reflist-utils.h File Reference

Functions
int	write_reflist (const char *filename, RefList *list)
int	write_reflist_2 (const char *filename, RefList *list, SymOpList *sym)
RefList *	read_reflections (const char *filename)
RefList *	read_reflections_2 (const char *filename, char **sym)
RefList *	read_reflections_3 (const char *filename, char **sym, UnitCell **cell)
int	check_list_symmetry (RefList *list, const SymOpList *sym)
int	find_equiv_in_list (RefList *list, signed int h, signed int k, signed int l, const SymOpList *sym, signed int *hu, signed int *ku, signed int *lu)
RefList *	asymmetric_indices (RefList *in, const SymOpList *sym)
void	resolution_limits (RefList *list, UnitCell *cell, double *rmin, double *rmax)
double	max_intensity (RefList *list)
RefList *	res_cutoff (RefList *list, UnitCell *cell, double min, double max)
RefList *	copy_reflist (RefList *list)
void	free_contribs (RefList *list)
void	reflist_add_command_and_version (RefList *list, int argcv, char *argv[])
int	write_to_mtz (RefList *reflist, SymOpList *sym, UnitCell *cell, double min_res, double max_res, const char *filename, const char *dataset_name, const char *crystal_name, const char *project_name, int bij)
int	write_to_xds (RefList *reflist, SymOpList *sym, UnitCell *cell, double min_res, double max_res, const char *filename)
int	libcrystfel_can_write_mtz (void)

Detailed Description

Reflection list utility functions.

Function Documentation

asymmetric_indices()

RefList * asymmetric_indices	(	RefList *	in,
		const SymOpList *	sym
	)

asymmetric_indices:

Parameters

in	A RefList
sym	A SymOpList

This function creates a newly allocated copy of in, but indexed using the asymmetric indices according to sym instead of the original indices. The original indices are stored and can be retrieved using get_symmetric_indices() if required.

Returns: the new RefList, or NULL on failure.

check_list_symmetry()

int check_list_symmetry	(	RefList *	list,
		const SymOpList *	sym
	)

Checks that the symmetry of list is indeed sym.

Parameters

list	A list of reflections
sym	Symmetry of the reflection list

Returns

0 if the symmetry is correct, otherwise 1

copy_reflist()

RefList * copy_reflist

(

RefList *

list

)

copy_reflist:

Parameters

list

A RefList

Returns: A copy of RefList.

free_contribs()

void free_contribs

(

RefList *

list

)

free_contribs:

Parameters

list

A RefList

Goes through list and frees all the reflection contribution structures.

max_intensity()

double max_intensity

(

RefList *

list

)

max_intensity:

Parameters

list

A RefList

Returns: The maximum intensity in list.

read_reflections()

RefList * read_reflections

(

const char *

filename

)

read_reflections:

Parameters

filename

Filename to read from

This function reads a reflection list from a file.

Returns: A RefList read from the file, or NULL on error

read_reflections_2()

RefList * read_reflections_2	(	const char *	filename,
		char **	sym
	)

read_reflections_2:

Parameters

filename	Filename to read from
sym	Pointer to a "char *" at which to store the symmetry

This function reads a reflection list from a file, including the point group name from the header (e.g. "4/mmm").

The file can be a CrystFEL reflection data file, or an MTZ file provided that CrystFEL has been compiled with libCCP4 available. MTZ files contain the unit cell parameters - if you want this information, use read_reflections_2 instead.

Returns: A RefList read from the file, or NULL on error

read_reflections_3()

RefList * read_reflections_3	(	const char *	filename,
		char **	sym,
		UnitCell **	cell
	)

read_reflections_3:

Parameters

filename	Filename to read from
sym	Pointer to a "char *" at which to store the symmetry
cell	Pointer to a "UnitCell *" at which to store the unit cell

This function reads a reflection list from a file, including the point group name from the header (e.g. "4/mmm").

The file can be a CrystFEL reflection data file, or an MTZ file provided that CrystFEL has been compiled with libCCP4 available. The unit cell will only be returned when reading from an MTZ file - CrystFEL reflection data files don't contain this information.

Returns: A RefList read from the file, or NULL on error

res_cutoff()

RefList * res_cutoff	(	RefList *	list,
		UnitCell *	cell,
		double	min,
		double	max
	)

res_cutoff:

Parameters

list	A RefList
cell	A UnitCell with which to calculate 1/d values for list
min	Minimum acceptable value of 1/d
max	Maximum acceptable value of 1/d

Applies a resolution cutoff to list, returning the new version and freeing the old version.

Returns: A new RefList with resolution cutoff applied

resolution_limits()

void resolution_limits	(	RefList *	list,
		UnitCell *	cell,
		double *	rmin,
		double *	rmax
	)

resolution_limits:

Parameters

list	A RefList
cell	A UnitCell
rmin	Place to store the minimum 1/d value
rmax	Place to store the maximum 1/d value

This function calculates the minimum and maximum values of 1/d, where 2dsin(theta) = wavelength. The answers are in m^-1.

write_reflist()

int write_reflist	(	const char *	filename,
		RefList *	list
	)

This function writes the contents of list to file,

Reflections which have a redundancy of zero will not be written.

The resulting list can be read back with read_reflections_from_file() or read_reflections().

This is a convenience function which simply opens filename and then calls write_reflections_to_file.

Deprecated:

Use write_reflist_2() instead.

Parameters

filename	Filename
list	The reflection list to write

Returns

Zero on success, non-zero on failure.

write_reflist_2()

int write_reflist_2	(	const char *	filename,
		RefList *	list,
		SymOpList *	sym
	)

This function writes the contents of list to file,

Reflections which have a redundancy of zero will not be written.

The resulting list can be read back with read_reflections_from_file() or read_reflections().

Parameters

filename	Filename
list	The reflection list to write
sym	A SymOpList describing the symmetry of the list

Returns

zero on success, non-zero on failure.