ObjCryst::CIFData Class Reference

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

List of all members.

Public Member Functions
	CIFData ()
void	ExtractAll (const bool verbose=false)
	Extract lattice parameters, spacegroup (symbol or number), atomic positions, chemical name and formula if available.
void	ExtractName (const bool verbose=false)
	Extract name & formula for the crystal.
void	ExtractUnitCell (const bool verbose=false)
	Extract unit cell.
void	ExtractSpacegroup (const bool verbose=false)
	Extract spacegroup number or symbol.
void	ExtractAtomicPositions (const bool verbose=false)
	Extract all atomic positions.
void	ExtractPowderPattern (const bool verbose=false)
	Extract Powder Diffraction data, with Iobs, sigma(Iobs) and either 2theta or time-of-flight position.
void	Cartesian2FractionalCoord ()
	Generate fractional coordinates from cartesian ones for all atoms CIFData::CalcMatrices() must be called first.
void	Fractional2CartesianCoord ()
	Generate cartesian coordinates from fractional ones for all atoms CIFData::CalcMatrices() must be called first.
void	f2c (float &x, float &y, float &z)
	Convert from fractional to cartesian coordinates CIFData::CalcMatrices() must be called first.
void	c2f (float &x, float &y, float &z)
	Convert from cartesia to fractional coordinates CIFData::CalcMatrices() must be called first.
void	CalcMatrices (const bool verbose=false)
	Calculate real space transformation matrices requires unit cell parameters.
Public Attributes
std::list< std::string >	mvComment
	Comments from CIF file, in the order they were read.
std::map< ci_string, std::string >	mvItem
	Individual CIF items.
std::map< std::set< ci_string >, std::map< ci_string, std::vector< std::string > > >	mvLoop
	CIF Loop data.
std::vector< float >	mvLatticePar
	Lattice parameters, in ansgtroem and degrees - vector size is 0 if no parameters have been obtained yet.
unsigned int	mSpacegroupNumberIT
	Spacegroup number from International Tables (_space_group_IT_number), or -1.
std::string	mSpacegroupSymbolHall
	Spacegroup Hall symbol (or empty string) (_space_group_name_Hall).
std::string	mSpacegroupHermannMauguin
	Spacegroup Hermann-Mauguin symbol (or empty string) (_space_group_name_H-M_alt).
std::string	mName
	Crystal name. Or empty string if none is available.
std::string	mFormula
	Formula. Or empty string if none is available.
std::vector< CIFAtom >	mvAtom
	Atoms, if any are found.
float	mOrthMatrix [3][3]
	Fractionnal2Cartesian matrix.
float	mOrthMatrixInvert [3][3]
	Cartesian2Fractionnal matrix.
std::vector< float >	mPowderPatternObs
	Powder pattern data.
std::vector< float >	mPowderPatternX
	Powder pattern data.
std::vector< float >	mPowderPatternSigma
	Powder pattern data.
WavelengthType	mDataType
	Is this X-Ray 2theta, time-of-flight ?

---

Detailed Description

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

It is a placeholder for all comments, item and loop data, as raw strings copied from a cif file.

It is also used to interpret this data to extract parts of the cif data, i.e. only part of the core cif dictionnary are recognized. CIF tags currently recognized include ("tag1 > tag2" means tag1 is preferred to tag2 when extracting the info, only one is reported):

• crystal name: _chemical_name_systematic > _chemical_name_mineral > _chemical_name_structure_type > _chemical_name_common
• crystal formula: _chemical_formula_analytical > _chemical_formula_structural > _chemical_formula_iupac > _chemical_formula_moiety
• unit cell: _cell_length_{a,b,c} ; _cell_angle_{alpha,beta,gamma}
• spacegroup number: _space_group_IT_number > _symmetry_Int_Tables_number
• spacegroup Hall symbol: _space_group_name_Hall > _symmetry_space_group_name_Hall
• spacegroup Hermann-Mauguin symbol:_space_group_name_H-M_alt > _symmetry_space_group_name_H-M
• atom coordinates: _atom_site_fract_{x} ; _atom_site_Cartn_{x,y,z}
• atom occupancy: _atom_site_occupancy
• atom label & symbol: _atom_site_type_symbol ; _atom_site_label

Cartesian coordinates are stored in Angstroems, angles in radians.

