atomes 1.1.14
atomes: an atomic scale modeling tool box
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Functions to create atomic objects. More...
#include "atom_edit.h"
Go to the source code of this file.
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 |
Functions to create atomic objects.
Definition in file atom_object.c.
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
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.
void adjust_object_frag_coord | ( | atomic_object * | object | ) |
adjust object number of fragment(s)
object | the target insert object |
Definition at line 973 of file atom_object.c.
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
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.
void clean_object_vois | ( | project * | this_proj, |
atomic_object * | object, | ||
int * | new_id, | ||
gboolean | movtion ) |
clean the object neigbours list
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.
void clean_this_object | ( | int | orig, |
int | act, | ||
project * | this_proj, | ||
atom_search * | asearch ) |
clean object data
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.
void correct_coordinates_for_object | ( | project * | this_proj, |
atomic_object * | this_object, | ||
gboolean | upcoord ) |
correct the atomic coordinates for 'this_object'
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.
void correct_pos_and_get_dim | ( | atomic_object * | object, |
gboolean | adjust ) |
get the barycenter of the atomic coordinates of an object
object | the target insert object |
adjust | center object coordinates or not |
Definition at line 104 of file atom_object.c.
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
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.
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
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.
void create_object_from_library | ( | int | p | ) |
create object using the molecular library
p | the project id of the library molecule in the workspace |
Definition at line 421 of file atom_object.c.
int create_object_from_open_project | ( | project * | this_proj, |
int | p ) |
create object from atom(s) of a project opened in the workspace
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.
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
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.
atomic_object * create_object_from_selection | ( | project * | this_proj | ) |
create object from atom selection
this_proj | the target project |
Definition at line 724 of file atom_object.c.
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
this_proj | the target project |
sid | the species id |
remove | remove search, if any |
Definition at line 683 of file atom_object.c.
atomic_object * duplicate_atomic_object | ( | atomic_object * | old_obj | ) |
duplicate an insert object
old_obj | the insert object to duplicate |
Definition at line 381 of file atom_object.c.
int * duplicate_z | ( | int | species, |
double * | old_z ) |
duplicate z table when creating an object, integer is preferred to avoid comparison errors during action
species | the number of chemical species |
old_z | the old z table to duplicate |
Definition at line 663 of file atom_object.c.
double get_object_dim | ( | atomic_object * | object | ) |
int in_object_bond_list | ( | atomic_object * | object, |
int | aid, | ||
int | bid ) |
is there a bond between atom aid and atom bid ?
object | the target insert object |
aid | 1st atom id |
bid | 2nd atom id |
Definition at line 466 of file atom_object.c.
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
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.
void reconstruct_bonds | ( | project * | this_proj, |
int | ifcl, | ||
int * | bcid ) |
reconstruct the project bond(s)/clone(s) lists after reconstruction using PBC
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.
void reconstruct_coordinates_for_object | ( | project * | this_proj, |
atomic_object * | this_object, | ||
gboolean | upcoord ) |
reconstruct object atomic coordinates using PBC
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.
void to_insert_in_project | ( | int | stat, |
int | orig, | ||
project * | this_proj, | ||
atom_search * | asearch, | ||
gboolean | visible ) |
to insert object in project
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.
shift insertion position for object not to have overlapping objects for multiple/repeated insertions
view | the target glwin |
Definition at line 354 of file atom_object.c.
int being_copied |
Definition at line 371 of file atom_object.c.
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extern |
Definition at line 280 of file read_cif.c.
atomic_object* lib_object |
Definition at line 372 of file atom_object.c.