atom_edit.h File Reference

Function declarations for the mode edition window. More...

#include "global.h"
#include "bind.h"
#include "callbacks.h"
#include "interface.h"
#include "initcoord.h"
#include "glview.h"
#include "glwindow.h"
#include "project.h"
#include "workspace.h"

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Macros
#define	IDCOL   0
#define	TOLAB   3
#define	TOPIC   4

Functions
GtkWidget *	selection_tab (atom_search *asearch, int nats)
	create the search widget
G_MODULE_EXPORT void	set_show_axis_toggle (GtkToggleButton *but, gpointer data)
	show / hide axis callback GTK3
void	save_rotation_quaternion (glwin *view)
	save the rotation quaternion of the last image
void	center_molecule (project *this_proj)
	center atomic coordinates around (0,0,0)
vec3_t	get_arc_ball_vector (glwin *view, int x, int y)
void	update_search_tree (atom_search *asearch)
	update search tree
chemical_data *	alloc_chem_data (int spec)
	allocate chemistry data
void	image_init_spec_data (image *img, project *this_proj, int nsp)
	initialize the chemical species related pointers in an image data structure
void	free_glwin_spec_data (project *this_proj, int spec)
	free the memory used by the chemical species related data in a glwin data structure
void	glwin_init_spec_data (project *this_proj, int nspec)
	initialize the glwin chemical species related pointers
void	prepare_opengl_menu_bar (glwin *view)
	update the OpenGL window menu bar
gboolean	test_vol (double box[2][3], double vect[3][3])
	is the cell properly described to use PBC ?
GtkTreeModel *	replace_combo_tree (gboolean insert, int proj)
	replace combo box in the tree view
int	get_selected_object_id (gboolean visible, int p, gchar *str, atom_search *asearch)
	get the id of the object selected (in contextual menu, or in combo box)
int	get_atom_id_from_periodic_table (atom_search *asearch)
	get atom Z from selection in the periodic table
G_MODULE_EXPORT void	set_mode (GtkWidget *widg, gpointer data)
	set mouse mode callback
GtkWidget *	coord_menu (glwin *view)
GtkWidget *	advanced_coord_properties (glwin *view, int page)
	create the environments configuration window
GtkWidget *	create_cell_edition_window (project *this_proj, gpointer data)
	create the cell editon window
G_MODULE_EXPORT void	window_spinner (GtkWidget *widg, gpointer data)
	create the spin window callback
gboolean	in_bond (int at, int bd[2])
	is atom at in bond bd
void	check_all_trees (project *this_proj)
	check all search trees
atomic_object *	get_atomic_object_by_origin (atomic_object *first, int oid, int aid)
	get insert object from a list by id
void	adjust_object_to_move (project *this_proj, atom_search *asearch, int mv, int id)
	adjust atom search parameters for motion cases
void	motion_to_zero (atom_search *asearch)
	reset motion to 0.0
int	get_asearch_num_objects (atom_search *asearch)
	the number of type of object(s) in this atom search
int	get_asearch_object (atom_search *asearch)
	get the number of object(s) in this atom search
int	get_asearch_filter (atom_search *asearch)
	get asearch filter
int	get_todo_size (atom_search *asearch)
	get the size of the atom search selection list
void	allocate_todo (atom_search *asearch, int tsize)
	allocate the selection list data buffer
void	clean_todo (atom_search *asearch)
	clean atom search selection list
void	clean_picked_and_labelled (atom_search *asearch, gboolean clean_msd)
	initialize atom search data buffers
void	adjust_search_param (atom_search *asearch, project *this_proj, int a, int s, int c, gboolean status)
	adjust parameters for this atom search
void	re_populate_tree_search (atom_search *asearch)
	re populate search tree after atom action if >= 10 000 atoms
G_MODULE_EXPORT void	set_search_mode (GtkComboBox *box, gpointer data)
	change search mode
G_MODULE_EXPORT void	set_object_changed (GtkComboBox *box, gpointer data)
	change the search object
G_MODULE_EXPORT void	set_filter_changed (GtkComboBox *box, gpointer data)
	change the search filter
G_MODULE_EXPORT void	set_spec_changed (GtkComboBox *box, gpointer data)
	change the search chemical species
void	add_bonds_to_list (int **new_bond_list, int nat, int nbd, atomic_object *object)
	add object bond(s) list to overall bond(s) list
void	add_bonds_to_project (project *this_proj, int removed, int nbd, int **new_bond_list)
	add bond list to project bond list
gboolean *	remove_bonds_from_project (project *this_proj, atomic_object *this_object, int *old_id, atom *new_list, gboolean remove, gboolean passivate)
	remove bond(s) from project
G_MODULE_EXPORT void	set_reset_transformation (GtkToggleButton *but, gpointer data)
	reset model transformation toggle callback GTK3
void	to_remove_this_list_of_objects (project *this_proj, atom_search *asearch)
	prepaer to remove a list of object(s) from a project, one object after another.
void	to_passivate_using_the_objects (project *this_proj, atom_search *asearch)
	prepare passivation (delete of an object, then insert of another one at the same location)
tint	ulam_coord (glwin *view)
	shift insertion position for object not to have overlapping objects for multiple/repeated insertions
void	correct_pos_and_get_dim (atomic_object *object, gboolean adjust)
	get the barycenter of the atomic coordinates of an object
atomic_object *	duplicate_atomic_object (atomic_object *old_obj)
	duplicate an insert object
atomic_object *	create_object_from_species (project *this_proj, int sid, atom_search *remove)
	create object from all atom(s) of the same chemical species
