Functions to create the molecular library
Functions to read the 'Simple chemical XML' files. More...

#include "global.h"
#include "bind.h"
#include "interface.h"
#include "project.h"
#include "glview.h"
#include "glwindow.h"
#include <libxml/xmlreader.h>

Include dependency graph for w_library.c:

Go to the source code of this file.

Macros
#define	FAMILY 26

Functions
gboolean	create_3d_model (int p, gboolean load)

G_MODULE_EXPORT void	on_realize (GtkGLArea *area, gpointer data)

xmlNodePtr	findnode (xmlNodePtr startnode, char *nname)
	find XML node

int	action_atoms_from_project (project this_proj, atom_search asearch, gboolean visible)
	apply atom edition action to project (motion, remove, replace, insert, random move)

void	to_insert_in_project (int stat, int orig, project this_proj, atom_search asearch, gboolean visible)
	to insert object in project

void	create_object_from_library (int p)
	create object using the molecular library

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

int	clean_xml_data (xmlDoc *doc, xmlTextReaderPtr reader)
	free XML data

gchar *	replace_markup (char init, char key, char *rep)
	replace pattern in string

gchar *	substitute_string (gchar init, gchar o_motif, gchar *n_motif)
	substitute all patterns in string

gchar *	check_xml_string (gchar *init)
	check for, and correct tags in XML string

int	sml_preview (const char *filetoread)
	retrieve preview information from 'Simple chemical library XML' file

gchar *	open_sml_file (const char *filetoread, int fam)
	open 'Simple chemical library XML' file

int	get_family (gchar *str)
	get molecular family id

void	sort_files (int num_f)
	sort file(s) by molecular family and name

int	get_sml_files ()
	get the library 'Simple chemical library XML' files

void	fill_molecule_tree (GtkListStore *store)
	fill molecule list store

void	fill_family_tree (GtkListStore *store)
	fill molecular family list store

void	insert_preview ()
	insert preview in library window and visualize

void	prepare_preview (int active, int id, gboolean visible)
	prepare library molecule preview

G_MODULE_EXPORT void	select_library_data (GtkTreeView tree_view, GtkTreePath path, GtkTreeViewColumn *column, gpointer data)
	select library element callback

G_MODULE_EXPORT void	set_library_markup (GtkTreeViewColumn col, GtkCellRenderer renderer, GtkTreeModel mod, GtkTreeIter iter, gpointer data)
	set font markup in the molecular library tree store

GtkWidget *	library_tree (GtkListStore store, int id, gchar name)
	create library tree store widget

G_MODULE_EXPORT void	run_select_from_library (GtkDialog *lib, gint response_id, gpointer data)
	select from library - running the dialog

int	select_from_library (gboolean visible, project this_proj, atom_search asearch)
	select object to insert from the library

int	insert_this_project_from_lib (int id, gboolean visible, project this_proj, atom_search asearch)
	insert object from the library

Variables
element_data	periodic_table_info []

insertion_menu	mol []

gchar *	family_list [FAMILY]

gchar *	family_dir [FAMILY]

atom_search *	remove_search

GtkListStore *	family_store

GtkTreeIter	first_family_iter

GtkListStore *	molecule_store

GtkTreeIter	first_mol_iter

GtkTreeSelection *	libselect [2]

int	the_family

gchar *	the_molecule

gchar **	sml_file_name

gchar **	mol_name

GtkWidget *	lib_preview_box = NULL

GtkWidget *	lib_preview_plot = NULL

project *	lib_proj = NULL

gchar *	other_name [5]

int	o_names

int	inserted_from_lib

gboolean	lib_res

gboolean	lib_visible

Detailed Description

Functions to create the molecular library
Functions to read the 'Simple chemical XML' 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 w_library.c.

Macro Definition Documentation

◆ FAMILY

#define FAMILY 26

Definition at line 214 of file w_library.c.

Function Documentation

◆ action_atoms_from_project()

int action_atoms_from_project	(	project *	this_proj,
		atom_search *	asearch,
		gboolean	visible )

extern

apply atom edition action to project (motion, remove, replace, insert, random move)

Parameters

this_proj	the target project
asearch	the target atom search
visible	is the 'model edition' window visible (1/0)

Definition at line 211 of file atom_action.c.

◆ check_xml_string()

gchar * check_xml_string ( gchar * init )

check for, and correct tags in XML string

Parameters

init	the XML string to check / correct

Definition at line 395 of file w_library.c.

◆ clean_xml_data()

int clean_xml_data	(	xmlDoc *	doc,
		xmlTextReaderPtr	reader )

free XML data

Parameters

doc	the XML doc pointer to free
reader	the XML reader to free

Definition at line 322 of file w_library.c.

◆ create_3d_model()

gboolean create_3d_model	(	int	p,
		gboolean	load )

extern

Definition at line 1399 of file glwindow.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.

◆ fill_family_tree()

void fill_family_tree ( GtkListStore * store )

fill molecular family list store

Parameters

store the list store to fill

Definition at line 805 of file w_library.c.

