Functions to add / remove molecule(s) to / from the force field. More...

#include "dlp_field.h"
#include "calc.h"
#include "interface.h"
#include "glview.h"

Include dependency graph for dlp_mol.c:

Functions
ColRGBA	init_color (int id, int numid)
	initialize color based id number over total number of elements

void	field_unselect_all ()
	unselect all atoms

gchar *	set_field_atom_name (field_atom ato, field_molecule mol)
	get name string for field atom

void	find_atom_id_in_field_molecule (field_molecule *fmol)

void	viz_fragment (field_molecule *fmol, int id, int viz)
	show / hide fragment

void	check_to_visualize_properties (int id)
	check if it is requried to update rendering

gchar *	remove_text (int i, int j, gchar *str)
	get removal information text

void	clean_up_molecules_info (gboolean usel)
	prepare molecule related widgets in the assistant

void	set_sensitive_mol (GtkTreeViewColumn col, GtkCellRenderer renderer, GtkTreeModel mod, GtkTreeIter iter, gpointer data)
	set renderer sensitivity in the force field molecule selection tree store

G_MODULE_EXPORT void	select_mol (GtkCellRendererToggle cell_renderer, gchar string_path, gpointer data)
	on select field molecule toggle callback

void	clear_field_atoms (field_molecule fmol, field_atom at, int mols, int *mol)
	clean the field atom from a list of atom(s)

void	molecule_set_color (GtkTreeViewColumn col, GtkCellRenderer renderer, GtkTreeModel mod, GtkTreeIter iter, gpointer data)
	set renderer color in the force field molecule selection tree store

G_MODULE_EXPORT void	run_add_molecule_to_field (GtkDialog *dialog, gint response_id, gpointer data)
	add molecule to force field - running the dialog

G_MODULE_EXPORT void	add_molecule_to_field (GSimpleAction action, GVariant parameter, gpointer data)
	add molecule to force field - creating the dialog

void	merge_all_atoms_to_mol (field_molecule *new_mol, int mstart)
	merge all field atoms to another field molecule

void	prepare_atoms_to_merge (field_atom at, field_molecule new_mol, field_molecule *old_mol)
	update the data for the newly 'merged' field atom

field_atom *	new_atom_to_merge (int id, field_molecule *fmol)
	merge field atoms from a field molecule

G_MODULE_EXPORT void	run_remove_molecule_from_field (GtkDialog *rmol, gint response_id, gpointer data)
	remove molecule from force field - running the dialog

G_MODULE_EXPORT void	remove_molecule_from_field (GSimpleAction action, GVariant parameter, gpointer data)
	remove molecule from force field - creating the dialog

Variables
int	active_col

int	a_mol

int	b_mol

int *	new_mol

field_molecule *	to_remove

GtkWidget *	remove_label

GtkCellRenderer *	remove_renderer [5]

GtkTreeViewColumn *	remove_col [5]

gboolean	removing = FALSE

int	old_viz_mol

dint **	atomd_id_save

Detailed Description

Functions to add / remove molecule(s) to / from the force field.

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 dlp_mol.c.

Function Documentation

◆ add_molecule_to_field()

G_MODULE_EXPORT void add_molecule_to_field	(	GSimpleAction *	action,
		GVariant *	parameter,
		gpointer	data )

add molecule to force field - creating the dialog

Parameters

action	the GAction sending the signal
parameter	GVariant parameter of the GAction, if any
data	the associated data pointer

Definition at line 470 of file dlp_mol.c.

◆ check_to_visualize_properties()

void check_to_visualize_properties ( int pid )

extern

check if it is requried to update rendering

Parameters

pid	the page number in the assistant

Definition at line 768 of file dlp_viz.c.

◆ clean_up_molecules_info()

void clean_up_molecules_info ( gboolean usel )

prepare molecule related widgets in the assistant

Parameters

usel	unselect all atom(s) (yes / no)

Definition at line 124 of file dlp_mol.c.

◆ clear_field_atoms()

void clear_field_atoms	(	field_molecule *	fmol,
		field_atom *	at,
		int	mols,
		int *	mol )

clean the field atom from a list of atom(s)

Parameters

fmol	the target fied molecule
at	the field atom to clean, remove specific atom(s) from it
mols	the number of fragment(s) for this molecule
mol	the list of fragment id

Definition at line 227 of file dlp_mol.c.

◆ field_unselect_all()

void field_unselect_all ( )

extern

unselect all atoms

Definition at line 130 of file dlp_viz.c.

◆ find_atom_id_in_field_molecule()

void find_atom_id_in_field_molecule ( field_molecule * fmol )

extern

◆ init_color()

ColRGBA init_color	(	int	id,
		int	numid )

extern

initialize color based id number over total number of elements

Parameters

id	the id number
numid	the total number of elements

Definition at line 81 of file initcoord.c.

◆ merge_all_atoms_to_mol()

void merge_all_atoms_to_mol	(	field_molecule *	new_mol,
		int	mstart )

merge all field atoms to another field molecule

Parameters

new_mol	the field molecule to merge the atom(s) with
mstart	the fragment id to start with

Definition at line 537 of file dlp_mol.c.

◆ molecule_set_color()

void molecule_set_color	(	GtkTreeViewColumn *	col,
		GtkCellRenderer *	renderer,
		GtkTreeModel *	mod,
		GtkTreeIter *	iter,
		gpointer	data )

set renderer color in the force field molecule selection tree store

Parameters

col	the target GtkTreeViewColumn
renderer	the target cell renderer
mod	the target tree model
iter	the target tree iter
data	the associated data pointer

Definition at line 301 of file dlp_mol.c.

