Unit cell. More...

#include <unitcell.hpp>

Inheritance diagram for gemmi::UnitCell:

Public Member Functions
	UnitCell ()=default

	UnitCell (double a_, double b_, double c_, double alpha_, double beta_, double gamma_)

	UnitCell (const std::array< double, 6 > &v)

bool	is_crystal () const

bool	is_similar (const UnitCell &o, double rel, double deg) const

void	calculate_properties ()

double	cos_alpha () const

Mat33	calculate_matrix_B () const
	B matrix following convention from Busing & Levy (1967), not from cctbx.

double	calculate_u_eq (const SMat33< double > &ani) const
	The equivalent isotropic displacement factor.

void	set_matrices_from_fract (const Transform &f)

void	set (double a_, double b_, double c_, double alpha_, double beta_, double gamma_)

void	set_from_parameters (const UnitCellParameters &p)

void	set_from_array (const std::array< double, 6 > &v)

void	set_from_vectors (const Vec3 &va, const Vec3 &vb, const Vec3 &vc)

UnitCell	changed_basis_backward (const Op &op, bool set_images)

UnitCell	changed_basis_forward (const Op &op, bool set_images)

bool	is_compatible_with_groupops (const GroupOps &gops, double eps=1e-3) const

bool	is_compatible_with_spacegroup (const SpaceGroup *sg, double eps=1e-3) const

void	set_cell_images_from_groupops (const GroupOps &group_ops)

void	set_cell_images_from_spacegroup (const SpaceGroup *sg)

void	add_ncs_images_to_cs_images (const std::vector< NcsOp > &ncs)

std::vector< FTransform >	get_ncs_transforms () const

Position	orthogonalize (const Fractional &f) const

Fractional	fractionalize (const Position &o) const

Position	orthogonalize_difference (const Fractional &delta) const
	orthogonalize_difference(a-b) == orthogonalize(a) - orthogonalize(b)

Fractional	fractionalize_difference (const Position &delta) const
	the inverse of orthogonalize_difference

Box< Position >	orthogonalize_box (const Box< Fractional > &f) const
	Returns box containing fractional box (a cuboid in fractional coordinates can be a parallelepiped in Cartesian coordinates).

Transform	orthogonalize_transform (const FTransform &ftr) const

Transform	op_as_transform (const Op &op) const

double	distance_sq (const Fractional &pos1, const Fractional &pos2) const

double	distance_sq (const Position &pos1, const Position &pos2) const

double	volume_per_image () const

bool	search_pbc_images (Fractional &&diff, NearestImage &image) const

NearestImage	find_nearest_image (const Position &ref, const Position &pos, Asu asu) const

void	apply_transform (Fractional &fpos, int image_idx, bool inverse) const

NearestImage	find_nearest_pbc_image (const Fractional &fref, Fractional fpos, int image_idx=0) const

NearestImage	find_nearest_pbc_image (const Position &ref, const Position &pos, int image_idx=0) const

std::vector< NearestImage >	find_nearest_pbc_images (const Fractional &fref, double dist, const Fractional &fpos, int image_idx) const

Position	orthogonalize_in_pbc (const Position &ref, const Fractional &fpos) const

Position	find_nearest_pbc_position (const Position &ref, const Position &pos, int image_idx, bool inverse=false) const

Fractional	fract_image (const NearestImage &im, Fractional fpos)

int	is_special_position (const Fractional &fpos, double max_dist) const
	Counts nearby symmetry mates (0 = none, 3 = 4-fold axis, etc).

int	is_special_position (const Position &pos, double max_dist=0.8) const

double	calculate_1_d2_double (double h, double k, double l) const
	Calculate 1/d^2 for specified hkl reflection.

double	calculate_1_d2 (const Miller &hkl) const

double	calculate_d (const Miller &hkl) const
	Calculate d-spacing.

double	calculate_stol_sq (const Miller &hkl) const
	Calculate (sin(theta)/lambda)^2 = d*^2/4.

SMat33< double >	metric_tensor () const
	https://dictionary.iucr.org/Metric_tensor

SMat33< double >	reciprocal_metric_tensor () const

UnitCell	reciprocal () const
	Returns reciprocal unit cell.

