diff options
| -rw-r--r-- | include/tng_io.h | 47 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 148 |
2 files changed, 194 insertions, 1 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index f13563b..8f6fcef 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1288,6 +1288,23 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add tng_chain_t *chain); /** + * @brief Add a bond between two atoms to a molecule. + * @param tng_data is the trajectory data container containing the molecule. + * @param molecule is the molecule containing the atoms to connect. + * @param from_atom_id is the id of one of the two atoms in the bond. + * @param to_atom_id is the id of the other atom in the bond. + * @param bond is a pointer to the newly created bond. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (!) if a minor error + * has occured or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add + (const tng_trajectory_t tng_data, + tng_molecule_t molecule, + const int64_t from_atom_id, + const int64_t to_atom_id, + tng_bond_t *bond); + +/** * @brief Set the name of a chain. * @param tng_data is the trajectory data container containing the atom.. * @param chain is the chain to rename. @@ -1443,6 +1460,19 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get int max_len); /** + * @brief Get the molecule id 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 id is will be set to the id of the molecule. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error + * has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + int64_t *id); + +/** * @brief Get the bonds of the current molecular system. * @param tng_data is the trajectory data container containing the molecular * system. @@ -1497,7 +1527,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get int max_len); /** - * @brief Get the residue id of real particle number (number in mol system). + * @brief Get the residue id (local to molecule) 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 id is a pointer to the variable, which will be set to the ID. @@ -1510,6 +1541,20 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get int64_t *id); /** + * @brief Get the residue id (based on other molecules and molecule counts) + * 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 id is a pointer to the variable, which will be set to the ID. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error + * has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + int64_t *id); + +/** * @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. diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index d7bc988..26c8986 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -7329,6 +7329,63 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add return(stat); } +tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add + (const tng_trajectory_t tng_data, + tng_molecule_t molecule, + const int64_t from_atom_id, + const int64_t to_atom_id, + tng_bond_t *bond) +{ + int64_t i; + tng_bond_t new_bonds; + tng_function_status stat; + + stat = tng_check_trajectory_container(tng_data); + if(stat != TNG_SUCCESS) + { + printf("Trajectory container not properly setup. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } + + for(i = 0; i < molecule->n_bonds; i++) + { + *bond = &molecule->bonds[i]; + /* Check if the bond already exists */ + if(((*bond)->from_atom_id == from_atom_id && (*bond)->to_atom_id == to_atom_id) || + ((*bond)->to_atom_id == from_atom_id && (*bond)->from_atom_id == to_atom_id)) + { + return(TNG_SUCCESS); + } + } + + new_bonds = realloc(molecule->bonds, + sizeof(struct tng_bond) * + (molecule->n_bonds + 1)); + + if(!new_bonds) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(struct tng_bond) * (molecule->n_bonds + 1), + __FILE__, __LINE__); + *bond = 0; + free(molecule->bonds); + molecule->bonds = 0; + return(TNG_CRITICAL); + } + + molecule->bonds = new_bonds; + + *bond = &new_bonds[molecule->n_bonds]; + + (*bond)->from_atom_id = from_atom_id; + (*bond)->to_atom_id = to_atom_id; + + molecule->n_bonds++; + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_chain_name_set (tng_trajectory_t tng_data, tng_chain_t chain, @@ -7768,6 +7825,47 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + int64_t *id) +{ + int64_t cnt = 0, i, *molecule_cnt_list = 0; + tng_molecule_t mol; + tng_bool found = TNG_FALSE; + tng_function_status stat; + + stat = tng_check_trajectory_container(tng_data); + if(stat != TNG_SUCCESS) + { + printf("Trajectory container not properly setup. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } + + tng_molecule_cnt_list_get(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; + } + found = TNG_TRUE; + break; + } + if(!found) + { + return(TNG_FAILURE); + } + + *id = mol->id; + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get (const tng_trajectory_t tng_data, int64_t *n_bonds, @@ -7989,6 +8087,56 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get + (const tng_trajectory_t tng_data, + const int64_t nr, + int64_t *id) +{ + int64_t cnt = 0, i, offset = 0, *molecule_cnt_list = 0; + tng_molecule_t mol; + tng_atom_t atom; + tng_bool found = TNG_FALSE; + tng_function_status stat; + + stat = tng_check_trajectory_container(tng_data); + if(stat != TNG_SUCCESS) + { + printf("Trajectory container not properly setup. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } + + tng_molecule_cnt_list_get(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]; + offset += mol->n_residues * molecule_cnt_list[i]; + continue; + } + atom = &mol->atoms[nr % mol->n_atoms]; + found = TNG_TRUE; + break; + } + if(!found) + { + return(TNG_FAILURE); + } + if(!atom->residue) + { + return(TNG_FAILURE); + } + + offset += mol->n_residues * ((nr - cnt) / mol->n_atoms); + + *id = atom->residue->id + offset; + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, |