◆ fill_molecule_tree()

void fill_molecule_tree ( GtkListStore * store )

fill molecule list store

Parameters

store the list store to fill

Definition at line 779 of file w_library.c.

◆ findnode()

xmlNodePtr findnode	(	xmlNodePtr	startnode,
		char *	nname )

extern

find XML node

Parameters

startnode	Starting node
nname	Node name to find

Definition at line 546 of file read_isaacs.c.

◆ get_family()

int get_family ( gchar * str )

get molecular family id

Parameters

str	the moecular family

Definition at line 609 of file w_library.c.

◆ get_sml_files()

int get_sml_files ( )

get the library 'Simple chemical library XML' files

Definition at line 656 of file w_library.c.

◆ get_z_from_periodic_table()

double get_z_from_periodic_table ( gchar * lab )

get Z from atom label

Parameters

lab	the atomic label

Definition at line 304 of file w_library.c.

◆ insert_preview()

void insert_preview ( )

insert preview in library window and visualize

Definition at line 829 of file w_library.c.

◆ insert_this_project_from_lib()

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

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 1160 of file w_library.c.

◆ library_tree()

GtkWidget * library_tree	(	GtkListStore *	store,
		int	id,
		gchar *	name )

create library tree store widget

Parameters

store	the list store model to use
id	selection id (0 = family, 1 = molecule)
name	column label

Definition at line 1015 of file w_library.c.

◆ on_realize()

G_MODULE_EXPORT void on_realize	(	GtkGLArea *	area,
		gpointer	data )

extern

◆ open_sml_file()

gchar * open_sml_file	(	const char *	filetoread,
		int	fam )

open 'Simple chemical library XML' file

Parameters

filetoread	the name of the file to open
fam	the molecular family

Definition at line 549 of file w_library.c.

◆ prepare_preview()

void prepare_preview	(	int	active,
		int	id,
		gboolean	visible )

prepare library molecule preview

Parameters

active	active project id
id	molecule id number
visible	is the 'model edition' window visible

Definition at line 912 of file w_library.c.

◆ replace_markup()

gchar * replace_markup	(	char *	init,
		char *	key,
		char *	rep )

replace pattern in string

Parameters

init	the string
key	the pattern to replace
rep	the new pattern

Definition at line 339 of file w_library.c.

◆ run_select_from_library()

G_MODULE_EXPORT void run_select_from_library	(	GtkDialog *	lib,
		gint	response_id,
		gpointer	data )

select from library - running the dialog

Parameters

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

Definition at line 1047 of file w_library.c.

◆ select_from_library()

int select_from_library	(	gboolean	visible,
		project *	this_proj,
		atom_search *	asearch )

select object to insert from the library

Parameters

visible	is the 'model edition' window visible
this_proj	the target project
asearch	the target atom search

Definition at line 1104 of file w_library.c.

◆ select_library_data()

G_MODULE_EXPORT void select_library_data	(	GtkTreeView *	tree_view,
		GtkTreePath *	path,
		GtkTreeViewColumn *	column,
		gpointer	data )

select library element callback

Parameters

tree_view	the GtkTreeView sending the signal
path	the path in the tree view
column	the column in the tree view
data	the associated data pointer

Definition at line 960 of file w_library.c.

◆ set_library_markup()

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

set font markup in the molecular library 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 998 of file w_library.c.

◆ sml_preview()

int sml_preview ( const char * filetoread )

retrieve preview information from 'Simple chemical library XML' file

Parameters

filetoread the name of the file to read

Definition at line 414 of file w_library.c.

◆ sort_files()

void sort_files ( int num_f )

sort file(s) by molecular family and name

Parameters

num_f number of file(s) to sort

Definition at line 626 of file w_library.c.

◆ substitute_string()

gchar * substitute_string	(	gchar *	init,
		gchar *	o_motif,
		gchar *	n_motif )

substitute all patterns in string

Parameters

init	the initial string
o_motif	the pattern to replace
n_motif	the new pattern

Definition at line 372 of file w_library.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.

Variable Documentation

◆ family_dir

gchar* family_dir[FAMILY]

Initial value:

={"Misc",
                            "Alcohols",
                            "Aldehydes",
                            "Alkanes",
                            "Alkenes",
                            "Alkynes",
                            "Amides",
                            "Amines",
                            "Amino_acids",
                            "Aromatics",
                            "Carboxylic_acids",
                            "Cyclic_alkanes",
                            "Cyclic_alkenes",
                            "Ethers",
                            "Fatty_acids",
                            "Fullerenes",
                            "Heterocyclics",
                            "Macrocycles",
                            "Ketones",
                            "Nitriles",
                            "Nucleobases",
                            "Steroids",
                            "Linear_sugars",
                            "Cyclic_sugars",
                            "Sulfoxides",
                            "Thiols"}

Definition at line 242 of file w_library.c.