Miller	get_hkl_limits (double dmin) const

Mat33	primitive_orth_matrix (char centring_type) const

Public Member Functions inherited from gemmi::UnitCellParameters
	UnitCellParameters ()=default

	UnitCellParameters (const double(&par)[6])

	UnitCellParameters (const std::array< double, 6 > &par)

bool	operator== (const UnitCellParameters &o) const

bool	operator!= (const UnitCellParameters &o) const

bool	approx (const UnitCellParameters &o, double epsilon) const

Public Attributes
Transform	orth

Transform	frac

double	volume = 1.0

double	ar = 1.0
	reciprocal parameters a, b, c, alpha, beta, gamma

double	br = 1.0

double	cr = 1.0

double	cos_alphar = 0.0

double	cos_betar = 0.0

double	cos_gammar = 0.0

bool	explicit_matrices = false

short	cs_count = 0

std::vector< FTransform >	images

Public Attributes inherited from gemmi::UnitCellParameters
double	a = 1.0

double	b = 1.0

double	c = 1.0

double	alpha = 90.0

double	beta = 90.0

double	gamma = 90.0

Detailed Description

Unit cell.

Contains cell parameters as well as pre-calculated orthogonalization and fractionalization matrices, volume, and more. Contains symmetry operations (incl. NCS) if they were set from outside.

Definition at line 165 of file unitcell.hpp.

Constructor & Destructor Documentation

◆ UnitCell() [1/3]

gemmi::UnitCell::UnitCell ( )

default

◆ UnitCell() [2/3]

gemmi::UnitCell::UnitCell	(	double	a_,
		double	b_,
		double	c_,
		double	alpha_,
		double	beta_,
		double	gamma_
	)

inline

Definition at line 167 of file unitcell.hpp.

◆ UnitCell() [3/3]

gemmi::UnitCell::UnitCell ( const std::array< double, 6 > & v )

inline

Definition at line 171 of file unitcell.hpp.

Member Function Documentation

◆ is_crystal()

bool gemmi::UnitCell::is_crystal ( ) const

inline

Definition at line 187 of file unitcell.hpp.

◆ is_similar()

bool gemmi::UnitCell::is_similar	(	const UnitCell &	o,
		double	rel,
		double	deg
	)		const

inline

Definition at line 190 of file unitcell.hpp.

◆ calculate_properties()

void gemmi::UnitCell::calculate_properties ( )

inline

Definition at line 197 of file unitcell.hpp.

◆ cos_alpha()

double gemmi::UnitCell::cos_alpha ( ) const

inline

Definition at line 247 of file unitcell.hpp.

◆ calculate_matrix_B()

Mat33 gemmi::UnitCell::calculate_matrix_B ( ) const

inline

B matrix following convention from Busing & Levy (1967), not from cctbx.

Cf. https://dials.github.io/documentation/conventions.html

Definition at line 251 of file unitcell.hpp.

◆ calculate_u_eq()

double gemmi::UnitCell::calculate_u_eq ( const SMat33< double > & ani ) const

inline

The equivalent isotropic displacement factor.

Based on Fischer & Tillmanns (1988). Acta Cryst. C44, 775-776. The argument is a non-orthogonalized tensor U, i.e. the one from SmallStructure::Site, but not from Atom.

Definition at line 263 of file unitcell.hpp.

◆ set_matrices_from_fract()

void gemmi::UnitCell::set_matrices_from_fract ( const Transform & f )

inline

Definition at line 276 of file unitcell.hpp.

◆ set()

void gemmi::UnitCell::set	(	double	a_,
		double	b_,
		double	c_,
		double	alpha_,
		double	beta_,
		double	gamma_
	)

inline

Definition at line 291 of file unitcell.hpp.

◆ set_from_parameters()

void gemmi::UnitCell::set_from_parameters ( const UnitCellParameters & p )

inline

Definition at line 304 of file unitcell.hpp.

◆ set_from_array()

void gemmi::UnitCell::set_from_array ( const std::array< double, 6 > & v )

inline

Definition at line 308 of file unitcell.hpp.