To import PowderPattern data, the following tags are used:

• observed intensity: _pd_meas_counts_total > _pd_meas_intensity_total > _pd_proc_intensity_total > _pd_proc_intensity_net
• uncertainty on intensity: deducted from _pd_proc_ls_weight or square root of intensity
• coordinates: _pd_proc_2theta_corrected > _pd_meas_angle_2theta > _pd_meas_time_of_flight > _pd_proc_2theta_range_{min,max,inc}
• intensity normalizer (optional): _pd_meas_intensity_monitor > _pd_meas_step_count_time

If another data field is needed, it is possible to directly access the string data (CIFData::mvComment , CIFData::mvItem and CIFData::mvLoop) to search for the correct tags.

---

Constructor & Destructor Documentation

ObjCryst::CIFData::CIFData (   )

---

Member Function Documentation

void ObjCryst::CIFData::c2f (  float &  x, float &  y, float &  z )

Convert from cartesia to fractional coordinates CIFData::CalcMatrices() must be called first.

void ObjCryst::CIFData::CalcMatrices (  const bool  verbose = false  )

Calculate real space transformation matrices requires unit cell parameters.

void ObjCryst::CIFData::Cartesian2FractionalCoord (   )

Generate fractional coordinates from cartesian ones for all atoms CIFData::CalcMatrices() must be called first.

void ObjCryst::CIFData::ExtractAll (  const bool  verbose = false  )

Extract lattice parameters, spacegroup (symbol or number), atomic positions, chemical name and formula if available. All other data is ignored

void ObjCryst::CIFData::ExtractAtomicPositions (  const bool  verbose = false  )

Extract all atomic positions. Will generate cartesian from fractional coordinates or vice-versa if only cartesian coordinates are available.

void ObjCryst::CIFData::ExtractName (  const bool  verbose = false  )

Extract name & formula for the crystal.

void ObjCryst::CIFData::ExtractPowderPattern (  const bool  verbose = false  )

Extract Powder Diffraction data, with Iobs, sigma(Iobs) and either 2theta or time-of-flight position.

void ObjCryst::CIFData::ExtractSpacegroup (  const bool  verbose = false  )

Extract spacegroup number or symbol.

void ObjCryst::CIFData::ExtractUnitCell (  const bool  verbose = false  )

Extract unit cell.

void ObjCryst::CIFData::f2c (  float &  x, float &  y, float &  z )

Convert from fractional to cartesian coordinates CIFData::CalcMatrices() must be called first.

void ObjCryst::CIFData::Fractional2CartesianCoord (   )

Generate cartesian coordinates from fractional ones for all atoms CIFData::CalcMatrices() must be called first.

---

Member Data Documentation

WavelengthType ObjCryst::CIFData::mDataType

Is this X-Ray 2theta, time-of-flight ?

std::string ObjCryst::CIFData::mFormula

Formula. Or empty string if none is available.

std::string ObjCryst::CIFData::mName

Crystal name. Or empty string if none is available.

float ObjCryst::CIFData::mOrthMatrix[3][3]

Fractionnal2Cartesian matrix.

float ObjCryst::CIFData::mOrthMatrixInvert[3][3]

Cartesian2Fractionnal matrix.

std::vector<float> ObjCryst::CIFData::mPowderPatternObs

Powder pattern data.

std::vector<float> ObjCryst::CIFData::mPowderPatternSigma

Powder pattern data.

std::vector<float> ObjCryst::CIFData::mPowderPatternX

Powder pattern data.

std::string ObjCryst::CIFData::mSpacegroupHermannMauguin

Spacegroup Hermann-Mauguin symbol (or empty string) (_space_group_name_H-M_alt).

unsigned int ObjCryst::CIFData::mSpacegroupNumberIT

Spacegroup number from International Tables (_space_group_IT_number), or -1.

std::string ObjCryst::CIFData::mSpacegroupSymbolHall

Spacegroup Hall symbol (or empty string) (_space_group_name_Hall).

std::vector<CIFAtom> ObjCryst::CIFData::mvAtom

Atoms, if any are found.

std::list<std::string> ObjCryst::CIFData::mvComment

Comments from CIF file, in the order they were read.

std::map<ci_string,std::string> ObjCryst::CIFData::mvItem

Individual CIF items.

std::vector<float> ObjCryst::CIFData::mvLatticePar

Lattice parameters, in ansgtroem and degrees - vector size is 0 if no parameters have been obtained yet.

std::map<std::set<ci_string>,std::map<ci_string,std::vector<std::string> > > ObjCryst::CIFData::mvLoop

CIF Loop data.

---

The documentation for this class was generated from the following file:

• CIF.h

---