diff options
| -rw-r--r-- | src/lib/tng_io.c | 150 |
1 files changed, 61 insertions, 89 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 222156a..658f9e4 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -7601,29 +7601,19 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add const char *name, tng_molecule_t *molecule) { - int64_t id, i; - tng_bool found_id = TNG_TRUE; + int64_t id; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); - /* Find an unused ID */ - id = 0; - while(found_id) + /* Set ID to the ID of the last molecule + 1 */ + if(tng_data->n_molecules) { - found_id = TNG_FALSE; - for(i = 0; i < tng_data->n_molecules; i++) - { - if(tng_data->molecules[i].id == id) - { - found_id = TNG_TRUE; - i = 0; - } - } - if(found_id) - { - id++; - } + id = tng_data->molecules[tng_data->n_molecules-1].id + 1; + } + else + { + id = 1; } return(tng_molecule_w_id_add(tng_data, name, id, molecule)); @@ -7636,7 +7626,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add tng_molecule_t *molecule) { tng_molecule_t new_molecules; - int64_t *new_molecule_cnt_list, i; + int64_t *new_molecule_cnt_list; tng_function_status stat = TNG_SUCCESS; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -7682,17 +7672,6 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add /* FIXME: Should this be a function argument instead? */ tng_data->molecule_cnt_list[tng_data->n_molecules] = 0; - for(i = 0; i < tng_data->n_molecules; i++) - { - if(tng_data->molecules[i].id == id) - { - stat = TNG_FAILURE; - fprintf(stderr, "TNG library: Molecule ID %"PRId64" already in use. %s: %d\n", id, - __FILE__, __LINE__); - break; - } - } - (*molecule)->id = id; tng_data->n_molecules++; @@ -7704,29 +7683,19 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add (tng_trajectory_t tng_data, tng_molecule_t *molecule_p) { - tng_bool found_id = TNG_TRUE; + int64_t *new_molecule_cnt_list, id; tng_molecule_t new_molecules, molecule; - int64_t *new_molecule_cnt_list, i, id; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - /* Find an unused ID */ - id = 0; - while(found_id) + /* Set ID to the ID of the last molecule + 1 */ + if(tng_data->n_molecules) { - found_id = TNG_FALSE; - for(i = 0; i < tng_data->n_molecules; i++) - { - if(tng_data->molecules[i].id == id) - { - found_id = TNG_TRUE; - i = 0; - } - } - if(found_id) - { - id++; - } + id = tng_data->molecules[tng_data->n_molecules-1].id + 1; + } + else + { + id = 1; } new_molecules = realloc(tng_data->molecules, @@ -7919,7 +7888,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_find n_molecules = tng_data->n_molecules; - for(i = 0; i < n_molecules; i++) + for(i = n_molecules - 1; i >= 0; i--) { *molecule = &tng_data->molecules[i]; if(name[0] == 0 || strcmp(name, (*molecule)->name) == 0) @@ -8197,7 +8166,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find n_chains = molecule->n_chains; - for(i = 0; i < n_chains; i++) + for(i = n_chains - 1; i > 0; i--) { *chain = &molecule->chains[i]; if(name[0] == 0 || strcmp(name, (*chain)->name) == 0) @@ -8220,11 +8189,23 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add const char *name, tng_chain_t *chain) { + int64_t id; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); + /* Set ID to the ID of the last chain + 1 */ + if(molecule->n_chains) + { + id = molecule->chains[molecule->n_chains-1].id + 1; + } + else + { + id = 1; + } + return(tng_molecule_chain_w_id_add(tng_data, molecule, name, - molecule->n_chains + 1, chain)); + id, chain)); } tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add @@ -8234,7 +8215,6 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add const int64_t id, tng_chain_t *chain) { - int64_t i; tng_chain_t new_chains; tng_function_status stat = TNG_SUCCESS; @@ -8265,16 +8245,6 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add (*chain)->molecule = molecule; (*chain)->n_residues = 0; - for(i = 0; i < molecule->n_chains; i++) - { - if(molecule->chains[i].id == id) - { - stat = TNG_FAILURE; - fprintf(stderr, "TNG library: Chain ID already in use. %s: %d\n", __FILE__, __LINE__); - break; - } - } - molecule->n_chains++; (*chain)->id = id; @@ -8345,7 +8315,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_find n_atoms = molecule->n_atoms; - for(i = 0; i < n_atoms; i++) + for(i = n_atoms - 1; i >= 0; i--) { *atom = &molecule->atoms[i]; if(name[0] == 0 || strcmp(name, (*atom)->name) == 0) @@ -8463,7 +8433,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find n_residues = chain->n_residues; - for(i = 0; i < n_residues; i++) + for(i = n_residues - 1; i >= 0; i--) { *residue = &chain->residues[i]; if(name[0] == 0 || strcmp(name, (*residue)->name) == 0) @@ -8486,11 +8456,23 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add const char *name, tng_residue_t *residue) { + int64_t id; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); + /* Set ID to the ID of the last residue + 1 */ + if(chain->n_residues) + { + id = chain->residues[chain->n_residues-1].id + 1; + } + else + { + id = 0; + } + return(tng_chain_residue_w_id_add(tng_data, chain, name, - chain->n_residues + 1, residue)); + id, residue)); } tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add @@ -8500,7 +8482,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add const int64_t id, tng_residue_t *residue) { - int64_t i, curr_index; + int64_t curr_index; tng_residue_t new_residues, temp_residue, last_residue; tng_molecule_t molecule = chain->molecule; tng_function_status stat = TNG_SUCCESS; @@ -8570,16 +8552,6 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add (*residue)->n_atoms = 0; (*residue)->atoms_offset = 0; - for(i = 0; i < chain->n_residues; i++) - { - if(chain->residues[i].id == id) - { - stat = TNG_FAILURE; - fprintf(stderr, "TNG library: Residue ID already in use. %s: %d\n", __FILE__, __LINE__); - break; - } - } - chain->n_residues++; molecule->n_residues++; @@ -8694,13 +8666,24 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add const char *atom_type, tng_atom_t *atom) { + int64_t id; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(atom_name, "TNG library: atom_name must not be a NULL pointer."); TNG_ASSERT(atom_type, "TNG library: atom_type must not be a NULL pointer."); + /* Set ID to the ID of the last atom + 1 */ + if(residue->chain->molecule->n_atoms) + { + id = residue->chain->molecule->atoms[residue->chain->molecule->n_atoms-1].id + 1; + } + else + { + id = 0; + } + return(tng_residue_atom_w_id_add(tng_data, residue, atom_name, atom_type, - residue->chain->molecule->n_atoms + 1, - atom)); + id, atom)); } tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add @@ -8711,7 +8694,6 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add const int64_t id, tng_atom_t *atom) { - int64_t i; tng_atom_t new_atoms; tng_molecule_t molecule = residue->chain->molecule; tng_function_status stat = TNG_SUCCESS; @@ -8749,16 +8731,6 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add (*atom)->residue = residue; - for(i = 0; i < molecule->n_atoms; i++) - { - if(molecule->atoms[i].id == id) - { - stat = TNG_FAILURE; - fprintf(stderr, "TNG library: Atom ID %"PRId64" already in use. %s: %d\n", id, __FILE__, __LINE__); - break; - } - } - residue->n_atoms++; molecule->n_atoms++; |