void	reconstruct_bonds (project *this_proj, int ifcl, int *bcid)
	reconstruct the project bond(s)/clone(s) lists after reconstruction using PBC
void	reconstruct_coordinates_for_object (project *this_proj, atomic_object *this_object, gboolean upcoord)
	reconstruct object atomic coordinates using PBC
atomic_object *	create_object_from_selection (project *this_proj)
	create object from atom selection
atomic_object *	create_object_from_atom_coordination (project *this_proj, int coord, int aid, atom_search *remove)
	create object from an atom and its nearest neighbors
atomic_object *	create_object_from_overall_coordination (project *this_proj, int coord, int aid, atom_search *remove)
	create object from all the atom(s) that have the same exact coordination than the target atom
atomic_object *	create_object_from_frag_mol (project *this_proj, int coord, int geo, atom_search *remove)
	create object from a fragment or a molecule
void	create_object_from_library (int p)
	create object using the molecular library
int	create_object_from_open_project (project *this_proj, int p)
	create object from atom(s) of a project opened in the workspace
void	clean_this_object (int orig, int act, project *this_proj, atom_search *asearch)
	clean object data
void	to_insert_in_project (int stat, int orig, project *this_proj, atom_search *asearch, gboolean visible)
	to insert object in project
int	insert_this_project_from_lib (int id, gboolean visible, project *this_proj, atom_search *asearch)
	insert object from the library
G_MODULE_EXPORT void	set_atoms_to_insert (GtkComboBox *box, gpointer data)
	change the object to insert
void	clean_other_window_after_edit (project *this_proj)
	update other windows after model edition if required
void	clean_coord_window (project *this_proj)
	update the environment configuration window after edtion
GtkWidget *	create_atom_notebook (project *this_proj, GtkWidget *vbox)
	create the model edition notebook
double **	save_coordinates (project *this_proj, int status)
	save atomic coordinates
void	reset_coordinates (project *this_proj, int status)
	reset transformation and restore saved atomic coordinates
vec3_t	get_bary (project *this_proj, int status)
	get barycenter of atomic coordinates
void	init_coordinates (project *this_proj, int status, gboolean win, gboolean init)
	preserve atomic coordinates
void	translate (project *this_proj, int status, int axis, vec3_t trans)
	translate
void	rotate_quat (project *this_proj, vec4_t q, int status, int axis)
	rotate using quaternion
void	rotate (project *this_proj, int i, int j, int k, float param)
	rotate
void	random_move (project *this_proj, atom_search *asearch)
	random move
void	update_coordinates (project *this_proj, int status, int axis, int action)
	update atomic coordinates on motion
G_MODULE_EXPORT void	repeat_move (GtkSpinButton *res, gpointer data)
	repeat motion callback
G_MODULE_EXPORT gboolean	to_set_move (GtkWidget *widg, GdkEventFocus *event, gpointer data)
G_MODULE_EXPORT void	set_move (GtkEntry *res, gpointer data)
	motion callback - entry
void	range_has_changed (gpointer data, double v)
	motion
void	update_range_and_entry (project *this_proj, int i, int j, int k)
	update motion range
G_MODULE_EXPORT gboolean	scroll_range_move (GtkRange *range, GtkScrollType scroll, gdouble value, gpointer data)
	motion callback - scroll
G_MODULE_EXPORT void	range_move (GtkRange *range, gpointer data)
	motion callback - range
void	check_motion_interactors (project *this_proj, atom_search *asearch)
	add motion check button
GtkWidget *	add_motion_interaction (atom_search *asearch, int axd, project *this_proj)
	add motion interaction widgets
void	apply_action (project *this_proj, atom_search *asearch)
	apply edition action
void	clean_all_trees (atom_search *asearch, project *this_proj)
	clean all tree models in the 'model edition' window
gboolean	do_we_have_objects_in_selection (project *this_proj, atom_search *asearch, gboolean editing)
	check for object(s) in selection to apply action
G_MODULE_EXPORT void	take_action (GtkButton *but, gpointer data)
	take edition action
GtkWidget *	action_tab (int aid, project *this_proj)
	create model edtion action tab
int	find_this_geo_id (int id, coord_info *obj, int *old_z, int old_geo, int old_sp, int new_sp, coord_info *coord, double *new_z)
	if required create a new geometry, stored in coord, for coordination type 'gid' and chemical species 'new_sp', return geometry id
void	check_coord_modification (project *this_proj, int old_id[], atom *new_list, atomic_object *this_object, gboolean movtion, gboolean passivating)
void	print_coord_info (project *this_proj, coord_info *coord)
	print coordination info
coord_info *	duplicate_coord_info (coord_info *old_coord)
	duplicate coordination information data structure
void	recover_opengl_data (project *this_proj, int nmols, int add, int rem, int *num, int *rec, int ***tmpgeo, gboolean *showfrag)
	recover image pointer data and OpenGL window menu structure
chemical_data *	duplicate_chemical_data (int spec, chemical_data *chem)
	duplicate chemical data information
int	find_spec_id (int s, int z, double *list_z)
	find species id based on Z
int	search_for_new_spec (atom_edition *edit, atomic_object *object)
	search for new chemical species
void	prepare_atom_edition (gpointer data, gboolean visible)
	prepare atom edition
G_MODULE_EXPORT void	action_window (GtkWidget *widg, gpointer data)
	open model edition window callback GTK3
G_MODULE_EXPORT void	close_build (GtkWidget *widg, gpointer data)

