ObjCryst::RadiationType

Type of radiation used.

Only neutrons and X-Rays are used so far, electrons would require a very different treatment.

Definition at line 94 of file General.h.

Function Documentation

void ObjCryst::BuildRingRecursive	(	MolAtom *	currentAtom,
		MolAtom *	previousAtom,
		const map< MolAtom , set< MolAtom > > &	connect,
		list< MolAtom * > &	atomlist,
		map< set< MolAtom * >, list< MolAtom * > > &	ringlist
	)

Find rings, starting from a one atom, and given a connectivity table.

The ring begins and ends with the given atom.

Parameters

atom	the current atom
connect	the connectivity table

Returns: : the list of atoms to which will be appended the atoms of the ring, if one is found. Otherwise, an empty set of atoms.

Parameters

atomlist the current list of atoms in the list.

Definition at line 5221 of file Molecule.cpp.

int ObjCryst::CIFNumeric2Int ( const std::string & s )

Convert one CIF value to a floating-point value Return 0 if no value can be converted (e.g.

if '.' or '?' is encountered)

REAL ObjCryst::CIFNumeric2REAL ( const std::string & s )

Convert one CIF value to a floating-point value Return 0 if no value can be converted (e.g.

if '.' or '?' is encountered)

Crystal * ObjCryst::CreateCrystalFromCIF	(	CIF &	cif,
		const bool	verbose = `true`,
		const bool	checkSymAsXYZ = `true`
	)

Extract Crystal object(s) from a CIF, if possible.

Returns a null pointer if no crystal structure could be extracted (the minimum data is the unit cell parameters).

Parameters

checkSymAsXYZ if true, and the CIF file does not have a Hall symbol but has a list of symmetry_equiv_pos_as_xyz, check we have the correct setting by trying different ones using cctbx

Definition at line 991 of file CIF.cpp.

Crystal * ObjCryst::CreateCrystalFromCIF	(	CIF &	cif,
		const bool	verbose,
		const bool	checkSymAsXYZ,
		const bool	oneScatteringPowerPerElement,
		const bool	connectAtoms
	)

Extract Crystal object(s) from a CIF, if possible.

Returns a null pointer if no crystal structure could be extracted (the minimum data is the unit cell parameters).

Parameters

checkSymAsXYZ	if true, and the CIF file does not have a Hall symbol but has a list of symmetry_equiv_pos_as_xyz, check we have the correct setting by trying different ones using cctbx
oneScatteringPowerPerElement	if false (the default), then there will be as many ScatteringPowerAtom created as there are different Debye-Waller parameters. If true, only one will be created per element, avoiding a large number of scattering powers e.g. when importing CIFs obtained from single crystal data refinement.
connectAtoms	if true, call Crystal::ConnectAtoms to try to create as many Molecules as possible from the list of imported atoms.

Definition at line 996 of file CIF.cpp.

PowderPattern * ObjCryst::CreatePowderPatternFromCIF ( CIF & cif )

Create PowderPattern object(s) from a CIF, if possible.

Returns a null pointer if no pattern could be extracted. No components (background, crystal data) are created.

Definition at line 1252 of file CIF.cpp.

DiffractionDataSingleCrystal * ObjCryst::CreateSingleCrystalDataFromCIF	(	CIF &	cif,
		Crystal *	pryst = `0`
	)

Create DiffractionDataSingleCrystal object(s) from a CIF, if possible.

Returns a null pointer if no data could be extracted. A Crystal object must be supplied - if none is given, the last Crystal object will be used. If no Cyrstal data exists, a new one will be created.

Definition at line 1266 of file CIF.cpp.

bool ObjCryst::DichoIndexed	(	const PeakList &	dhkl,
		const RecUnitCell &	par,
		const RecUnitCell &	dpar,
		const unsigned int	nbUnindexed = `0`,
		const bool	verbose = `false`,
		unsigned int	useStoredHKL = `0`,
		const unsigned int	maxNbMissingBelow5 = `0`
	)

Number of reflexions found in the intervals calculated between par+dpar and par-dpar.

Parameters

useStoredHKL	if equal to 0, explore all possible hkl values to find possible Miller indices. if useStoredHKL=1, use the Miller indices already stored in hkl.vDicVolHKL for each observed line as the only possible indices. if useStoredHKL=2, search all the possible Miller indices for all reflections and store them in hkl.vDicVolHKL for each observed line.
maxNbMissingBelow5	the maximum number of lines that have been calculated before the d-value of the 5th observed line, but which have not been observed. If nbMissingBelow5>0 and more than nbMissingBelow5 lines have not been observed, return false. Recommended to speed up triclinic, with nbMissingBelow5=5

Definition at line 1562 of file Indexing.cpp.

float ObjCryst::EstimateCellVolume	(	const float	dmin,
		const float	dmax,
		const float	nbrefl,
		const CrystalSystem	system,
		const CrystalCentering	centering,
		const float	kappa = `1`
	)

Estimate volume from number of peaks at a given dmin See J.

