Functions to read CIF files. More...

#include "global.h"
#include "bind.h"
#include "interface.h"
#include "project.h"
#include "atom_edit.h"
#include "cbuild_edit.h"
#include "readers.h"
#include <ctype.h>

Include dependency graph for read_cif.c:

Go to the source code of this file.

Functions
int	get_atom_id_from_periodic_table (atom_search *asearch)
	get atom Z from selection in the periodic table

double	get_z_from_periodic_table (gchar *lab)
	get Z from atom label

void	get_origin (space_group *spg)
	get space group origin matrices

void	compute_lattice_properties (cell_info *cell, int box_id)
	compute lattice parameters following cell description

int	test_lattice (builder_edition cbuilder, cell_info cif_cell)
	test lattice parameters

int	read_space_group (builder_edition *cbuilder, int spg)
	read space group N°spg data from file

void	get_wyck_char (float val, int ax, int bx)
	convert wyckoff value to string

space_group *	duplicate_space_group (space_group *spg)
	duplicate space ground information

distance	distance_3d (cell_info cell, int mdstep, atom at, atom *bt)
	distance between atom a and b in 3D

void	sort (int dim, int *tab)
	sort, nim to max, a table by integer value

gchar *	get_cif_word (gchar *mot)
	get string from CIF file, EOL can be ugly

float	get_atom_coord (gchar *line, int mid)
	read atom coordinates from CIF file

gchar *	get_atom_label (gchar *line, int lid)
	read atom label from CIF file

int	get_atom_wyckoff (gchar *line, int wid)
	read Wyckoff position from CIF file

gchar *	get_atom_disorder (gchar *line, int lid)
	read atom disorder group from CIF file

G_MODULE_EXPORT void	set_cif_to_insert (GtkComboBox *box, gpointer data)
	change the object to insert at an empty cif position

gboolean	get_missing_object_from_user ()
	get missing atomic number in CIF file from the user

void	file_get_to_line (int line_id)
	reach line in CIF file

int	cif_get_value (gchar kroot, gchar keyw, int lstart, int lend, gchar *cif_word, gboolean rec_val, gboolean all_ligne, gboolean total_num, gboolean record_position, int line_position)
	read pattern in CIF file

int	cif_file_get_data_in_loop (int linec, int lid)
	get the number of "_" motifs in a line

int	get_loop_line_id (int lid)
	reach a line in the CIF file

int	get_loop_line_for_key (int linec, int conf, gchar key_a, gchar key_b)
	search a string

gchar *	cif_retrieve_value (int linec, int conf, gchar key_a, gchar key_b, gboolean all_ligne, gboolean in_loop, gboolean warning)
	retrieve a field value as string in the CIF file

int	cif_file_get_number_of_atoms (int linec, int lid, int nelem)
	get the number of atom(s) in a CIF file

void	check_for_to_lab (int ato, gchar *stlab)
	check atom label

gboolean	cif_file_get_atoms_data (int conf, int lin, int cid[9])

gboolean	cif_get_atomic_coordinates (int linec, int conf)

int	cif_file_get_number_of_positions (int lid)
	get the number of symmetry positions

gboolean	cif_get_symmetry_positions (int linec, int conf)
	read the symmetry positions from the CIF file

int	get_space_group_from_hm (gchar *hmk)
	retrieve space group using the HM Key

gchar *	get_string_from_origin (space_group *spg)
	get the space group origin from its name

int	get_setting_from_hm (gchar *hmk, int end)
	Getting the space group parameters using the HM Key.

int	group_info_from_hm_key (int spg, gchar *key_hm)
	get the space group information using the HM key from the CIF file

gboolean	cif_get_cell_data (int linec, int conf)
	get the cell data from the CIF file

int	cif_get_space_group (int linec, int conf)
	get the space group from the CIF file

int	open_cif_configuration (int linec, int conf)

int	open_cif_file (int linec)
	open CIF file

Variables
gchar *	wnpos [3]

gchar *	tmp_pos

FILE *	cifp

char *	line_ptr

int *	keylines = NULL

int	saved_group

int	cif_atoms

int	cif_nspec

int *	cif_lot = NULL

int *	cif_nsps = NULL

gboolean	cif_multiple = FALSE

gchar **	cif_strings = NULL

gchar *	cif_coord_opts [40][2]

GtkWidget **	img_cif

atom_search *	cif_search = NULL

atomic_object *	cif_object = NULL

Detailed Description

Functions to read CIF files.

