diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 125 |
1 files changed, 125 insertions, 0 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 536403d..9c6ce0f 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -7291,6 +7291,131 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_of_index_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t tng_data_src, + tng_trajectory_t tng_data_dest) +{ + tng_molecule_t molecule, molecule_temp; + tng_chain_t chain, chain_temp; + tng_residue_t residue, residue_temp; + tng_atom_t atom, atom_temp; + tng_bond_t bond_temp; + tng_function_status stat; + int64_t i, j, k, l, *list_temp; + + TNG_ASSERT(tng_data_src, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(tng_data_dest, "TNG library: Trajectory container not properly setup."); + + for(i = 0; i < tng_data_dest->n_molecules; i++) + { + molecule = &tng_data_dest->molecules[i]; + tng_molecule_destroy(tng_data_dest, molecule); + } + + tng_data_dest->n_molecules = tng_data_src->n_molecules; + + molecule_temp = realloc(tng_data_dest->molecules, + sizeof(struct tng_molecule) * tng_data_dest->n_molecules); + if(!molecule_temp) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(struct tng_molecule) * tng_data_dest->n_molecules, + __FILE__, __LINE__); + free(tng_data_dest->molecules); + tng_data_dest->molecules = 0; + return(TNG_CRITICAL); + } + list_temp = realloc(tng_data_dest->molecule_cnt_list, + sizeof(int64_t) * tng_data_dest->n_molecules); + if(!list_temp) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * tng_data_dest->n_molecules, + __FILE__, __LINE__); + free(tng_data_dest->molecule_cnt_list); + tng_data_dest->molecule_cnt_list = 0; + free(molecule_temp); + return(TNG_CRITICAL); + } + + tng_data_dest->molecules = molecule_temp; + tng_data_dest->molecule_cnt_list = list_temp; + + for(i = 0; i < tng_data_dest->n_molecules; i++) + { + molecule = &tng_data_src->molecules[i]; + stat = tng_molecule_w_id_add(tng_data_dest, molecule->name, molecule->id, + &molecule_temp); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Cannot create new molecule to make a copy."); + return(stat); + } + molecule_temp->quaternary_str = molecule->quaternary_str; + for(j = 0; j < molecule->n_chains; j++) + { + chain = &molecule->chains[j]; + stat = tng_molecule_chain_w_id_add(tng_data_dest, molecule_temp, + chain->name, chain->id, + &chain_temp); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Cannot create new chain to make a copy."); + return(stat); + } + for(k = 0; k < chain->n_residues; k++) + { + residue = &chain->residues[k]; + stat = tng_chain_residue_w_id_add(tng_data_dest, chain_temp, + residue->name, residue->id, + &residue_temp); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Cannot create new residue to make a copy."); + return(stat); + } + for(l = 0; l < residue->n_atoms; l++) + { + atom = &molecule->atoms[residue->atoms_offset + l]; + stat = tng_residue_atom_w_id_add(tng_data_dest, residue_temp, + atom->name, atom->atom_type, + atom->id, &atom_temp); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Cannot create new atom to make a copy."); + return(stat); + } + } + } + } + molecule_temp->n_bonds = molecule->n_bonds; + bond_temp = realloc(molecule_temp->bonds, sizeof(struct tng_bond) * + molecule->n_bonds); + if(!bond_temp) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(struct tng_bond) * molecule->n_bonds, + __FILE__, __LINE__); + free(molecule_temp->bonds); + molecule_temp->n_bonds = 0; + return(TNG_CRITICAL); + } + molecule_temp->bonds = bond_temp; + for(j = 0; j < molecule->n_bonds; j++) + { + molecule_temp->bonds[j] = molecule->bonds[j]; + } + stat = tng_molecule_cnt_set(tng_data_dest, molecule_temp, + tng_data_src->molecule_cnt_list[i]); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Cannot set molecule count. %s: %d.\n", + __FILE__, __LINE__); + return(stat); + } + } + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find (tng_trajectory_t tng_data, tng_molecule_t molecule, |