Appl. Cryst. 20 (1987), 161

Parameters

dmin,dmax	1/d limits between which the number of reflections has been observed
nbrefl	number of observed reflections
kappa	estimated percentage of reflections actually observed (default=1.0)

Definition at line 45 of file Indexing.cpp.

void ObjCryst::ExpandAtomGroupRecursive	(	MolAtom *	atom,
		const map< MolAtom , set< MolAtom > > &	connect,
		set< MolAtom * > &	atomlist,
		const MolAtom *	finalAtom = `0`
	)

Build recursively a list of atoms, starting from a one atom, and given a connectivity table.

Parameters

atom	the starting atom
connect	the connectivity table
atomlist	the list of atoms to which will be appended the atoms newly found.
finalAtom	if specified, the list buildin will stop after finding this atom. This can be used to build the list of atoms between two given atoms. Otherwise, the list is expanded until the end of the chain(s), or until an atom already in the list is encountered (i.e. a ring has been found).

Definition at line 151 of file Molecule.cpp.

void ObjCryst::ExpandAtomGroupRecursive	(	MolAtom *	atom,
		const map< MolAtom , set< MolAtom > > &	connect,
		map< MolAtom *, unsigned long > &	atomlist,
		const unsigned long	maxdepth,
		unsigned long	depth = `0`
	)

Build recursively a list of atoms, starting from a one atom, and given a connectivity table, until a certain depth (number of bonds) is reached.

Parameters

atom	the starting atom
connect	the connectivity table
atomlist	the list of atoms to which will be appended the atoms newly found.
finalAtom	if specified, the list buildin will stop after finding this atom. This can be used to build the list of atoms between two given atoms. Otherwise, the list is expanded until the end of the chain(s), or until an atom already in the list is encountered (i.e. a ring has been found).

Definition at line 166 of file Molecule.cpp.

template<class T >

std::complex< T > ObjCryst::ExponentialIntegral1 ( const complex< T > z )

Complex exponential integral E1(z) (Abramowitz & Stegun, chap.

5)

Using A&S 5.1.11 (series) and 5.1.51 (asymptotic) expansions

Definition at line 1601 of file ReflectionProfile.cpp.

template<class T >

std::complex< T > ObjCryst::ExponentialIntegral1_ExpZ ( const complex< T > z )

E1(z)*exp(z)

This can be computed for large z values to avoid floating-point exceptions.

Definition at line 1606 of file ReflectionProfile.cpp.

void ObjCryst::ImagGeomStructFactor	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 44 of file geomStructFactor.cpp.

void ObjCryst::ImagGeomStructFactor_1	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	isf
	)

Deprecated:

Definition at line 63 of file geomStructFactor_001.cpp.

void ObjCryst::ImagGeomStructFactor_2	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	isf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_230	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	isf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_67	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	isf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_67_cba	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_67a_cb	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_67ba_c	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_67bca	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_67cab	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

void ObjCryst::ImagGeomStructFactor_97	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	isf
	)

Deprecated:

Definition at line 64 of file geomStructFactor_097.cpp.

void ObjCryst::ImagGeomStructFactor_centro	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	isf
	)

Deprecated:

Definition at line 46 of file geomStructFactor_centro.cpp.

float ObjCryst::InputFloat	(	istream &	is,
		const char	endchar = `' '`
	)

Safely read a floating-point value from a stream.

Parameters

endchar the character ending the input. On return, the stream will be placed at this character (i.e. it will be the next to be read). Note that the input will stop when encoutering a space character, even if the endchar has not been found.

Returns: : the value - NaN will be returned as NaN, but probably only if the value was written on the same platform

Definition at line 68 of file ObjCryst/IO.cpp.

REAL ObjCryst::LorentzianBiasedRandomMove	(	const REAL	x0,
		const REAL	sigma,
		const REAL	delta,
		const REAL	amplitude
	)

Random move respecting a gaussian probability distribution with a flat top.

i.e. x in [-delta;+delta], P(x)=1 outside, P(x)=1/(1+(abs(x)-delta)^2/sigma^2)

If sigma<1e-6, it is treated as a step-like probability non-null only in [-delta;+delta]

Definition at line 4695 of file Molecule.cpp.

CrystVector_REAL ObjCryst::PowderProfileGauss	(	const CrystVector_REAL	theta,
		const REAL	fwhm,
		const REAL	center,
		const REAL	asym = `1.0`
	)

Gaussian, normalized (ie integral is equal to 1), as a function of theta and of the FWHM.