Author: Sébastien Le Roux sebas.nosp@m.tien.nosp@m..lero.nosp@m.ux@i.nosp@m.pcms..nosp@m.unis.nosp@m.tra.f.nosp@m.r

Definition in file read_cif.c.

Function Documentation

◆ check_for_to_lab()

void check_for_to_lab	(	int	ato,
		gchar *	stlab )

check atom label

Parameters

ato	atom id
stlab	label to read in the CIF file

Definition at line 941 of file read_cif.c.

◆ cif_file_get_atoms_data()

gboolean cif_file_get_atoms_data	(	int	conf,
		int	lin,
		int	cid[9] )

Definition at line 992 of file read_cif.c.

◆ cif_file_get_data_in_loop()

int cif_file_get_data_in_loop	(	int	linec,
		int	lid )

get the number of "_" motifs in a line

Parameters

linec	total number of lines
lid	line to reach

Definition at line 635 of file read_cif.c.

◆ cif_file_get_number_of_atoms()

int cif_file_get_number_of_atoms	(	int	linec,
		int	lid,
		int	nelem )

get the number of atom(s) in a CIF file

Parameters

linec	total number of lines
lid	line to reach
nelem	number of element(s) the line

Definition at line 874 of file read_cif.c.

◆ cif_file_get_number_of_positions()

int cif_file_get_number_of_positions ( int lid )

get the number of symmetry positions

Parameters

lid	line to reach

Definition at line 1403 of file read_cif.c.

◆ cif_get_atomic_coordinates()

gboolean cif_get_atomic_coordinates	(	int	linec,
		int	conf )

Definition at line 1105 of file read_cif.c.

◆ cif_get_cell_data()

gboolean cif_get_cell_data	(	int	linec,
		int	conf )

get the cell data from the CIF file

Parameters

linec	total number of lines
conf	configuration to read

Definition at line 1780 of file read_cif.c.

◆ cif_get_space_group()

int cif_get_space_group	(	int	linec,
		int	conf )

get the space group from the CIF file

Parameters

linec	total number of lines
conf	configuration to read

Definition at line 1842 of file read_cif.c.

◆ cif_get_symmetry_positions()

gboolean cif_get_symmetry_positions	(	int	linec,
		int	conf )

read the symmetry positions from the CIF file

Parameters

linec	total number of lines
conf	configuration to read

Definition at line 1497 of file read_cif.c.

◆ cif_get_value()

int cif_get_value	(	gchar *	kroot,
		gchar *	keyw,
		int	lstart,
		int	linec,
		gchar **	cif_word,
		gboolean	rec_val,
		gboolean	all_ligne,
		gboolean	total_num,
		gboolean	record_position,
		int *	line_position )

read pattern in CIF file

Parameters

kroot	string key (first part)
keyw	string key (second part)
lstart	starting line to reach
lend	final line
cif_word	pointer to store the data to read
rec_val	record position on the line
all_ligne	browse all line (1/0)
total_num	get the total number of occurrences
record_position	record line position of each occurrences
line_position	line position of each occurrences

Definition at line 436 of file read_cif.c.

◆ cif_retrieve_value()

gchar * cif_retrieve_value	(	int	linec,
		int	conf,
		gchar *	key_a,
		gchar *	key_b,
		gboolean	all_ligne,
		gboolean	in_loop,
		gboolean	warning )

retrieve a field value as string in the CIF file

Parameters

linec	total number of lines
conf	configuration to read
keya	string key (first part)
keyb	string key (second part)
all_ligne	browse all line (1/0)
in_loop	is field in a loop (1/0)
warning	show warning (1/0)

Definition at line 802 of file read_cif.c.

◆ compute_lattice_properties()

void compute_lattice_properties	(	cell_info *	cell,
		int	box_id )

extern

compute lattice parameters following cell description

Parameters

cell	the target cell description
box_id	the target box description to fill

Definition at line 209 of file cbuild_action.c.

◆ distance_3d()

distance distance_3d	(	cell_info *	cell,
		int	mdstep,
		atom *	at,
		atom *	bt )

extern

distance between atom a and b in 3D

Parameters

cell	unit cell
mdstep	the MD step
at	atom a
bt	atom b

Definition at line 81 of file ogl_utils.c.

