atom_object.c File Reference

Functions to create atomic objects. More...

#include "atom_edit.h"

Include dependency graph for atom_object.c:

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Functions
double	get_object_dim (atomic_object *object)
	get estimate of an object dimension
void	correct_pos_and_get_dim (atomic_object *object, gboolean adjust)
	get the barycenter of the atomic coordinates of an object
gboolean	rebuild_atom_neighbors (project *this_proj, int step, atomic_object *object, int target, int aid, atom *at, gboolean *checked_at)
	rebuild target atom id coordinates using PBC
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
void	correct_coordinates_for_object (project *this_proj, atomic_object *this_object, gboolean upcoord)
	correct the atomic coordinates for 'this_object'
tint	ulam_coord (glwin *view)
	shift insertion position for object not to have overlapping objects for multiple/repeated insertions
atomic_object *	duplicate_atomic_object (atomic_object *old_obj)
	duplicate an insert object
void	create_object_from_library (int p)
	create object using the molecular library
int	in_object_bond_list (atomic_object *object, int aid, int bid)
	is there a bond between atom aid and atom bid ?
void	clean_object_vois (project *this_proj, atomic_object *object, int *new_id, gboolean movtion)
	clean the object neigbours list
void	clean_object_bonds (project *proj, int o_step, atomic_object *object, int *new_id, gboolean movtion)
	create the object bond list, and adjust the bond's atom id
void	add_object_atoms (atomic_object *this_object, project *this_proj, int o_step, int numa, int *old_id, gboolean check_bonding, atom_search *remove)
	add atom list to insert object
int *	duplicate_z (int species, double *old_z)
	duplicate z table when creating an object, integer is preferred to avoid comparison errors during action
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
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	adjust_object_frag_coord (atomic_object *object)
	adjust object number of fragment(s)
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

Variables
atomic_object *	cif_object
int	being_copied
atomic_object *	lib_object

Detailed Description

Functions to create atomic objects.

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_object.c.

Function Documentation

add_object_atoms()

void add_object_atoms	(	atomic_object *	this_object,
		project *	this_proj,
		int	o_step,
		int	numa,
		int *	old_id,
		gboolean	alloc_new_id,
		atom_search *	remove )

add atom list to insert object

Parameters

this_object	the target insert object
this_proj	the target project
o_step	the MD step
numa	number of atom(s)
old_id	list of atom's old id in the project 'this_proj'
alloc_new_id	check_bonding check bonding ? (partial copy or not)
remove	remove search, if any

Definition at line 621 of file atom_object.c.

adjust_object_frag_coord()

void adjust_object_frag_coord

(

atomic_object *

object

)

adjust object number of fragment(s)

Parameters

object

the target insert object

Definition at line 973 of file atom_object.c.

clean_object_bonds()

void clean_object_bonds	(	project *	proj,
		int	o_step,
		atomic_object *	object,
		int *	new_id,
		gboolean	movtion )

create the object bond list, and adjust the bond's atom id

Parameters

proj	the target project
o_step	the MD step
object	the target insert object
new_id	list of atom's old id in the project 'this_proj'
movtion	reconstruction of atomic coordinates using PBC ?

Definition at line 542 of file atom_object.c.

clean_object_vois()

void clean_object_vois	(	project *	this_proj,
		atomic_object *	object,
		int *	new_id,
		gboolean	movtion )

clean the object neigbours list

Parameters

this_proj	the target project
object	the target insert object
new_id	list of atom's old id in the project 'this_proj'
movtion	reconstruction of atomic coordinates using PBC ?

Definition at line 487 of file atom_object.c.

clean_this_object()

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

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.

correct_coordinates_for_object()

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

correct the atomic coordinates for 'this_object'

Parameters

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

Definition at line 325 of file atom_object.c.

correct_pos_and_get_dim()

void correct_pos_and_get_dim	(	atomic_object *	object,
		gboolean	adjust )

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_object_from_atom_coordination()

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

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 )

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

)

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 )

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 )

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

)

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 )

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.

duplicate_atomic_object()

atomic_object * duplicate_atomic_object

(

atomic_object *

old_obj

)

duplicate an insert object

Parameters

old_obj

the insert object to duplicate

Definition at line 381 of file atom_object.c.

duplicate_z()

int * duplicate_z	(	int	species,
		double *	old_z )

duplicate z table when creating an object, integer is preferred to avoid comparison errors during action

Parameters

species	the number of chemical species
old_z	the old z table to duplicate

Definition at line 663 of file atom_object.c.

get_object_dim()

double get_object_dim

(

atomic_object *

object

)

get estimate of an object dimension

Parameters

object

Definition at line 77 of file atom_object.c.

in_object_bond_list()

int in_object_bond_list	(	atomic_object *	object,
		int	aid,
		int	bid )

is there a bond between atom aid and atom bid ?

Parameters

object	the target insert object
aid	1st atom id
bid	2nd atom id

Definition at line 466 of file atom_object.c.

rebuild_atom_neighbors()

gboolean rebuild_atom_neighbors	(	project *	this_proj,
		int	step,
		atomic_object *	object,
		int	target,
		int	aid,
		atom *	at,
		gboolean *	checked_at )

rebuild target atom id coordinates using PBC

Parameters

this_proj	the target project
step	the MD step
object	the target insert object
target	the target atom id to correct
aid	the atom id
at	the target atom
checked_at	the list of already checked/corrected atom coordinates id

Definition at line 141 of file atom_object.c.

reconstruct_bonds()

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

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 )

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.

to_insert_in_project()

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

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.

ulam_coord()

tint ulam_coord

(

glwin *

view

)

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.

Variable Documentation

being_copied

int being_copied

Definition at line 371 of file atom_object.c.

cif_object

atomic_object* cif_object

extern

Definition at line 282 of file read_cif.c.

lib_object

atomic_object* lib_object

Definition at line 372 of file atom_object.c.