The input is an array of the theta values. The maximum of the function is in theta=center. If asymmetry is used, negative tth values must be first.

Definition at line 1422 of file ReflectionProfile.cpp.

CrystVector_REAL ObjCryst::PowderProfileLorentz	(	const CrystVector_REAL	theta,
		const REAL	fwhm,
		const REAL	center,
		const REAL	asym = `1.0`
	)

Lorentzian, normalized (ie integral is equal to 1), as a function of theta and of the FWHM.

The input is an array of the theta values. The maximum of the function is in theta=center. If asymmetry is used, negative tth values must be first.

Definition at line 1501 of file ReflectionProfile.cpp.

void ObjCryst::ReadFHLine	(	const char *	buf,
		const unsigned int	nb,
		string &	symbol,
		int &	n1,
		float &	v1,
		int &	n2,
		float &	v2,
		int &	n3,
		float &	v3
	)

Function to parse one line from a Fenske-Hall zmatrix file.

The function first trie to read the line by assuming that all fields are separated by at least one space. If the correct number of fields is not found, it then uses the strict formatting (%2s%3u%6f%3u%6f%3u%6f) to find all fields. This is needed for example when there are more than 100 atoms since the atom number fields are only 3-character wide.

Definition at line 1190 of file ZScatterer.cpp.

void ObjCryst::RealGeomStructFactor	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 34 of file geomStructFactor.cpp.

void ObjCryst::RealGeomStructFactor_1	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 46 of file geomStructFactor_001.cpp.

void ObjCryst::RealGeomStructFactor_2	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 46 of file geomStructFactor_002.cpp.

void ObjCryst::RealGeomStructFactor_230	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 46 of file geomStructFactor_230.cpp.

void ObjCryst::RealGeomStructFactor_67	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 46 of file geomStructFactor_067.cpp.

void ObjCryst::RealGeomStructFactor_67_cba	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 91 of file geomStructFactor_067.cpp.

void ObjCryst::RealGeomStructFactor_67a_cb	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 121 of file geomStructFactor_067.cpp.

void ObjCryst::RealGeomStructFactor_67ba_c	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 61 of file geomStructFactor_067.cpp.

void ObjCryst::RealGeomStructFactor_67bca	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 106 of file geomStructFactor_067.cpp.

void ObjCryst::RealGeomStructFactor_67cab	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 76 of file geomStructFactor_067.cpp.

void ObjCryst::RealGeomStructFactor_97	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l,
		CrystVector_REAL &	rsf
	)

Deprecated:

Definition at line 47 of file geomStructFactor_097.cpp.

template<class T >

void ObjCryst::RefObjRegisterRecursive	(	T &	obj,
		ObjRegistry< T > &	reg
	)

Register a new object in a registry, and recursively include all included (sub)objects.

Definition at line 1147 of file RefinableObj.cpp.

SpeedTestReport ObjCryst::SpeedTest	(	const unsigned int	nbAtom,
		const int	nbAtomType,
		const string	spacegroup,
		const RadiationType	radiation,
		const unsigned long	nbReflections,
		const unsigned int	dataType,
		const REAL	time
	)

Parameters

nbAtom	total number of unique atoms.
nbAtomType	total number of atom types. Must be smaller than nbAtom.
spacegroup	the symbol or spacegroup number for the spacegroup to be tested.
radiation	the type of radiation to do the test with (neutron, x-ray).
nbReflections	total number of reflections to use.
time	duration of the test (10s is usually enough).
dataType	0= single crystal, 1= powder pattern (1 background + 1 crystal phase)

Definition at line 35 of file test.cpp.

float ObjCryst::string2floatC ( const string & s )

Function to convert a substring to a floating point value, imposing a C locale (using '.

' as decimal separator). This is used for input/output from data file, which are only using the C locale, contrary to the GUI.

Definition at line 59 of file ObjCryst/IO.cpp.

void ObjCryst::WXCrystValidateAllUserInput ( )

This function validates all user input (in a WXField) not yet taken into account, if needs be.

This should be called by ALL functions using data stored in fields (basically all functions !)

Definition at line 257 of file wxCryst.cpp.

template<class T >

T * ObjCryst::WXDialogChooseFromRegistry	(	ObjRegistry< T > &	reg,
		wxWindow *	parent,
		const string &	message,
		int &
	)

This function allows to pick up one object in a registry.

Shows a modal dialog with a list of objects

Definition at line 437 of file wxRefinableObj.cpp.

template<class T >

const T * ObjCryst::WXDialogChooseFromRegistry	(	const ObjRegistry< T > &	reg,
		wxWindow *	parent,
		const string &	message,
		int &
	)

This function allows to pick up one object in a registry.

