diff options
| -rw-r--r-- | include/tng_io.h | 156 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 137 |
2 files changed, 221 insertions, 72 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index c713fbd..16ba849 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1616,66 +1616,102 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t tng_trajectory_t tng_data_dest); /** - * @brief Get the chains of a molecule. + * @brief Get the number of chains in a molecule. * @param tng_data is the trajectory containing the molecule. - * @param molecule is the molecule of which to get the chains. - * @param chains is pointing to the list of chains. This is a pointer - * to the list of the molecule, which means that it should be handled - * carefully, e.g. not freed. + * @param molecule is the molecule of which to get the number of chains. * @param n is pointing to a value set to the number of chains. * @pre \code molecule != 0 \endcode The molecule must not be NULL. - * @pre \code chains != 0 \endcode The pointer to the list of chains must not - * be a NULL pointer. * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_chains_get +tng_function_status DECLSPECDLLEXPORT tng_molecule_num_chains_get (tng_trajectory_t tng_data, tng_molecule_t molecule, - tng_chain_t *chains, int64_t *n); /** - * @brief Get the residues of a molecule. + * @brief Retrieve the chain of a molecule with specified index in the list + * of chains. + * @param tng_data is the trajectory data container containing the molecule. + * @param index is the index (in molecule->chains) of the chain to return + * @param molecule is the molecule from which to get the chain. + * @param chain is a pointer to the chain if it was found - otherwise 0. + * @pre \code molecule != 0 \endcode molecule must not be a NULL pointer. + * @pre \code chain != 0 \endcode chain must not be a NULL pointer. + * @return TNG_SUCCESS (0) if the chain is found or TNG_FAILURE (1) if the + * chain is not found. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_of_index_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t index, + tng_chain_t *chain); + +/** + * @brief Get the number of residues in a molecule. * @param tng_data is the trajectory containing the molecule. - * @param molecule is the molecule of which to get the residues. - * @param residues is pointing to the list of residues. This is a pointer - * to the list of the molecule, which means that it should be handled - * carefully, e.g. not freed. + * @param molecule is the molecule of which to get the number residues. * @param n is pointing to a value set to the number of residues. * @pre \code molecule != 0 \endcode The molecule must not be NULL. - * @pre \code residues != 0 \endcode The pointer to the list of residues must not - * be a NULL pointer. * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_residues_get +tng_function_status DECLSPECDLLEXPORT tng_molecule_num_residues_get (tng_trajectory_t tng_data, tng_molecule_t molecule, - tng_residue_t *residues, int64_t *n); /** - * @brief Get the atoms of a molecule. + * @brief Retrieve the residue of a molecule with specified index in the list + * of chains. + * @param tng_data is the trajectory data container containing the molecule. + * @param index is the index (in molecule->residues) of the residue to return + * @param molecule is the molecule from which to get the residue. + * @param residue is a pointer to the residue if it was found - otherwise 0. + * @pre \code molecule != 0 \endcode molecule must not be a NULL pointer. + * @pre \code residue != 0 \endcode residue must not be a NULL pointer. + * @return TNG_SUCCESS (0) if the residue is found or TNG_FAILURE (1) if the + * residue is not found. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_residue_of_index_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t index, + tng_residue_t *residue); + +/** + * @brief Get the number of atoms in a molecule. * @param tng_data is the trajectory containing the molecule. - * @param molecule is the molecule of which to get the atoms. - * @param atoms is pointing to the list of atoms. This is a pointer - * to the list of the molecule, which means that it should be handled - * carefully, e.g. not freed. + * @param molecule is the molecule of which to get the number of atoms. * @param n is pointing to a value set to the number of atoms. * @pre \code molecule != 0 \endcode The molecule must not be NULL. - * @pre \code atoms != 0 \endcode The pointer to the list of atoms must not - * be a NULL pointer. * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_atoms_get +tng_function_status DECLSPECDLLEXPORT tng_molecule_num_atoms_get (tng_trajectory_t tng_data, tng_molecule_t molecule, - tng_atom_t *atoms, int64_t *n); /** + * @brief Retrieve the atom of a molecule with specified index in the list + * of atoms. + * @param tng_data is the trajectory data container containing the molecule. + * @param index is the index (in molecule->atoms) of the atom to return + * @param molecule is the molecule from which to get the atom. + * @param atom is a pointer to the atom if it was found - otherwise 0. + * @pre \code molecule != 0 \endcode molecule must not be a NULL pointer. + * @pre \code atom != 0 \endcode atom must not be a NULL pointer. + * @return TNG_SUCCESS (0) if the atom is found or TNG_FAILURE (1) if the + * atom is not found. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_of_index_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t index, + tng_atom_t *atom); + +/** * @brief Find a chain in a molecule. * @param tng_data is the trajectory data container containing the molecule. * @param molecule is the molecule in which to search for the chain. @@ -1818,26 +1854,38 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set const char *new_name); /** - * @brief Get the residues of a chain. + * @brief Get the number of residues in a molecule chain. * @param tng_data is the trajectory containing the chain. - * @param chain is the chain of which to get the residues. - * @param residues is pointing to the list of residues. This is a pointer - * to the list of the molecule, which means that it should be handled - * carefully, e.g. not freed. + * @param chain is the chain of which to get the number of residues. * @param n is pointing to a value set to the number of residues. * @pre \code chain != 0 \endcode The chain must not be NULL. - * @pre \code residues != 0 \endcode The pointer to the list of residues must not - * be a NULL pointer. * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_residues_get +tng_function_status DECLSPECDLLEXPORT tng_chain_num_residues_get (const tng_trajectory_t tng_data, const tng_chain_t chain, - tng_residue_t *residues, int64_t *n); /** + * @brief Retrieve the residue of a chain with specified index in the list + * of residues. + * @param tng_data is the trajectory data container containing the chain. + * @param index is the index (in chain->residues) of the residue to return + * @param chain is the chain from which to get the residue. + * @param residue is a pointer to the residue if it was found - otherwise 0. + * @pre \code chain != 0 \endcode chain must not be a NULL pointer. + * @pre \code residue != 0 \endcode residue must not be a NULL pointer. + * @return TNG_SUCCESS (0) if the residue is found or TNG_FAILURE (1) if the + * residue is not found. + */ +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_of_index_get + (tng_trajectory_t tng_data, + tng_chain_t chain, + int64_t index, + tng_residue_t *residue); + +/** * @brief Find a residue in a chain. * @param tng_data is the trajectory data container containing the chain. * @param chain is the chain in which to search for the residue. @@ -1938,28 +1986,38 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set const char *new_name); /** - * @brief Get the atoms of a residue. + * @brief Get the number of atoms in a residue. * @param tng_data is the trajectory containing the residue. - * @param molecule is the molecule containing the residue. - * @param residue is the residue of which to get the atoms. - * @param atoms is pointing to the list of atoms. This is a pointer - * to the list of the molecule, which means that it should be handled - * carefully, e.g. not freed. + * @param residue is the residue of which to get the number atoms. * @param n is pointing to a value set to the number of atoms. * @pre \code residue != 0 \endcode The residue must not be NULL. - * @pre \code atoms != 0 \endcode The pointer to the list of atoms must not - * be a NULL pointer. * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_residue_atoms_get +tng_function_status DECLSPECDLLEXPORT tng_residue_num_atoms_get (const tng_trajectory_t tng_data, - const tng_molecule_t molecule, const tng_residue_t residue, - tng_atom_t *atoms, int64_t *n); /** + * @brief Retrieve the atom of a residue with specified index in the list + * of atoms. + * @param tng_data is the trajectory data container containing the residue. + * @param index is the index (in residue->atoms) of the atom to return + * @param residue is the residue from which to get the atom. + * @param atom is a pointer to the atom if it was found - otherwise 0. + * @pre \code residue != 0 \endcode residue must not be a NULL pointer. + * @pre \code atom != 0 \endcode atom must not be a NULL pointer. + * @return TNG_SUCCESS (0) if the atom is found or TNG_FAILURE (1) if the + * atom is not found. + */ +tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get + (tng_trajectory_t tng_data, + tng_residue_t residue, + int64_t index, + tng_atom_t *atom); + +/** * @brief Add an atom to a residue. * @param tng_data is the trajectory containing the residue. * @param residue is the residue to add an atom to. @@ -3191,12 +3249,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get * not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get +/*tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get (tng_trajectory_t tng_data, int64_t *n_mols, int64_t **molecule_cnt_list, tng_molecule_t *mols); - +*/ /* * @brief High-level function for adding a molecule to the mol system. * @param tng_data is the trajectory containing the mol system. diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 5a6386d..abb0592 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -7590,57 +7590,105 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_molecule_chains_get +tng_function_status DECLSPECDLLEXPORT tng_molecule_num_chains_get (const tng_trajectory_t tng_data, const tng_molecule_t molecule, - tng_chain_t *chains, int64_t *n) { (void) tng_data; TNG_ASSERT(molecule, "TNG library: molecule must not be NULL"); - TNG_ASSERT(chains, "TNG library: chains must not be a NULL pointer"); TNG_ASSERT(n, "TNG library: n must not be a NULL pointer"); - *chains = molecule->chains; *n = molecule->n_chains; return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_molecule_residues_get +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_of_index_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t index, + tng_chain_t *chain) +{ + (void) tng_data; + TNG_ASSERT(molecule, "TNG library: molecule must not be a NULL pointer."); + TNG_ASSERT(chain, "TNG library: chain must not be a NULL pointer."); + + if(index >= molecule->n_chains) + { + *chain = 0; + return(TNG_FAILURE); + } + *chain = &molecule->chains[index]; + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_molecule_num_residues_get (const tng_trajectory_t tng_data, const tng_molecule_t molecule, - tng_residue_t *residues, int64_t *n) { (void) tng_data; TNG_ASSERT(molecule, "TNG library: molecule must not be NULL"); - TNG_ASSERT(residues, "TNG library: residues must not be a NULL pointer"); TNG_ASSERT(n, "TNG library: n must not be a NULL pointer"); - *residues = molecule->residues; *n = molecule->n_residues; return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_molecule_atoms_get +tng_function_status DECLSPECDLLEXPORT tng_molecule_residue_of_index_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t index, + tng_residue_t *residue) +{ + (void) tng_data; + TNG_ASSERT(molecule, "TNG library: molecule must not be a NULL pointer."); + TNG_ASSERT(residue, "TNG library: residue must not be a NULL pointer."); + + if(index >= molecule->n_residues) + { + *residue = 0; + return(TNG_FAILURE); + } + *residue = &molecule->residues[index]; + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_molecule_num_atoms_get (const tng_trajectory_t tng_data, const tng_molecule_t molecule, - tng_atom_t *atoms, int64_t *n) { (void) tng_data; TNG_ASSERT(molecule, "TNG library: molecule must not be NULL"); - TNG_ASSERT(atoms, "TNG library: atoms must not be a NULL pointer"); TNG_ASSERT(n, "TNG library: n must not be a NULL pointer"); - *atoms = molecule->atoms; *n = molecule->n_atoms; return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_of_index_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t index, + tng_atom_t *atom) +{ + (void) tng_data; + TNG_ASSERT(molecule, "TNG library: molecule must not be a NULL pointer."); + TNG_ASSERT(atom, "TNG library: atom must not be a NULL pointer."); + + if(index >= molecule->n_atoms) + { + *atom = 0; + return(TNG_FAILURE); + } + *atom = &molecule->atoms[index]; + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find (tng_trajectory_t tng_data, tng_molecule_t molecule, @@ -7875,23 +7923,39 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_chain_residues_get +tng_function_status DECLSPECDLLEXPORT tng_chain_num_residues_get (const tng_trajectory_t tng_data, const tng_chain_t chain, - tng_residue_t *residues, int64_t *n) { (void) tng_data; TNG_ASSERT(chain, "TNG library: chain must not be NULL"); - TNG_ASSERT(residues, "TNG library: residues must not be a NULL pointer"); TNG_ASSERT(n, "TNG library: n must not be a NULL pointer"); - *residues = chain->residues; *n = chain->n_residues; return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_of_index_get + (tng_trajectory_t tng_data, + tng_chain_t chain, + int64_t index, + tng_residue_t *residue) +{ + (void) tng_data; + TNG_ASSERT(chain, "TNG library: chain must not be a NULL pointer."); + TNG_ASSERT(residue, "TNG library: residue must not be a NULL pointer."); + + if(index >= chain->n_residues) + { + *residue = 0; + return(TNG_FAILURE); + } + *residue = &chain->residues[index]; + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find (tng_trajectory_t tng_data, tng_chain_t chain, @@ -8085,25 +8149,51 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_ return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_residue_atoms_get +tng_function_status DECLSPECDLLEXPORT tng_residue_num_atoms_get (const tng_trajectory_t tng_data, - const tng_molecule_t molecule, const tng_residue_t residue, - tng_atom_t *atoms, int64_t *n) { (void) tng_data; TNG_ASSERT(residue, "TNG library: residue must not be NULL"); - TNG_ASSERT(atoms, "TNG library: atoms must not be a NULL pointer"); TNG_ASSERT(n, "TNG library: n must not be a NULL pointer"); - *atoms = molecule->atoms; - *atoms += residue->atoms_offset; *n = residue->n_atoms; return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get + (tng_trajectory_t tng_data, + tng_residue_t residue, + int64_t index, + tng_atom_t *atom) +{ + tng_chain_t chain; + tng_molecule_t molecule; + + (void) tng_data; + TNG_ASSERT(residue, "TNG library: residue must not be a NULL pointer."); + TNG_ASSERT(atom, "TNG library: atom must not be a NULL pointer."); + + if(index >= residue->n_atoms) + { + *atom = 0; + return(TNG_FAILURE); + } + chain = residue->chain; + molecule = chain->molecule; + + if(index + residue->atoms_offset >= molecule->n_atoms) + { + *atom = 0; + return(TNG_FAILURE); + } + + *atom = &molecule->atoms[residue->atoms_offset + index]; + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add (tng_trajectory_t tng_data, tng_residue_t residue, @@ -15708,6 +15798,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get return(TNG_SUCCESS); } +/* tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get (tng_trajectory_t tng_data, int64_t *n_mols, @@ -15735,7 +15826,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get return(TNG_SUCCESS); } - +*/ /* tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add (tng_trajectory_t tng_data, |