◆ set_from_vectors()

void gemmi::UnitCell::set_from_vectors	(	const Vec3 &	va,
		const Vec3 &	vb,
		const Vec3 &	vc
	)

inline

Definition at line 310 of file unitcell.hpp.

◆ changed_basis_backward()

UnitCell gemmi::UnitCell::changed_basis_backward	(	const Op &	op,
		bool	set_images
	)

inline

Definition at line 315 of file unitcell.hpp.

◆ changed_basis_forward()

UnitCell gemmi::UnitCell::changed_basis_forward	(	const Op &	op,
		bool	set_images
	)

inline

Definition at line 331 of file unitcell.hpp.

◆ is_compatible_with_groupops()

bool gemmi::UnitCell::is_compatible_with_groupops	(	const GroupOps &	gops,
		double	eps = `1e-3`
	)		const

inline

Definition at line 335 of file unitcell.hpp.

◆ is_compatible_with_spacegroup()

bool gemmi::UnitCell::is_compatible_with_spacegroup	(	const SpaceGroup *	sg,
		double	eps = `1e-3`
	)		const

inline

Definition at line 350 of file unitcell.hpp.

◆ set_cell_images_from_groupops()

void gemmi::UnitCell::set_cell_images_from_groupops ( const GroupOps & group_ops )

inline

Definition at line 354 of file unitcell.hpp.

◆ set_cell_images_from_spacegroup()

void gemmi::UnitCell::set_cell_images_from_spacegroup ( const SpaceGroup * sg )

inline

Definition at line 363 of file unitcell.hpp.

◆ add_ncs_images_to_cs_images()

void gemmi::UnitCell::add_ncs_images_to_cs_images ( const std::vector< NcsOp > & ncs )

inline

Definition at line 372 of file unitcell.hpp.

◆ get_ncs_transforms()

std::vector< FTransform > gemmi::UnitCell::get_ncs_transforms ( ) const

inline

Definition at line 384 of file unitcell.hpp.

◆ orthogonalize()

Position gemmi::UnitCell::orthogonalize ( const Fractional & f ) const

inline

Definition at line 391 of file unitcell.hpp.

◆ fractionalize()

Fractional gemmi::UnitCell::fractionalize ( const Position & o ) const

inline

Definition at line 394 of file unitcell.hpp.

◆ orthogonalize_difference()

Position gemmi::UnitCell::orthogonalize_difference ( const Fractional & delta ) const

inline

orthogonalize_difference(a-b) == orthogonalize(a) - orthogonalize(b)

Definition at line 401 of file unitcell.hpp.

◆ fractionalize_difference()

Fractional gemmi::UnitCell::fractionalize_difference ( const Position & delta ) const

inline

the inverse of orthogonalize_difference

Definition at line 405 of file unitcell.hpp.

◆ orthogonalize_box()

Box< Position > gemmi::UnitCell::orthogonalize_box ( const Box< Fractional > & f ) const

inline

Returns box containing fractional box (a cuboid in fractional coordinates can be a parallelepiped in Cartesian coordinates).

Definition at line 411 of file unitcell.hpp.

◆ orthogonalize_transform()

Transform gemmi::UnitCell::orthogonalize_transform ( const FTransform & ftr ) const

inline

Definition at line 426 of file unitcell.hpp.

◆ op_as_transform()

Transform gemmi::UnitCell::op_as_transform ( const Op & op ) const

inline

Definition at line 429 of file unitcell.hpp.

◆ distance_sq() [1/2]

double gemmi::UnitCell::distance_sq	(	const Fractional &	pos1,
		const Fractional &	pos2
	)		const

inline

Definition at line 433 of file unitcell.hpp.

◆ distance_sq() [2/2]

double gemmi::UnitCell::distance_sq	(	const Position &	pos1,
		const Position &	pos2
	)		const

inline

Definition at line 437 of file unitcell.hpp.

◆ volume_per_image()

double gemmi::UnitCell::volume_per_image ( ) const

inline

Definition at line 441 of file unitcell.hpp.

◆ search_pbc_images()

bool gemmi::UnitCell::search_pbc_images	(	Fractional &&	diff,
		NearestImage &	image
	)		const

inline

Definition at line 446 of file unitcell.hpp.