◆ duplicate_space_group()

space_group * duplicate_space_group ( space_group * spg )

extern

duplicate space ground information

Parameters

spg	the space group to duplicate

Definition at line 596 of file cbuild_action.c.

◆ file_get_to_line()

void file_get_to_line ( int line_id )

reach line in CIF file

Parameters

line_id Line to reach

Definition at line 411 of file read_cif.c.

◆ get_atom_coord()

float get_atom_coord	(	gchar *	line,
		int	mid )

read atom coordinates from CIF file

Parameters

line	the string that contains the data
mid	the position to reach on the line

Definition at line 220 of file read_cif.c.

◆ get_atom_disorder()

gchar * get_atom_disorder	(	gchar *	line,
		int	lid )

read atom disorder group from CIF file

Parameters

line	the string that contains the data
lid	the position to reach on the line

Definition at line 300 of file read_cif.c.

◆ get_atom_id_from_periodic_table()

int get_atom_id_from_periodic_table ( atom_search * asearch )

extern

get atom Z from selection in the periodic table

Parameters

asearch target atom search, if any

Definition at line 672 of file w_periodic.c.

◆ get_atom_label()

gchar * get_atom_label	(	gchar *	line,
		int	lid )

read atom label from CIF file

Parameters

line	the string that contains the data
lid	the position to reach on the line

Definition at line 243 of file read_cif.c.

◆ get_atom_wyckoff()

int get_atom_wyckoff	(	gchar *	line,
		int	wid )

read Wyckoff position from CIF file

Parameters

line	the string that contains the data
wid	the position to reach on the line

Definition at line 272 of file read_cif.c.

◆ get_cif_word()

gchar * get_cif_word ( gchar * mot )

get string from CIF file, EOL can be ugly

Parameters

mot	the string that was read in the file

Definition at line 205 of file read_cif.c.

◆ get_loop_line_for_key()

int get_loop_line_for_key	(	int	linec,
		int	conf,
		gchar *	key_a,
		gchar *	key_b )

search a string

Parameters

linec	total number of lines
conf	configuration to read
key_a	string root (first part)
key_b	string end (second part)

Definition at line 756 of file read_cif.c.

◆ get_loop_line_id()

int get_loop_line_id ( int lid )

reach a line in the CIF file

Parameters

lid	line to reach

Definition at line 699 of file read_cif.c.

◆ get_missing_object_from_user()

gboolean get_missing_object_from_user ( )

get missing atomic number in CIF file from the user

Definition at line 358 of file read_cif.c.

◆ get_origin()

void get_origin ( space_group * spg )

extern

get space group origin matrices

Parameters

spg	the target space group

Definition at line 161 of file cbuild_action.c.

◆ get_setting_from_hm()

int get_setting_from_hm	(	gchar *	hmk,
		int	end )

Getting the space group parameters using the HM Key.

Parameters

hmk	the HM key
end	use origin (number of possible SP origins), or not (-1)

Definition at line 1609 of file read_cif.c.

◆ get_space_group_from_hm()

int get_space_group_from_hm ( gchar * hmk )

retrieve space group using the HM Key

Parameters

hmk

Definition at line 1525 of file read_cif.c.

◆ get_string_from_origin()

gchar * get_string_from_origin ( space_group * spg )

get the space group origin from its name

Parameters

spg	space group

Definition at line 1579 of file read_cif.c.

◆ get_wyck_char()

void get_wyck_char	(	float	val,
		int	ax,
		int	bx )

extern

convert wyckoff value to string

Parameters

val	the target value
ax	axis id, x = 0, y = 1, z = 2
bx	axis label 0 = "x", 1 = "y", 2 = "z"

Definition at line 139 of file cbuild_info.c.

◆ get_z_from_periodic_table()

double get_z_from_periodic_table ( gchar * lab )

extern

get Z from atom label

Parameters

lab	the atomic label

Definition at line 304 of file w_library.c.

◆ group_info_from_hm_key()

int group_info_from_hm_key	(	int	spg,
		gchar *	key_hm )

get the space group information using the HM key from the CIF file

Parameters

spg	space group
key_hm	HM key

Definition at line 1697 of file read_cif.c.

◆ open_cif_configuration()

int open_cif_configuration	(	int	linec,
		int	conf )

Definition at line 2082 of file read_cif.c.

◆ open_cif_file()

int open_cif_file ( int linec )

open CIF file

Parameters

linec Total number of lines

Definition at line 2547 of file read_cif.c.