Variables
int	selected_aspec
int	is_selected
insertion_menu	mol []
atom_search *	remove_search
gchar *	mot [2][2]
int	being_copied
atomic_object *	lib_object
float	limit [2]
gchar *	action_name [5]
gchar *	action_atoms [3]

Detailed Description

Function declarations for the mode edition window.

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 atom_edit.h.

Macro Definition Documentation

IDCOL

#define IDCOL   0

Definition at line 44 of file atom_edit.h.

TOLAB

#define TOLAB   3

Definition at line 45 of file atom_edit.h.

TOPIC

#define TOPIC   4

Definition at line 46 of file atom_edit.h.

Function Documentation

action_tab()

GtkWidget * action_tab ( int aid, project * this_proj )

extern

create model edtion action tab

Parameters

aid	the action id
this_proj	the target project

Definition at line 281 of file atom_search.c.

action_window()

G_MODULE_EXPORT void action_window	(	GtkWidget *	widg,
		gpointer	data )

open model edition window callback GTK3

Parameters

widg	the GtkWidget sending the signal
data	the associated data pointer

Definition at line 535 of file atom_edit.c.

add_bonds_to_list()

void add_bonds_to_list ( int ** new_bond_list, int nat, int nbd, atomic_object * object )

extern

add object bond(s) list to overall bond(s) list

Parameters

new_bond_list	the bond list in the model
nat	the number of atom(s) in the model
nbd	the number of bond(s) in the model
object	the target insert object

Definition at line 81 of file atom_insert.c.

add_bonds_to_project()

void add_bonds_to_project ( project * this_proj, int removed, int nbd, int ** new_bond_list )

extern

add bond list to project bond list

Parameters

this_proj	the target project
removed	the number of atom(s) removed
nbd	the number of bond(s) to add
new_bond_list	the bond list to add

Definition at line 53 of file atom_insert.c.

add_motion_interaction()

GtkWidget * add_motion_interaction ( atom_search * asearch, int axd, project * this_proj )

extern

add motion interaction widgets

Parameters

asearch	the target atom search
axd	translation (0) or rotation (1)
this_proj	the target project

Definition at line 1230 of file atom_move.c.

adjust_object_to_move()

void adjust_object_to_move ( project * this_proj, atom_search * asearch, int mv, int id )

extern

adjust atom search parameters for motion cases

Parameters

this_proj	the target project
asearch	the target atom search
mv	motion id (0 = standard, 1 = random)
id	object id

Definition at line 523 of file w_search.c.

adjust_search_param()

void adjust_search_param ( atom_search * asearch, project * this_proj, int a, int s, int c, gboolean status )

extern

adjust parameters for this atom search

Parameters

asearch	the target atom search
this_proj	the target project
a	the atom id
s	the chemical species, or object id
c	the column id
status	the new toogle status

Definition at line 1745 of file w_search.c.

advanced_coord_properties()

GtkWidget * advanced_coord_properties ( glwin * view, int page )

extern

create the environments configuration window

Parameters

view	the target glwin
page	the page of the notebook to display

Definition at line 1310 of file w_coord.c.