◆ find_nearest_image()

NearestImage gemmi::UnitCell::find_nearest_image	(	const Position &	ref,
		const Position &	pos,
		Asu	asu
	)		const

inline

Definition at line 466 of file unitcell.hpp.

◆ apply_transform()

void gemmi::UnitCell::apply_transform	(	Fractional &	fpos,
		int	image_idx,
		bool	inverse
	)		const

inline

Definition at line 486 of file unitcell.hpp.

◆ find_nearest_pbc_image() [1/2]

NearestImage gemmi::UnitCell::find_nearest_pbc_image	(	const Fractional &	fref,
		Fractional	fpos,
		int	image_idx = `0`
	)		const

inline

Definition at line 496 of file unitcell.hpp.

◆ find_nearest_pbc_image() [2/2]

NearestImage gemmi::UnitCell::find_nearest_pbc_image	(	const Position &	ref,
		const Position &	pos,
		int	image_idx = `0`
	)		const

inline

Definition at line 505 of file unitcell.hpp.

◆ find_nearest_pbc_images()

std::vector< NearestImage > gemmi::UnitCell::find_nearest_pbc_images	(	const Fractional &	fref,
		double	dist,
		const Fractional &	fpos,
		int	image_idx
	)		const

inline

Definition at line 510 of file unitcell.hpp.

◆ orthogonalize_in_pbc()

Position gemmi::UnitCell::orthogonalize_in_pbc	(	const Position &	ref,
		const Fractional &	fpos
	)		const

inline

Definition at line 526 of file unitcell.hpp.

◆ find_nearest_pbc_position()

Position gemmi::UnitCell::find_nearest_pbc_position	(	const Position &	ref,
		const Position &	pos,
		int	image_idx,
		bool	inverse = `false`
	)		const

inline

Definition at line 532 of file unitcell.hpp.

◆ fract_image()

Fractional gemmi::UnitCell::fract_image	(	const NearestImage &	im,
		Fractional	fpos
	)

inline

Definition at line 540 of file unitcell.hpp.

◆ is_special_position() [1/2]

int gemmi::UnitCell::is_special_position	(	const Fractional &	fpos,
		double	max_dist
	)		const

inline

Counts nearby symmetry mates (0 = none, 3 = 4-fold axis, etc).

Precondition: is_crystal()

Definition at line 547 of file unitcell.hpp.

◆ is_special_position() [2/2]

int gemmi::UnitCell::is_special_position	(	const Position &	pos,
		double	max_dist = `0.8`
	)		const

inline

Definition at line 557 of file unitcell.hpp.

◆ calculate_1_d2_double()

double gemmi::UnitCell::calculate_1_d2_double	(	double	h,
		double	k,
		double	l
	)		const

inline

Calculate 1/d^2 for specified hkl reflection.

1/d^2 = (2*sin(theta)/lambda)^2

Definition at line 565 of file unitcell.hpp.

◆ calculate_1_d2()

double gemmi::UnitCell::calculate_1_d2 ( const Miller & hkl ) const

inline

Definition at line 573 of file unitcell.hpp.

◆ calculate_d()

double gemmi::UnitCell::calculate_d ( const Miller & hkl ) const

inline

Calculate d-spacing.

d = lambda/(2*sin(theta))

Definition at line 579 of file unitcell.hpp.

◆ calculate_stol_sq()

double gemmi::UnitCell::calculate_stol_sq ( const Miller & hkl ) const

inline

Calculate (sin(theta)/lambda)^2 = d*^2/4.

Definition at line 584 of file unitcell.hpp.

◆ metric_tensor()

SMat33< double > gemmi::UnitCell::metric_tensor ( ) const

inline

https://dictionary.iucr.org/Metric_tensor

Definition at line 589 of file unitcell.hpp.

◆ reciprocal_metric_tensor()

SMat33< double > gemmi::UnitCell::reciprocal_metric_tensor ( ) const

inline

Definition at line 594 of file unitcell.hpp.