◆ read_space_group()

int read_space_group	(	builder_edition *	cbuilder,
		int	spg )

extern

read space group N°spg data from file

Parameters

cbuilder	the target builder edition
spg	the space group id

Definition at line 772 of file cbuild_edit.c.

◆ set_cif_to_insert()

G_MODULE_EXPORT void set_cif_to_insert	(	GtkComboBox *	box,
		gpointer	data )

change the object to insert at an empty cif position

Parameters

box	the GtkComboBox sending the signal
data	the associated data pointer

Definition at line 323 of file read_cif.c.

◆ sort()

void sort	(	int	dim,
		int *	tab )

extern

sort, nim to max, a table by integer value

Parameters

dim	the number of value
tab	the table to sort

Definition at line 391 of file glview.c.

◆ test_lattice()

int test_lattice	(	builder_edition *	cbuilder,
		cell_info *	cif_cell )

extern

test lattice parameters

Parameters

cbuilder	the builder edition with the lattice parameters
cif_cell	the cell information when testing CIF file

Definition at line 328 of file cbuild_action.c.

Variable Documentation

◆ cif_atoms

int cif_atoms

Definition at line 98 of file read_cif.c.

◆ cif_coord_opts

gchar* cif_coord_opts[40][2]

Definition at line 107 of file read_cif.c.

◆ cif_lot

int* cif_lot = NULL

Definition at line 100 of file read_cif.c.

◆ cif_multiple

gboolean cif_multiple = FALSE

Definition at line 103 of file read_cif.c.

◆ cif_nspec

int cif_nspec

Definition at line 99 of file read_cif.c.

◆ cif_nsps

int* cif_nsps = NULL

Definition at line 101 of file read_cif.c.

◆ cif_object

atomic_object* cif_object = NULL

Definition at line 313 of file read_cif.c.

◆ cif_search

atom_search* cif_search = NULL

Definition at line 312 of file read_cif.c.

◆ cif_strings

gchar** cif_strings = NULL

Definition at line 105 of file read_cif.c.

◆ cifp

FILE* cifp

Definition at line 94 of file read_cif.c.

◆ img_cif

GtkWidget** img_cif

Definition at line 311 of file read_cif.c.

◆ keylines

int* keylines = NULL

Definition at line 96 of file read_cif.c.

◆ line_ptr

char* line_ptr

Definition at line 95 of file read_cif.c.

◆ saved_group

int saved_group

Definition at line 97 of file read_cif.c.

◆ tmp_pos

gchar* tmp_pos

extern

Definition at line 73 of file cbuild_action.c.

◆ wnpos

gchar* wnpos[3]

extern

Definition at line 74 of file cbuild_info.c.

Functions

Variables

Detailed Description

Function Documentation

◆ check_for_to_lab()

◆ cif_file_get_atoms_data()

◆ cif_file_get_data_in_loop()

◆ cif_file_get_number_of_atoms()

◆ cif_file_get_number_of_positions()

◆ cif_get_atomic_coordinates()

◆ cif_get_cell_data()

◆ cif_get_space_group()

◆ cif_get_symmetry_positions()

◆ cif_get_value()

◆ cif_retrieve_value()

◆ compute_lattice_properties()

◆ distance_3d()

◆ duplicate_space_group()

◆ file_get_to_line()

◆ get_atom_coord()

◆ get_atom_disorder()

◆ get_atom_id_from_periodic_table()

◆ get_atom_label()

◆ get_atom_wyckoff()

◆ get_cif_word()

◆ get_loop_line_for_key()

◆ get_loop_line_id()

◆ get_missing_object_from_user()

◆ get_origin()

◆ get_setting_from_hm()

◆ get_space_group_from_hm()

◆ get_string_from_origin()

◆ get_wyck_char()

◆ get_z_from_periodic_table()

◆ group_info_from_hm_key()

◆ open_cif_configuration()

◆ open_cif_file()

◆ read_space_group()

◆ set_cif_to_insert()

◆ sort()

◆ test_lattice()

Variable Documentation

◆ cif_atoms

◆ cif_coord_opts

◆ cif_lot

◆ cif_multiple

◆ cif_nspec

◆ cif_nsps

◆ cif_object

◆ cif_search

◆ cif_strings

◆ cifp

◆ img_cif

◆ keylines

◆ line_ptr

◆ saved_group

◆ tmp_pos

◆ wnpos