◆ new_atom_to_merge()

field_atom * new_atom_to_merge	(	int	id,
		field_molecule *	fmol )

merge field atoms from a field molecule

Parameters

id	the id of the new field atom
fmol	the field molecule for of the atoms

Definition at line 613 of file dlp_mol.c.

◆ prepare_atoms_to_merge()

void prepare_atoms_to_merge	(	field_atom *	at,
		field_molecule *	new_mol,
		field_molecule *	old_mol )

update the data for the newly 'merged' field atom

Parameters

at	the target field atom
new_mol	the target molecule to merge with
old_mol	the molecule to remove

Definition at line 573 of file dlp_mol.c.

◆ remove_molecule_from_field()

G_MODULE_EXPORT void remove_molecule_from_field	(	GSimpleAction *	action,
		GVariant *	parameter,
		gpointer	data )

remove molecule from force field - creating the dialog

Parameters

action	the GAction sending the signal
parameter	GVariant parameter of the GAction, if any
data	the associated data pointer

Definition at line 752 of file dlp_mol.c.

◆ remove_text()

gchar * remove_text	(	int	i,
		int	j,
		gchar *	str )

get removal information text

Parameters

i	-2 = remove field atom, -1 = remove field molecule
j	-1 = remove field molecule, else remove field atom
str	the name of the object to remove

Definition at line 81 of file dlp_mol.c.

◆ run_add_molecule_to_field()

G_MODULE_EXPORT void run_add_molecule_to_field	(	GtkDialog *	dialog,
		gint	response_id,
		gpointer	data )

add molecule to force field - running the dialog

Parameters

dialog	the GtkDialog sending the signal
response_id	the response id
data	the associated data pointer

Definition at line 318 of file dlp_mol.c.

◆ run_remove_molecule_from_field()

G_MODULE_EXPORT void run_remove_molecule_from_field	(	GtkDialog *	rmol,
		gint	response_id,
		gpointer	data )

remove molecule from force field - running the dialog

Parameters

rmol	the GtkDialog sending the signal
response_id	the response id
data	the associated data pointer

Definition at line 647 of file dlp_mol.c.

◆ select_mol()

G_MODULE_EXPORT void select_mol	(	GtkCellRendererToggle *	cell_renderer,
		gchar *	string_path,
		gpointer	data )

on select field molecule toggle callback

Parameters

cell_renderer	the GtkCellRendererToggle sending the signal
string_path	the path in the tree store
data	the associated data pointer

Definition at line 178 of file dlp_mol.c.

◆ set_field_atom_name()

gchar * set_field_atom_name	(	field_atom *	ato,
		field_molecule *	mol )

extern

get name string for field atom

Parameters

ato	the target field atom
mol	the target field molecule

Definition at line 247 of file dlp_init.c.

◆ set_sensitive_mol()

void set_sensitive_mol	(	GtkTreeViewColumn *	col,
		GtkCellRenderer *	renderer,
		GtkTreeModel *	mod,
		GtkTreeIter *	iter,
		gpointer	data )

set renderer sensitivity in the force field molecule selection tree store

Parameters

col	the target GtkTreeViewColumn
renderer	the target cell renderer
mod	the target tree model
iter	the target tree iter
data	the associated data pointer

Definition at line 153 of file dlp_mol.c.

◆ viz_fragment()

void viz_fragment	(	field_molecule *	fmol,
		int	id,
		int	viz )

extern

show / hide fragment

Parameters

fmol	the target field molecule
id	the fragment id
viz	visualization status (0 = hide, 1 = show)

Definition at line 115 of file dlp_viz.c.

Variable Documentation

◆ a_mol

int a_mol

Definition at line 58 of file dlp_mol.c.

◆ active_col

int active_col

Definition at line 57 of file dlp_mol.c.

◆ atomd_id_save

dint** atomd_id_save

Definition at line 215 of file dlp_mol.c.

◆ b_mol

int b_mol

Definition at line 58 of file dlp_mol.c.

◆ new_mol

int* new_mol

Definition at line 59 of file dlp_mol.c.

◆ old_viz_mol

int old_viz_mol

Definition at line 167 of file dlp_mol.c.

◆ remove_col

GtkTreeViewColumn* remove_col[5]

Definition at line 64 of file dlp_mol.c.

◆ remove_label

GtkWidget* remove_label

Definition at line 62 of file dlp_mol.c.

◆ remove_renderer

GtkCellRenderer* remove_renderer[5]

Definition at line 63 of file dlp_mol.c.

◆ removing

gboolean removing = FALSE

Definition at line 65 of file dlp_mol.c.

◆ to_remove

field_molecule* to_remove

Definition at line 61 of file dlp_mol.c.

Functions

Variables

Detailed Description

Function Documentation

◆ add_molecule_to_field()

◆ check_to_visualize_properties()

◆ clean_up_molecules_info()

◆ clear_field_atoms()

◆ field_unselect_all()

◆ find_atom_id_in_field_molecule()

◆ init_color()

◆ merge_all_atoms_to_mol()

◆ molecule_set_color()

◆ new_atom_to_merge()

◆ prepare_atoms_to_merge()

◆ remove_molecule_from_field()

◆ remove_text()

◆ run_add_molecule_to_field()

◆ run_remove_molecule_from_field()

◆ select_mol()

◆ set_field_atom_name()

◆ set_sensitive_mol()

◆ viz_fragment()

Variable Documentation

◆ a_mol

◆ active_col

◆ atomd_id_save

◆ b_mol

◆ new_mol

◆ old_viz_mol

◆ remove_col

◆ remove_label

◆ remove_renderer

◆ removing

◆ to_remove