alloc_chem_data()

chemical_data * alloc_chem_data ( int spec )

extern

allocate chemistry data

Parameters

spec	the number of chemical species

Definition at line 186 of file open_p.c.

allocate_todo()

void allocate_todo ( atom_search * asearch, int tsize )

extern

allocate the selection list data buffer

Parameters

asearch	the target atom search
tsize	the target size

Definition at line 3717 of file w_search.c.

apply_action()

void apply_action ( project * this_proj, atom_search * asearch )

extern

apply edition action

Parameters

this_proj	the target project
asearch	the target atom search

Definition at line 1100 of file atom_action.c.

center_molecule()

void center_molecule ( project * this_proj )

extern

center atomic coordinates around (0,0,0)

Parameters

this_proj

the target project

Definition at line 1441 of file glview.c.

check_all_trees()

void check_all_trees ( project * this_proj )

extern

check all search trees

Parameters

this_proj

the target project

Definition at line 450 of file w_search.c.

check_coord_modification()

void check_coord_modification ( project * this_proj, int old_id[], atom * new_list, atomic_object * this_object, gboolean movtion, gboolean passivating )

extern

check_motion_interactors()

void check_motion_interactors ( project * this_proj, atom_search * asearch )

extern

add motion check button

Parameters

this_proj	the target project
asearch	the target atom search

Definition at line 1160 of file atom_move.c.

clean_all_trees()

void clean_all_trees ( atom_search * asearch, project * this_proj )

extern

clean all tree models in the 'model edition' window

Parameters

asearch	the target atom search
this_proj	the target project

Definition at line 1018 of file atom_action.c.

clean_coord_window()

void clean_coord_window ( project * this_proj )

extern

update the environment configuration window after edtion

Parameters

this_proj

the target project

Definition at line 87 of file atom_edit.c.

clean_other_window_after_edit()

void clean_other_window_after_edit ( project * this_proj )

extern

update other windows after model edition if required

Parameters

this_proj

the target project

Definition at line 110 of file atom_edit.c.

clean_picked_and_labelled()

void clean_picked_and_labelled ( atom_search * asearch, gboolean clean_msd )

extern

initialize atom search data buffers

Parameters

asearch	the target atom search
clean_msd	clean msd all data (1) or not (0)

Definition at line 3791 of file w_search.c.

clean_this_object()

void clean_this_object ( int orig, int act, project * this_proj, atom_search * asearch )

extern

clean object data

Parameters

orig	- (fragmol id/species id +1), -1, or, orgin atom id
act	action in enum 'actions'
this_proj	the target project
asearch	the target atom search

Definition at line 1102 of file atom_object.c.

clean_todo()

void clean_todo ( atom_search * asearch )

extern

clean atom search selection list

Parameters

asearch

the target atom search

Definition at line 3730 of file w_search.c.

close_build()

G_MODULE_EXPORT void close_build	(	GtkWidget *	widg,
		gpointer	data )

coord_menu()

GtkWidget * coord_menu ( glwin * view )

extern

correct_pos_and_get_dim()

void correct_pos_and_get_dim ( atomic_object * object, gboolean adjust )

extern

get the barycenter of the atomic coordinates of an object

Parameters

object	the target insert object
adjust	center object coordinates or not

Definition at line 104 of file atom_object.c.

create_atom_notebook()

GtkWidget * create_atom_notebook ( project * this_proj, GtkWidget * vbox )

extern

create the model edition notebook

Parameters

this_proj	the target project
vbox	the GtkWidget sending the signal

Definition at line 365 of file atom_edit.c.

create_cell_edition_window()

GtkWidget * create_cell_edition_window ( project * this_proj, gpointer data )

extern

create the cell editon window

Parameters

this_proj	the target project
data	the associated data pointer

Definition at line 182 of file cell_edit.c.

create_object_from_atom_coordination()

atomic_object * create_object_from_atom_coordination ( project * this_proj, int coord, int aid, atom_search * remove )

extern

create object from an atom and its nearest neighbors

Parameters

this_proj	the target project
coord	0 = total coordination, 1 = partial coordination
aid	the atom id
remove	remove search, if any

Definition at line 777 of file atom_object.c.

create_object_from_frag_mol()

atomic_object * create_object_from_frag_mol ( project * this_proj, int coord, int geo, atom_search * remove )

extern

create object from a fragment or a molecule

Parameters

this_proj	the target project
coord	2 = fragment, 3 = molecule
geo	fragment or molecule id
remove	remove search, if any

Definition at line 928 of file atom_object.c.

create_object_from_library()

void create_object_from_library ( int p )

extern

create object using the molecular library

Parameters

p	the project id of the library molecule in the workspace

Definition at line 421 of file atom_object.c.