Shows a modal dialog with a list of objects. This is a const access.

Definition at line 488 of file wxRefinableObj.cpp.

void ObjCryst::XMLCrystFileLoadAllObject ( std::istream & is )

Load all 'top' objects from a file (Crystal, PowderPattern, DiffDataSingleCrystal and GlobalOptimObj objects).

All objects are directly allocated, and can be accessed through their respective global registry (eg gCrystalRegistry fro a Crysta, etc...)

Parameters

file	the filename from which the objects will be loaded.

void ObjCryst::XMLCrystFileLoadAllObject ( const string & file )

Load all 'top' objects from a file (Crystal, PowderPattern, DiffDataSingleCrystal and GlobalOptimObj objects).

All objects are directly allocated, and can be accessed through their respective global registry (eg gCrystalRegistry fro a Crysta, etc...)

Parameters

file	the filename from which the objects will be loaded.

Definition at line 223 of file ObjCryst/IO.cpp.

template<class T >

void ObjCryst::XMLCrystFileLoadObject	(	const string &	file,
		const string &	tagName,
		const string &	name,
		T *	obj
	)

Load an object from a file, identifying it from its tag.

Parameters

file	the filename from which the object will be loaded.
tagName	the name of the tag
name	the name of the object to be found (in a 'Name' attribute)
obj	the pointer to the object to be loaded. The allocation will be done by the function, and the pointer changed accordingly.

NOT TESTED YET !

Definition at line 175 of file ObjCryst/IO.cpp.

ObjRegistry< XMLCrystTag > ObjCryst::XMLCrystFileLoadObjectList ( const string & filename )

Get the list (tags) of ObjCryst objects in a file.

This will recognize only certain tags in the file (Crystal,PowderPattern, DiffDataSingleCrystal, GlobalOptimObj). Eventually it should include also the ZScatterer objects.

Note: It will be the duty of the caller to destroy all the tags which have been allocated.

NOT TESTED YET !

Definition at line 146 of file ObjCryst/IO.cpp.

void ObjCryst::XMLCrystFileSaveGlobal ( std::ostream & out )

Save all Objcryst++ objects.

This saves all Crystal, PowderPattern, DiffDataSingleCrystal and GlobalOptimObj objects, using the global registries for these classes. All other objects (Scatterer, ScatteringPower, PowderPatternComponent are saved as well since they are sub-objects of Crystal or PowderPattern objects).

Saving is done in well-formed xml format.

void ObjCryst::XMLCrystFileSaveGlobal ( const string & filename )

Save all Objcryst++ objects.

This saves all Crystal, PowderPattern, DiffDataSingleCrystal and GlobalOptimObj objects, using the global registries for these classes. All other objects (Scatterer, ScatteringPower, PowderPatternComponent are saved as well since they are sub-objects of Crystal or PowderPattern objects).

Saving is done in well-formed xml format.

Definition at line 106 of file ObjCryst/IO.cpp.

Molecule * ObjCryst::ZScatterer2Molecule ( ZScatterer * scatt )

Conversion from ZScatterer to the newer Molecule object. (in WXZScatterer.cpp)

Conversion from ZScatterer to the newer Molecule object.

Definition at line 51 of file wxZScatterer.cpp.

Variable Documentation

REAL ObjCryst::defaultWavelength =1.0

static

This is the default wavelength - whenever a "_diffrn_radiation_wavelength" or "_pd_proc_wavelength"entry is found, it is used as a new value for the default wavelength.

Since the powder CIFs do not include the wavelength, this could be useful if the crystal structure CIF (including the wavelength) is parsed right before the powder pattern one.

Definition at line 466 of file CIF.cpp.

void(* ObjCryst::fpObjCrystInformUser)(const string &) =ObjCrystInformUserStdOut

Pointer to a function for passing info to the user during or after long/important processes (use scarcely!)

This function pointer is by default assigned to ObjCrystInformUserStdOut, which outputs the message to the standard output. If a user interface is used (eg in Fox), this pointer should be reassigned at the beginning of the application to a more user-suitable function.

Definition at line 76 of file Exception.cpp.

ObjRegistry< RefinableObj > ObjCryst::gTopRefinableObjRegistry

This is a special registry for 'top' object for an optimization.

In the ObjCryst++ class, this currently includes Crystal, PowderPattern and DiffractionDataSingleCrystal.

Definition at line 1316 of file RefinableObj.h.

std::map< wxWindowID, std::pair< wxPoint, wxSize > > ObjCryst::gvWindowPosition

Used to remember window positions.

Definition at line 51 of file wxCryst.cpp.

Classes

Enumerations

Functions

Variables

Detailed Description

Enumeration Type Documentation

Function Documentation

Variable Documentation