diff options
Diffstat (limited to 'include')
| -rw-r--r-- | include/tng_io.h | 808 |
1 files changed, 507 insertions, 301 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index f2ae1c9..57ae8a4 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -499,90 +499,6 @@ extern "C" { #endif -tng_function_status tng_util_trajectory_open(const char *filename, - const char mode, - tng_trajectory_t *tng_data_p); - -tng_function_status tng_util_trajectory_close(tng_trajectory_t *tng_data_p); - -tng_function_status tng_util_trajectory_molecules_get(tng_trajectory_t tng_data, - int64_t *n_mols, - int64_t *molecule_cnt_list, - tng_molecule_t *mols); - -tng_function_status tng_util_trajectory_molecule_add(tng_trajectory_t tng_data, - const char *name, - const int64_t cnt, - tng_molecule_t *mol); - -tng_function_status tng_util_molecule_particles_get(tng_trajectory_t tng_data, - const tng_molecule_t mol, - int64_t *n_particles, - char ***names, - char ***types, - char ***res_names, - int64_t **res_ids, - char ***chain_names, - int64_t **chain_ids); - -tng_function_status tng_util_molecule_particles_set(tng_trajectory_t tng_data, - tng_molecule_t mol, - const int64_t n_particles, - const char **names, - const char **types, - const char **res_names, - const int64_t *res_ids, - const char **chain_names, - const int64_t *chain_ids); - -tng_function_status tng_util_pos_read(tng_trajectory_t tng_data, - float *positions); - -tng_function_status tng_util_vel_read(tng_trajectory_t tng_data, - float *velocities); - -tng_function_status tng_util_force_read(tng_trajectory_t tng_data, - float *forces); - -tng_function_status tng_util_box_shape_read(tng_trajectory_t tng_data, - float *box_shape); - -tng_function_status tng_util_pos_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *positions); - -tng_function_status tng_util_vel_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *velocities); - -tng_function_status tng_util_force_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *forces); - -tng_function_status tng_util_box_shape_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *box_shape); - -tng_function_status tng_util_pos_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *positions); - -tng_function_status tng_util_vel_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *velocities); - -tng_function_status tng_util_force_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *forces); - -tng_function_status tng_util_box_shape_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *box_shape); - /** * @brief Setup a trajectory data container. @@ -591,7 +507,8 @@ tng_function_status tng_util_box_shape_write(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_data_p); +tng_function_status DECLSPECDLLEXPORT tng_trajectory_init + (tng_trajectory_t *tng_data_p); /** * @brief Clean up a trajectory data container. @@ -600,7 +517,8 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_ * tng_data_p itself. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *tng_data_p); +tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy + (tng_trajectory_t *tng_data_p); /** * @brief Copy a trajectory data container (dest is setup as well). @@ -614,8 +532,8 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajectory_t src, - tng_trajectory_t *dest_p); +tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src + (tng_trajectory_t src, tng_trajectory_t *dest_p); /** * @brief Get the name of the input file. @@ -627,8 +545,9 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_input_file_get(const tng_trajectory_t tng_data, - char *file_name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_input_file_get + (const tng_trajectory_t tng_data, + char *file_name, const int max_len); /** * @brief Set the name of the input file. @@ -637,8 +556,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_get(const tng_trajectory_t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_input_file_set(tng_trajectory_t tng_data, - const char *file_name); +tng_function_status DECLSPECDLLEXPORT tng_input_file_set + (tng_trajectory_t tng_data, + const char *file_name); /** * @brief Get the name of the output file. @@ -650,8 +570,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_set(tng_trajectory_t tng_da * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_output_file_get(const tng_trajectory_t tng_data, - char *file_name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_output_file_get + (const tng_trajectory_t tng_data, + char *file_name, const int max_len); /** * @brief Set the name of the output file. @@ -660,8 +581,9 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_get(const tng_trajectory_t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_output_file_set(tng_trajectory_t tng_data, - const char *file_name); +tng_function_status DECLSPECDLLEXPORT tng_output_file_set + (tng_trajectory_t tng_data, + const char *file_name); /** * @brief Get the endianness of the output file. @@ -698,8 +620,9 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_set * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the program used when creating the trajectory. @@ -708,8 +631,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get(const tng_traje * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the program used when last modifying the trajectory. @@ -721,8 +645,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set(tng_trajectory_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the program used when last modifying the trajectory. @@ -731,8 +656,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get(const tng_trajec * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the user who created the trajectory. @@ -744,8 +670,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set(tng_trajectory_t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the user who created the trajectory. @@ -754,8 +681,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get(const tng_trajecto * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the user who last modified the trajectory. @@ -767,8 +695,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the user who last modified the trajectory. @@ -777,8 +706,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get(const tng_trajector * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the computer used when creating the trajectory. @@ -790,8 +720,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the computer used when creating the trajectory. @@ -800,8 +731,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get(const tng_traj * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the computer used when last modifying the trajectory. @@ -813,8 +745,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set(tng_trajectory * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the computer used when last modifying the trajectory. @@ -823,8 +756,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get(const tng_traje * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the