create_object_from_open_project()

int create_object_from_open_project ( project * this_proj, int p )

extern

create object from atom(s) of a project opened in the workspace

Parameters

this_proj	the target project
p	the project id of the project that contains the atom(s) to copy

Definition at line 1015 of file atom_object.c.

create_object_from_overall_coordination()

atomic_object * create_object_from_overall_coordination ( project * this_proj, int coord, int aid, atom_search * remove )

extern

create object from all the atom(s) that have the same exact coordination than the target atom

Parameters

this_proj	the target project
coord	0 = total coordination, 1 = partial coordination
aid	target atom id
remove	remove search, if any

Definition at line 848 of file atom_object.c.

create_object_from_selection()

atomic_object * create_object_from_selection ( project * this_proj )

extern

create object from atom selection

Parameters

this_proj

the target project

Definition at line 724 of file atom_object.c.

create_object_from_species()

atomic_object * create_object_from_species ( project * this_proj, int sid, atom_search * remove )

extern

create object from all atom(s) of the same chemical species

Parameters

this_proj	the target project
sid	the species id
remove	remove search, if any

Definition at line 683 of file atom_object.c.

do_we_have_objects_in_selection()

gboolean do_we_have_objects_in_selection ( project * this_proj, atom_search * asearch, gboolean editing )

extern

check for object(s) in selection to apply action

Parameters

this_proj	the target project
asearch	the target atom search
editing	actually going for action (1) or simply counting elements (0)

Definition at line 1369 of file atom_action.c.

duplicate_atomic_object()

atomic_object * duplicate_atomic_object ( atomic_object * old_obj )

extern

duplicate an insert object

Parameters

old_obj

the insert object to duplicate

Definition at line 381 of file atom_object.c.

duplicate_chemical_data()

chemical_data * duplicate_chemical_data ( int spec, chemical_data * chem )

extern

duplicate chemical data information

Parameters

spec	the number of chemical species
chem	the chemical data to duplicate

Definition at line 50 of file atom_species.c.

duplicate_coord_info()

coord_info * duplicate_coord_info ( coord_info * old_coord )

extern

duplicate coordination information data structure

Parameters

old_coord

the coordination info to duplicate

Definition at line 190 of file atom_coord.c.

find_spec_id()

int find_spec_id ( int s, int z, double * list_z )

extern

find species id based on Z

Parameters

s	the number of chemical species
z	the target Z
list_z	the list of Z values

Definition at line 83 of file atom_species.c.

find_this_geo_id()

int find_this_geo_id ( int gid, coord_info * obj, int * old_z, int old_geo, int old_sp, int new_sp, coord_info * coord, double * new_z )

extern

if required create a new geometry, stored in coord, for coordination type 'gid' and chemical species 'new_sp', return geometry id

Parameters

gid	the new coordination type (0 = total, 1 = partial)
obj	the new coordination info to update
old_z	old Z list
old_geo	the old coordination id for this coordination type
old_sp	the old chemical species id
new_sp	the new chemical species id
coord	the old coordination info
new_z	new Z list

Definition at line 209 of file atom_geo.c.

free_glwin_spec_data()

void free_glwin_spec_data ( project * this_proj, int spec )

extern

free the memory used by the chemical species related data in a glwin data structure

Parameters

this_proj	the target project
spec	the number of chemical species

Definition at line 1543 of file glview.c.

get_arc_ball_vector()

vec3_t get_arc_ball_vector ( glwin * view, int x, int y )

extern

Definition at line 46 of file arcball.c.

get_asearch_filter()

int get_asearch_filter ( atom_search * asearch )

extern

get asearch filter

Parameters

asearch

the target atom search

Definition at line 170 of file w_search.c.

get_asearch_num_objects()

int get_asearch_num_objects ( atom_search * asearch )

extern

the number of type of object(s) in this atom search

Parameters

asearch

the target atom search

Definition at line 125 of file w_search.c.

get_asearch_object()

int get_asearch_object ( atom_search * asearch )

extern

get the number of object(s) in this atom search

Parameters

asearch

the target atom search

Definition at line 149 of file w_search.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_atomic_object_by_origin()

atomic_object * get_atomic_object_by_origin ( atomic_object * first, int oid, int aid )

extern

get insert object from a list by id

Parameters

first	the first insert object of the list
oid	object origin id (type of origin)
aid	object id

Definition at line 474 of file w_search.c.

get_bary()

vec3_t get_bary ( project * this_proj, int status )

extern

get barycenter of atomic coordinates

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)

Definition at line 170 of file atom_move.c.

get_selected_object_id()

int get_selected_object_id ( gboolean visible, int p, gchar * str, atom_search * asearch )

extern

get the id of the object selected (in contextual menu, or in combo box)