◆ family_list

gchar* family_list[FAMILY]

Initial value:

={"Misc",
                             "Alcohols",
                             "Aldehydes",
                             "Alkanes",
                             "Alkenes",
                             "Alkynes",
                             "Amides",
                             "Amines",
                             "Amino acids",
                             "Aromatics",
                             "Carboxylic acids",
                             "Cyclic alkanes",
                             "Cyclic alkenes",
                             "Ethers",
                             "Fatty acids",
                             "Fullerenes",
                             "Heterocyclics",
                             "Macrocycles",
                             "Ketones",
                             "Nitriles",
                             "Nucleobases",
                             "Steroids",
                             "Sugars (Linears)",
                             "Sugars (Cyclics)",
                             "Sulfoxides",
                             "Thiols"}

Definition at line 215 of file w_library.c.

◆ family_store

GtkListStore* family_store

Definition at line 281 of file w_library.c.

◆ first_family_iter

GtkTreeIter first_family_iter

Definition at line 282 of file w_library.c.

◆ first_mol_iter

GtkTreeIter first_mol_iter

Definition at line 284 of file w_library.c.

◆ inserted_from_lib

int inserted_from_lib

Definition at line 295 of file w_library.c.

◆ lib_preview_box

GtkWidget* lib_preview_box = NULL

Definition at line 290 of file w_library.c.

◆ lib_preview_plot

GtkWidget* lib_preview_plot = NULL

Definition at line 291 of file w_library.c.

◆ lib_proj

project* lib_proj = NULL

Definition at line 292 of file w_library.c.

◆ lib_res

gboolean lib_res

Definition at line 1035 of file w_library.c.

◆ lib_visible

gboolean lib_visible

Definition at line 1036 of file w_library.c.

◆ libselect

GtkTreeSelection* libselect[2]

Definition at line 285 of file w_library.c.

◆ mol

insertion_menu mol[]

Initial value:

= {
    { "Atom", NULL, -1, 0 },
    { NULL, "H", 1, 1 },
    { NULL, "B", 5, 1 },
    { NULL, "C", 6, 1 },
    { NULL, "N", 7, 1 },
    { NULL, "O", 8, 1 },
    { NULL, "F", 9, 1 },
    { NULL, "S", 16, 1 },
    { NULL, "Cl", 17, 1 },
    { NULL, "Other ...", -1, 1 },
    { "Library", NULL, -1, 0 },
    { NULL, "H<sub>2</sub>O", -1, 3 },
    { NULL, "CH<sub>4</sub>", -1, 5 },
    { NULL, "Toluene", -1, 15 },
    { NULL, "Cp", -1, 10 },
    { NULL, "C<sub>60</sub>", -1,  60},
    { NULL, "Ni-Phthalocyanine", -1, 57 },
    { NULL, "More ...", -1, -1 },
    { NULL, NULL, -1, 0 }}

Definition at line 193 of file w_library.c.

◆ mol_name

gchar** mol_name

Definition at line 289 of file w_library.c.

◆ molecule_store

GtkListStore* molecule_store

Definition at line 283 of file w_library.c.

◆ o_names

int o_names

Definition at line 294 of file w_library.c.

◆ other_name

gchar* other_name[5]

Definition at line 293 of file w_library.c.

◆ periodic_table_info

element_data periodic_table_info[]

Definition at line 71 of file w_library.c.

◆ remove_search

atom_search* remove_search

extern

Definition at line 174 of file popup.c.

◆ sml_file_name

gchar** sml_file_name

Definition at line 288 of file w_library.c.

◆ the_family

int the_family

Definition at line 286 of file w_library.c.

◆ the_molecule

gchar* the_molecule

Definition at line 287 of file w_library.c.

Macros

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ FAMILY

Function Documentation

◆ action_atoms_from_project()

◆ check_xml_string()

◆ clean_xml_data()

◆ create_3d_model()

◆ create_object_from_library()

◆ fill_family_tree()

◆ fill_molecule_tree()

◆ findnode()

◆ get_family()

◆ get_sml_files()

◆ get_z_from_periodic_table()

◆ insert_preview()

◆ insert_this_project_from_lib()

◆ library_tree()

◆ on_realize()

◆ open_sml_file()

◆ prepare_preview()

◆ replace_markup()

◆ run_select_from_library()

◆ select_from_library()

◆ select_library_data()

◆ set_library_markup()

◆ sml_preview()

◆ sort_files()

◆ substitute_string()

◆ to_insert_in_project()

Variable Documentation

◆ family_dir

◆ family_list

◆ family_store

◆ first_family_iter

◆ first_mol_iter

◆ inserted_from_lib

◆ lib_preview_box

◆ lib_preview_plot

◆ lib_proj

◆ lib_res

◆ lib_visible

◆ libselect

◆ mol

◆ mol_name

◆ molecule_store

◆ o_names

◆ other_name

◆ periodic_table_info

◆ remove_search

◆ sml_file_name

◆ the_family

◆ the_molecule