diff options
| -rw-r--r-- | src/lib/tng_io.c | 152 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 72 | ||||
| -rw-r--r-- | src/tests/tng_io_read_pos.c | 10 |
3 files changed, 231 insertions, 3 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 708fc3d..47f215b 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -5471,6 +5471,110 @@ tng_function_status tng_molecule_name_of_particle_nr_get return(TNG_SUCCESS); } +tng_function_status tng_chain_name_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + char *name, + int max_len) +{ + int64_t cnt = 0, i, *molecule_cnt_list; + tng_molecule_t mol; + tng_atom_t atom; + tng_bool found = FALSE; + + if(tng_data->var_num_atoms_flag) + { + molecule_cnt_list = tng_data->current_trajectory_frame_set. + molecule_cnt_list; + } + else + { + molecule_cnt_list = tng_data->molecule_cnt_list; + } + + for(i = 0; i < tng_data->n_molecules; i++) + { + mol = &tng_data->molecules[i]; + if(cnt + mol->n_atoms * molecule_cnt_list[i] - 1 < nr) + { + cnt += mol->n_atoms * molecule_cnt_list[i]; + continue; + } + atom = &mol->atoms[nr % mol->n_atoms]; + found = TRUE; + break; + } + if(!found) + { + return(TNG_FAILURE); + } + if(!atom->residue || atom->residue->chain) + { + return(TNG_FAILURE); + } + + strncpy(name, atom->residue->chain->name, max_len - 1); + name[max_len - 1] = 0; + + if(strlen(atom->residue->chain->name) > max_len - 1) + { + return(TNG_FAILURE); + } + return(TNG_SUCCESS); +} + +tng_function_status tng_residue_name_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + char *name, + int max_len) +{ + int64_t cnt = 0, i, *molecule_cnt_list; + tng_molecule_t mol; + tng_atom_t atom; + tng_bool found = FALSE; + + if(tng_data->var_num_atoms_flag) + { + molecule_cnt_list = tng_data->current_trajectory_frame_set. + molecule_cnt_list; + } + else + { + molecule_cnt_list = tng_data->molecule_cnt_list; + } + + for(i = 0; i < tng_data->n_molecules; i++) + { + mol = &tng_data->molecules[i]; + if(cnt + mol->n_atoms * molecule_cnt_list[i] - 1 < nr) + { + cnt += mol->n_atoms * molecule_cnt_list[i]; + continue; + } + atom = &mol->atoms[nr % mol->n_atoms]; + found = TRUE; + break; + } + if(!found) + { + return(TNG_FAILURE); + } + if(!atom->residue) + { + return(TNG_FAILURE); + } + + strncpy(name, atom->residue->name, max_len - 1); + name[max_len - 1] = 0; + + if(strlen(atom->residue->name) > max_len - 1) + { + return(TNG_FAILURE); + } + return(TNG_SUCCESS); +} + tng_function_status tng_atom_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, @@ -5519,6 +5623,54 @@ tng_function_status tng_atom_name_of_particle_nr_get return(TNG_SUCCESS); } +tng_function_status tng_atom_type_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + char *type, + int max_len) +{ + int64_t cnt = 0, i, *molecule_cnt_list; + tng_molecule_t mol; + tng_atom_t atom; + tng_bool found = FALSE; + + if(tng_data->var_num_atoms_flag) + { + molecule_cnt_list = tng_data->current_trajectory_frame_set. + molecule_cnt_list; + } + else + { + molecule_cnt_list = tng_data->molecule_cnt_list; + } + + for(i = 0; i < tng_data->n_molecules; i++) + { + mol = &tng_data->molecules[i]; + if(cnt + mol->n_atoms * molecule_cnt_list[i] - 1 < nr) + { + cnt += mol->n_atoms * molecule_cnt_list[i]; + continue; + } + atom = &mol->atoms[nr % mol->n_atoms]; + found = TRUE; + break; + } + if(!found) + { + return(TNG_FAILURE); + } + + strncpy(type, atom->atom_type, max_len - 1); + type[max_len - 1] = 0; + + if(strlen(atom->atom_type) > max_len - 1) + { + return(TNG_FAILURE); + } + return(TNG_SUCCESS); +} + tng_function_status tng_particle_mapping_add (tng_trajectory_t tng_data, const int64_t num_first_particle, diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index c00abc0..0530112 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -1341,6 +1341,54 @@ tng_function_status tng_molecule_name_of_particle_nr_get_ } /** + * @brief Get the chain name of real particle number (number in mol system). + * @param tng_data is the trajectory data container containing the atom. + * @param nr is the real number of the particle in the molecular system. + * @param name is a string, which is set to the name of the chain. Memory + * must be reserved beforehand. + * @param max_len is the maximum length of name. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error + * has occured. + */ +tng_function_status tng_chain_name_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + char *name, + int max_len); +tng_function_status tng_chain_name_of_particle_nr_get_ + (const tng_trajectory_t tng_data, + const int64_t nr, + char *name, + int max_len) +{ + return(tng_chain_name_of_particle_nr_get(tng_data, nr, name, max_len)); +} + +/** + * @brief Get the residue name of real particle number (number in mol system). + * @param tng_data is the trajectory data container containing the atom. + * @param nr is the real number of the particle in the molecular system. + * @param name is a string, which is set to the name of the residue. Memory + * must be reserved beforehand. + * @param max_len is the maximum length of name. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error + * has occured. + */ +tng_function_status tng_residue_name_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + char *name, + int max_len); +tng_function_status tng_residue_name_of_particle_nr_get_ + (const tng_trajectory_t tng_data, + const int64_t nr, + char *name, + int max_len) +{ + return(tng_residue_name_of_particle_nr_get(tng_data, nr, name, max_len)); +} + +/** * @brief Get the atom name of real particle number (number in mol system). * @param tng_data is the trajectory data container containing the atom. * @param nr is the real number of the particle in the molecular system. @@ -1365,6 +1413,30 @@ tng_function_status tng_atom_name_of_particle_nr_get_ } /** + * @brief Get the atom type of real particle number (number in mol system). + * @param tng_data is the trajectory data container containing the atom. + * @param nr is the real number of the particle in the molecular system. + * @param type is a string, which is set to the type of the atom. Memory + * must be reserved beforehand. + * @param max_len is the maximum length of type. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error + * has occured. + */ +tng_function_status tng_atom_type_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + char *type, + int max_len); +tng_function_status tng_atom_type_of_particle_nr_get_ + (const tng_trajectory_t tng_data, + const int64_t nr, + char *type, + int max_len) +{ + return(tng_atom_type_of_particle_nr_get(tng_data, nr, type, max_len)); +} + +/** * @brief Add a particle mapping table. * @details Each particle mapping table will be written as a separate block, * followed by the data blocks for the corresponding particles. In most cases diff --git a/src/tests/tng_io_read_pos.c b/src/tests/tng_io_read_pos.c index 5d3be64..54193eb 100644 --- a/src/tests/tng_io_read_pos.c +++ b/src/tests/tng_io_read_pos.c @@ -12,7 +12,7 @@ int main(int argc, char **argv) int64_t particle = 0; // Set a default frame range int first_frame = 0, last_frame = 50; - char name[64]; + char atom_name[64], res_name[64]; if(argc <= 1) { @@ -50,10 +50,14 @@ int main(int argc, char **argv) n_frames = last_frame - first_frame + 1; - if(tng_atom_name_of_particle_nr_get(traj, particle, name, sizeof(name)) == + if(tng_atom_name_of_particle_nr_get(traj, particle, atom_name, + sizeof(atom_name)) == + TNG_SUCCESS && + tng_residue_name_of_particle_nr_get(traj, particle, res_name, + sizeof(res_name)) == TNG_SUCCESS) { - printf("Particle: %s\n", name); + printf("Particle: %s (%s)\n", atom_name, res_name); } else { |