Parameters

visible	is the 'model edition' window visible (1/0)
p	the target project id
str	the string that describing the selection
asearch	the target atom search

Definition at line 2385 of file w_search.c.

get_todo_size()

int get_todo_size ( atom_search * asearch )

extern

get the size of the atom search selection list

Parameters

asearch

the target atom search

Definition at line 3681 of file w_search.c.

glwin_init_spec_data()

void glwin_init_spec_data ( project * this_proj, int nspec )

extern

initialize the glwin chemical species related pointers

Parameters

this_proj	the target project
nspec	the number of chemical species

Definition at line 1588 of file glview.c.

image_init_spec_data()

void image_init_spec_data ( image * img, project * this_proj, int nsp )

extern

initialize the chemical species related pointers in an image data structure

Parameters

img	the target image
this_proj	the target project
nsp	the number of chemical species

Definition at line 1190 of file glview.c.

in_bond()

gboolean in_bond ( int at, int bd[2] )

extern

is atom at in bond bd

Parameters

at	the target atom id
bd	the bond atoms id

Definition at line 892 of file dlp_init.c.

init_coordinates()

void init_coordinates ( project * this_proj, int status, gboolean win, gboolean init )

extern

preserve atomic coordinates

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)
win	is the model edition window opened ?
init	preserve atomic coordinates

Definition at line 197 of file atom_move.c.

insert_this_project_from_lib()

int insert_this_project_from_lib ( int id, gboolean visible, project * this_proj, atom_search * asearch )

extern

insert object from the library

Parameters

id	object id to insert
visible	is the 'model edition window' visible
this_proj	the target project
asearch	the target atom search

Definition at line 1158 of file w_library.c.

motion_to_zero()

void motion_to_zero ( atom_search * asearch )

extern

reset motion to 0.0

Parameters

asearch

the target atom search

Definition at line 493 of file w_search.c.

prepare_atom_edition()

void prepare_atom_edition ( gpointer data, gboolean visible )

extern

prepare atom edition

Parameters

data	the associated data pointer
visible	is the window visible (1/0)

Definition at line 459 of file atom_edit.c.

prepare_opengl_menu_bar()

void prepare_opengl_menu_bar ( glwin * view )

extern

update the OpenGL window menu bar

Parameters

view	the target glwin

Definition at line 600 of file glwindow.c.

print_coord_info()

void print_coord_info ( project * this_proj, coord_info * coord )

extern

print coordination info

Parameters

this_proj	the target project
coord	the target coordination info

Definition at line 87 of file atom_coord.c.

random_move()

void random_move ( project * this_proj, atom_search * asearch )

extern

random move

Parameters

this_proj	the target project
asearch	the target atom search

Definition at line 657 of file atom_move.c.

range_has_changed()

void range_has_changed ( gpointer data, double v )

extern

motion

Parameters

data	the associated data pointer
v	the value for motion

Definition at line 1016 of file atom_move.c.

range_move()

G_MODULE_EXPORT void range_move ( GtkRange * range, gpointer data )

extern

motion callback - range

Parameters

range	the GtkRange sending the signal
data	the associated data pointer

Definition at line 1061 of file atom_move.c.

re_populate_tree_search()

void re_populate_tree_search ( atom_search * asearch )

extern

re populate search tree after atom action if >= 10 000 atoms

Parameters

asearch

the target atom search

Definition at line 1608 of file w_search.c.

reconstruct_bonds()

void reconstruct_bonds ( project * this_proj, int ifcl, int * bcid )

extern

reconstruct the project bond(s)/clone(s) lists after reconstruction using PBC

Parameters

this_proj	the target project
ifcl	number of clone bond(s) removed
bcid	the removed clone bond(s) atoms id

Definition at line 180 of file atom_object.c.

reconstruct_coordinates_for_object()

void reconstruct_coordinates_for_object ( project * this_proj, atomic_object * this_object, gboolean upcoord )

extern

reconstruct object atomic coordinates using PBC

Parameters

this_object	the target project
this_proj	the target insert object
upcoord	reconstruction of atomic coordinates using PBC ?