◆ reciprocal()

UnitCell gemmi::UnitCell::reciprocal ( ) const

inline

Returns reciprocal unit cell.

Definition at line 599 of file unitcell.hpp.

◆ get_hkl_limits()

Miller gemmi::UnitCell::get_hkl_limits ( double dmin ) const

inline

Definition at line 605 of file unitcell.hpp.

◆ primitive_orth_matrix()

Mat33 gemmi::UnitCell::primitive_orth_matrix ( char centring_type ) const

inline

Definition at line 609 of file unitcell.hpp.

Member Data Documentation

◆ orth

Transform gemmi::UnitCell::orth

Definition at line 173 of file unitcell.hpp.

◆ frac

Transform gemmi::UnitCell::frac

Definition at line 174 of file unitcell.hpp.

◆ volume

double gemmi::UnitCell::volume = 1.0

Definition at line 175 of file unitcell.hpp.

◆ ar

double gemmi::UnitCell::ar = 1.0

reciprocal parameters a*, b*, c*, alpha*, beta*, gamma*

Definition at line 177 of file unitcell.hpp.

◆ br

double gemmi::UnitCell::br = 1.0

Definition at line 177 of file unitcell.hpp.

◆ cr

double gemmi::UnitCell::cr = 1.0

Definition at line 177 of file unitcell.hpp.

◆ cos_alphar

double gemmi::UnitCell::cos_alphar = 0.0

Definition at line 178 of file unitcell.hpp.

◆ cos_betar

double gemmi::UnitCell::cos_betar = 0.0

Definition at line 178 of file unitcell.hpp.

◆ cos_gammar

double gemmi::UnitCell::cos_gammar = 0.0

Definition at line 178 of file unitcell.hpp.

◆ explicit_matrices

bool gemmi::UnitCell::explicit_matrices = false

Definition at line 179 of file unitcell.hpp.

◆ cs_count

short gemmi::UnitCell::cs_count = 0

Definition at line 180 of file unitcell.hpp.

◆ images

std::vector<FTransform> gemmi::UnitCell::images

Definition at line 181 of file unitcell.hpp.

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

include/gemmi/unitcell.hpp

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ UnitCell() [1/3]

◆ UnitCell() [2/3]

◆ UnitCell() [3/3]

Member Function Documentation

◆ is_crystal()

◆ is_similar()

◆ calculate_properties()

◆ cos_alpha()

◆ calculate_matrix_B()

◆ calculate_u_eq()

◆ set_matrices_from_fract()

◆ set()

◆ set_from_parameters()

◆ set_from_array()

◆ set_from_vectors()

◆ changed_basis_backward()

◆ changed_basis_forward()

◆ is_compatible_with_groupops()

◆ is_compatible_with_spacegroup()

◆ set_cell_images_from_groupops()

◆ set_cell_images_from_spacegroup()

◆ add_ncs_images_to_cs_images()

◆ get_ncs_transforms()

◆ orthogonalize()

◆ fractionalize()

◆ orthogonalize_difference()

◆ fractionalize_difference()

◆ orthogonalize_box()

◆ orthogonalize_transform()

◆ op_as_transform()

◆ distance_sq() [1/2]

◆ distance_sq() [2/2]

◆ volume_per_image()

◆ search_pbc_images()

◆ find_nearest_image()

◆ apply_transform()

◆ find_nearest_pbc_image() [1/2]

◆ find_nearest_pbc_image() [2/2]

◆ find_nearest_pbc_images()

◆ orthogonalize_in_pbc()

◆ find_nearest_pbc_position()

◆ fract_image()

◆ is_special_position() [1/2]

◆ is_special_position() [2/2]

◆ calculate_1_d2_double()

◆ calculate_1_d2()

◆ calculate_d()

◆ calculate_stol_sq()

◆ metric_tensor()

◆ reciprocal_metric_tensor()

◆ reciprocal()

◆ get_hkl_limits()

◆ primitive_orth_matrix()

Member Data Documentation

◆ orth

◆ frac

◆ volume

◆ ar

◆ br

◆ cr

◆ cos_alphar

◆ cos_betar

◆ cos_gammar

◆ explicit_matrices

◆ cs_count

◆ images