Definition at line 263 of file atom_object.c.

recover_opengl_data()

void recover_opengl_data ( project * this_proj, int nmols, int add, int rem, int * num, int * rec, int *** tmpgeo, gboolean * showfrag )

extern

recover image pointer data and OpenGL window menu structure

Parameters

this_proj	the target project
nmols	the number of molecules
add	the number of new chemical species
rem	the number of chemical species to remove
num	the number of atom(s) by chemical species
rec	the lsit of removed chemical species, if any
tmpgeo	the new number of coordination [c] by chemical species [s] 'coorrd -> ntg[c][s]'
showfrag	the saved fragment(s) show information

Definition at line 549 of file atom_coord.c.

remove_bonds_from_project()

gboolean * remove_bonds_from_project ( project * this_proj, atomic_object * this_object, int * old_id, atom * new_list, gboolean remove, gboolean passivate )

extern

remove bond(s) from project

Parameters

this_proj	the target project
this_object	the target insert object, if any
old_id	the atom(s) id list
new_list	the new atom list
remove	remove (1) or motion (0) action
passivate	passivate (1) or not (0)

Definition at line 224 of file atom_remove.c.

repeat_move()

G_MODULE_EXPORT void repeat_move ( GtkSpinButton * res, gpointer data )

extern

repeat motion callback

Parameters

res	the GtkSpinButton sending the signal
data	the associated data pointer

Definition at line 963 of file atom_move.c.

replace_combo_tree()

GtkTreeModel * replace_combo_tree ( gboolean insert, int proj )

extern

replace combo box in the tree view

Parameters

insert	add 'Select ...' combo box item
proj	target crystal builder project id

Definition at line 2615 of file w_search.c.

reset_coordinates()

void reset_coordinates ( project * this_proj, int status )

extern

reset transformation and restore saved atomic coordinates

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)

Definition at line 143 of file atom_move.c.

rotate()

void rotate ( project * this_proj, int status, int axis, int raxis, float param )

extern

rotate

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)
axis	0 = model, 1 = eye
raxis	rotation axis 0 = x, 1 = y, 2 = z
param	rotation angle

Definition at line 309 of file atom_move.c.

rotate_quat()

void rotate_quat ( project * this_proj, vec4_t q, int status, int axis )

extern

rotate using quaternion

Parameters

this_proj	the target project
q	rotation quaternion
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)
axis	0 = model, 1 = eye

Definition at line 269 of file atom_move.c.

save_coordinates()

double ** save_coordinates ( project * this_proj, int status )

extern

save atomic coordinates

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)

Definition at line 91 of file atom_move.c.

save_rotation_quaternion()

void save_rotation_quaternion ( glwin * view )

extern

save the rotation quaternion of the last image

Parameters

view	the target glwin

Definition at line 543 of file glview.c.

scroll_range_move()

G_MODULE_EXPORT gboolean scroll_range_move ( GtkRange * range, GtkScrollType scroll, gdouble value, gpointer data )

extern

motion callback - scroll

Parameters

range	the GtkRange sending the signal
scroll	the associated scroll type
value	the range value
data	the associated data pointer

Definition at line 1076 of file atom_move.c.

search_for_new_spec()

int search_for_new_spec ( atom_edition * edit, atomic_object * object )

extern

search for new chemical species

Parameters

edit	the edition window
object	the target insert object

Definition at line 107 of file atom_species.c.

selection_tab()

GtkWidget * selection_tab ( atom_search * asearch, int nats )

extern

create the search widget

Parameters

asearch	the target atom search
nats	the total number of atoms

Definition at line 4130 of file w_search.c.

set_atoms_to_insert()

G_MODULE_EXPORT void set_atoms_to_insert ( GtkComboBox * box, gpointer data )

extern

change the object to insert

Parameters

box	the GtkComboBox sending the signal
data	the associated data pointer

Definition at line 118 of file atom_insert.c.

set_filter_changed()

G_MODULE_EXPORT void set_filter_changed ( GtkComboBox * box, gpointer data )

extern

change the search filter

Parameters

box	the GtkComboBox sending the signal
data	the associated data pointer

Definition at line 3858 of file w_search.c.

set_mode()

G_MODULE_EXPORT void set_mode ( GtkWidget * widg, gpointer data )

extern

set mouse mode callback

Parameters

widg	the GtkWidget sending the signal
data	the associated data pointer

Definition at line 172 of file m_tools.c.

set_move()

G_MODULE_EXPORT void set_move ( GtkEntry * res, gpointer data )

extern

motion callback - entry

Parameters

res	the GtkEntry sending the signal
data	the associated data pointer

Definition at line 1046 of file atom_move.c.

set_object_changed()

G_MODULE_EXPORT void set_object_changed ( GtkComboBox * box, gpointer data )

extern

change the search object

Parameters

box	the GtkComboBox sending the signal
data	the associated data pointer

Definition at line 3884 of file w_search.c.

set_reset_transformation()

G_MODULE_EXPORT void set_reset_transformation ( GtkToggleButton * but, gpointer data )

extern

reset model transformation toggle callback GTK3

Parameters

but	the GtkToggleButton sending the signal
data	the associated data pointer

Definition at line 277 of file atom_edit.c.

set_search_mode()

G_MODULE_EXPORT void set_search_mode ( GtkComboBox * box, gpointer data )

extern

change search mode

Parameters

box	the GtkComboBox sending the signal
data	the associated data pointer

Definition at line 3983 of file w_search.c.

set_show_axis_toggle()

G_MODULE_EXPORT void set_show_axis_toggle ( GtkToggleButton * but, gpointer data )

extern

show / hide axis callback GTK3

Parameters

but	the GtkToggleButton sending the signal
data	the associated data pointer

Definition at line 193 of file w_axis.c.

set_spec_changed()

G_MODULE_EXPORT void set_spec_changed ( GtkComboBox * box, gpointer data )

extern

change the search chemical species

Parameters

box	the GtkComboBox sending the signal
data	the associated data pointer

Definition at line 3829 of file w_search.c.

take_action()

G_MODULE_EXPORT void take_action ( GtkButton * but, gpointer data )

extern

take edition action

Parameters

but	the GtkButton sending the signal
data	the associated data pointer

Definition at line 2011 of file atom_action.c.

test_vol()

gboolean test_vol ( double box[2][3], double vect[3][3] )

extern

is the cell properly described to use PBC ?

Parameters

box	lattice parameters
vect	lattice vectors

Definition at line 498 of file edit_menu.c.

to_insert_in_project()

void to_insert_in_project ( int stat, int orig, project * this_proj, atom_search * asearch, gboolean visible )

extern

to insert object in project

Parameters

stat	in enum object_types
orig	- (fragmol id/species id +1), -1, or, orgin atom id
this_proj	the target project
asearch	the target atom search
visible	is the model edition window visible ?

Definition at line 1214 of file atom_object.c.

to_passivate_using_the_objects()

void to_passivate_using_the_objects ( project * this_proj, atom_search * asearch )

extern

prepare passivation (delete of an object, then insert of another one at the same location)

Parameters

this_proj	the target project
asearch	the target atom search

Definition at line 650 of file atom_remove.c.

to_remove_this_list_of_objects()

void to_remove_this_list_of_objects ( project * this_proj, atom_search * asearch )

extern

prepaer to remove a list of object(s) from a project, one object after another.

Parameters

this_proj	the target project
asearch	the target atom search

Definition at line 580 of file atom_remove.c.

to_set_move()

G_MODULE_EXPORT gboolean to_set_move ( GtkWidget * widg, GdkEventFocus * event, gpointer data )

extern

translate()

void translate ( project * this_proj, int status, int axis, vec3_t trans )

extern

translate

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)
axis	0 = model, 1 = eye
trans	translation vector

Definition at line 230 of file atom_move.c.

ulam_coord()

tint ulam_coord ( glwin * view )

extern

shift insertion position for object not to have overlapping objects for multiple/repeated insertions

Parameters

view	the target glwin

Definition at line 354 of file atom_object.c.

update_coordinates()

void update_coordinates ( project * this_proj, int status, int axis, int action )

extern

update atomic coordinates on motion

Parameters

this_proj	the target project
status	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)
axis	axis, 0 = model, 1 = eye
action	0 = translation, 1 = rotation

Definition at line 939 of file atom_move.c.

update_range_and_entry()

void update_range_and_entry ( project * this_proj, int i, int j, int k )

extern

update motion range

Parameters

this_proj	the target project
i	selection status, 0 = non selected atom(s), 1 = selected atom(s), 2 = all atom(s)
j	axis, 0 = model, 1 = eye
k	parameter to update: x, y, z or alpha, beta, gamma

Definition at line 979 of file atom_move.c.

update_search_tree()

void update_search_tree ( atom_search * asearch )

extern

update search tree

Parameters

asearch

the target atom search

Definition at line 1294 of file w_search.c.

window_spinner()

G_MODULE_EXPORT void window_spinner ( GtkWidget * widg, gpointer data )

extern

create the spin window callback

Parameters

widg	the GtkWidget sending the signal
data	the associated data pointer

Definition at line 158 of file w_spiner.c.

Variable Documentation

action_atoms

gchar* action_atoms[3]

extern

Definition at line 61 of file atom_edit.c.

action_name

gchar* action_name[5]

extern

Definition at line 60 of file atom_edit.c.

being_copied

int being_copied

extern

Definition at line 371 of file atom_object.c.

is_selected

int is_selected

extern

Definition at line 182 of file popup.c.

lib_object

atomic_object* lib_object

extern

Definition at line 372 of file atom_object.c.

limit

float limit[2]

extern

Definition at line 59 of file atom_edit.c.

mol

insertion_menu mol[]

extern

Definition at line 193 of file w_library.c.

mot

gchar* mot[2][2]

extern

Definition at line 3293 of file popup.c.

remove_search

atom_search* remove_search

extern

Definition at line 175 of file popup.c.

selected_aspec

int selected_aspec

extern

Definition at line 180 of file popup.c.