pgp_signature of the user creating the trajectory. @@ -836,8 +770,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set(tng_trajectory_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_signature_get(const tng_trajectory_t tng_data, - char *signature, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_signature_get + (const tng_trajectory_t tng_data, + char *signature, const int max_len); /** * @brief Set the pgp_signature of the user creating the trajectory. @@ -846,8 +781,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_get(const tng_trajecto * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_signature_set(tng_trajectory_t tng_data, - const char *signature); +tng_function_status DECLSPECDLLEXPORT tng_first_signature_set + (tng_trajectory_t tng_data, + const char *signature); /** * @brief Get the pgp_signature of the user last modifying the trajectory. @@ -859,8 +795,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_set(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_signature_get(const tng_trajectory_t tng_data, - char *signature, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_signature_get + (const tng_trajectory_t tng_data, + char *signature, const int max_len); /** * @brief Set the pgp_signature of the user last modifying the trajectory. @@ -869,8 +806,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_get(const tng_trajector * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_signature_set(tng_trajectory_t tng_data, - const char *signature); +tng_function_status DECLSPECDLLEXPORT tng_last_signature_set + (tng_trajectory_t tng_data, + const char *signature); /** * @brief Get the name of the forcefield used in the trajectory. @@ -882,8 +820,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_set(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the forcefield used in the trajectory. @@ -892,8 +831,9 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get(const tng_trajecto * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the medium stride length of the trajectory. @@ -901,8 +841,9 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set(tng_trajectory_t t * @param len is pointing to a value set to the stride length. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get(const tng_trajectory_t tng_data, - int64_t *len); +tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get + (const tng_trajectory_t tng_data, + int64_t *len); /** * @brief Set the medium stride length of the trajectory. @@ -911,8 +852,9 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get(const tng_tra * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ -tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set(tng_trajectory_t tng_data, - const int64_t len); +tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set + (tng_trajectory_t tng_data, + const int64_t len); /** * @brief Get the long stride length of the trajectory. @@ -920,8 +862,9 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set(tng_trajector * @param len is pointing to a value set to the stride length. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get(const tng_trajectory_t tng_data, - int64_t *len); +tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get + (const tng_trajectory_t tng_data, + int64_t *len); /** * @brief Set the long stride length of the trajectory. @@ -930,8 +873,9 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get(const tng_traje * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ -tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set(tng_trajectory_t tng_data, - const int64_t len); +tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set + (tng_trajectory_t tng_data, + const int64_t len); /** * @brief Get the length of the input file. @@ -939,8 +883,9 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set(tng_trajectory_ * @param len is pointing to a value set to the file length. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get(const tng_trajectory_t tng_data, - int64_t *len); +tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get + (const tng_trajectory_t tng_data, + int64_t *len); /** * @brief Get the number of frames in the trajectory @@ -949,8 +894,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get(const tng_trajector * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (could not find last frame set). */ -tng_function_status DECLSPECDLLEXPORT tng_num_frames_get(const tng_trajectory_t tng_data, - int64_t *n); +tng_function_status DECLSPECDLLEXPORT tng_num_frames_get + (const tng_trajectory_t tng_data, + int64_t *n); /** * @brief Get the current number of particles. @@ -960,8 +906,9 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_get(const tng_trajectory_t * the number of particles in the current frame set. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_num_particles_get(const tng_trajectory_t tng_data, - int64_t *n); +tng_function_status DECLSPECDLLEXPORT tng_num_particles_get + (const tng_trajectory_t tng_data, + int64_t *n); /** * @brief Get the current total number of molecules. @@ -971,8 +918,9 @@ tng_function_status DECLSPECDLLEXPORT tng_num_particles_get(const tng_trajectory * the total number of molecules in the current frame set. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get(const tng_trajectory_t tng_data, - int64_t *n); +tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get + (const tng_trajectory_t tng_data, + int64_t *n); /** * @brief Get the number of frames per frame set. @@ -1031,8 +979,9 @@ tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find(tng_trajectory_t tng_data, - const int64_t nr); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find + (tng_trajectory_t tng_data, + const int64_t nr); /** * @brief Find the frame set containing a specific frame. @@ -1043,8 +992,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find(tng_trajectory_t tng_data, - const int64_t frame); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find + (tng_trajectory_t tng_data, + const int64_t frame); /** * @brief Get the file position of the next frame set in the input file. @@ -1093,8 +1043,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_frame_range_get * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t tng_data, - tng_molecule_t molecule); +tng_function_status DECLSPECDLLEXPORT tng_molecule_init + (const tng_trajectory_t tng_data, + tng_molecule_t molecule); /** * @brief Clean up a molecule container. @@ -1105,8 +1056,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_t tng_data, - tng_molecule_t molecule); +tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy + (const tng_trajectory_t tng_data, + tng_molecule_t molecule); /** * @brief Add a molecule to the trajectory. @@ -1116,9 +1068,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_ * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_add(tng_trajectory_t tng_data, - const char *name, - tng_molecule_t *molecule); +tng_function_status DECLSPECDLLEXPORT tng_molecule_add + (tng_trajectory_t tng_data, + const char *name, + tng_molecule_t *molecule); /** * @brief Set the name of a molecule. @@ -1128,9 +1081,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add(tng_trajectory_t tng_data * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *new_name); /** * @brief Get the count of a molecule. @@ -1140,9 +1094,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get(tng_trajectory_t tng_data, - tng_molecule_t molecule, - int64_t *cnt); +tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t *cnt); /** * @brief Set the count of a molecule. @@ -1152,9 +1107,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get(tng_trajectory_t tng_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const int64_t cnt); +tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const int64_t cnt); /** * @brief Find a chain in a molecule. @@ -1170,11 +1126,12 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set(tng_trajectory_t tng_ * @details If name is an empty string and id is -1 the first chain will be * found. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const char *name, - int64_t id, - tng_chain_t *chain); +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *name, + int64_t id, + tng_chain_t *chain); /** * @brief Add a chain to a molecule. @@ -1185,10 +1142,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const char *name, - tng_chain_t *chain); +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *name, + tng_chain_t *chain); /** * @brief Set the name of a chain. @@ -1198,9 +1156,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_name_set(tng_trajectory_t tng_data, - tng_chain_t chain, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_chain_name_set + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *new_name); /** * @brief Find a residue in a chain. @@ -1212,11 +1171,12 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set(tng_trajectory_t tng_da * residue is not found. * @details If name is an empty string the first residue will be found. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find(tng_trajectory_t tng_data, - tng_chain_t chain, - const char *name, - int64_t id, - tng_residue_t *residue); +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *name, + int64_t id, + tng_residue_t *residue); /** * @brief Add a residue to a chain. @@ -1227,10 +1187,11 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add(tng_trajectory_t tng_data, - tng_chain_t chain, - const char *name, - tng_residue_t *residue); +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *name, + tng_residue_t *residue); /** * @brief Set the name of a residue. @@ -1240,9 +1201,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_data, - tng_residue_t residue, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_residue_name_set + (tng_trajectory_t tng_data, + tng_residue_t residue, + const char *new_name); /** * @brief Add an atom to a residue. @@ -1254,11 +1216,12 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_ * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add(tng_trajectory_t tng_data, - tng_residue_t residue, - const char *atom_name, - const char *atom_type, - tng_atom_t *atom); +tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add + (tng_trajectory_t tng_data, + tng_residue_t residue, + const char *atom_name, + const char *atom_type, + tng_atom_t *atom); /** * @brief Set the name of an atom. @@ -1268,9 +1231,10 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add(tng_trajectory_t tng_ * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_atom_name_set(tng_trajectory_t tng_data, - tng_atom_t atom, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_atom_name_set + (tng_trajectory_t tng_data, + tng_atom_t atom, + const char *new_name); /** * @brief Set the atom type of an atom. @@ -1280,9 +1244,10 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_set(tng_trajectory_t tng_dat * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_atom_type_set(tng_trajectory_t tng_data, - tng_atom_t atom, - const char *new_type); +tng_function_status DECLSPECDLLEXPORT tng_atom_type_set + (tng_trajectory_t tng_data, + tng_atom_t atom, + const char *new_type); /** * @brief Get the molecume name of real particle number (number in mol system). @@ -1403,8 +1368,9 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_file_headers_read(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_file_headers_read + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Write the header blocks to the output_file of tng_data. @@ -1419,8 +1385,9 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_file_headers_write(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_file_headers_write + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Read one (the next) block (of any kind) from the input_file of tng_data. @@ -1438,9 +1405,10 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_write(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_data, - tng_gen_block_t block_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_block_read_next + (tng_trajectory_t tng_data, + tng_gen_block_t block_data, + const tng_hash_mode hash_mode); /** * @brief Read one (the next) frame set, including mapping and related data blocks @@ -1455,8 +1423,9 @@ tng_function_status DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_d * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Write one frame set, including mapping and related data blocks @@ -1470,8 +1439,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_set_write(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_write + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Create and initialise a frame set. @@ -1482,9 +1452,10 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_write(tng_trajectory_t tng_d * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_set_new(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t n_frames); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_new + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t n_frames); /** * @brief Add a non-particle dependent data block. @@ -1507,16 +1478,17 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new(tng_trajectory_t tng_dat * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_data_block_add(tng_trajectory_t tng_data, - const int64_t id, - const char *block_name, - const tng_data_type datatype, - const tng_block_type block_type_flag, - int64_t n_frames, - const int64_t n_values_per_frame, - int64_t stride_length, - const int64_t codec_id, - void *new_data); +tng_function_status DECLSPECDLLEXPORT tng_data_block_add + (tng_trajectory_t tng_data, + const int64_t id, + const char *block_name, + const tng_data_type datatype, + const tng_block_type block_type_flag, + int64_t n_frames, + const int64_t n_values_per_frame, + int64_t stride_length, + const int64_t codec_id, + void *new_data); /** * @brief Add a particle dependent data block. @@ -1542,18 +1514,19 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add(tng_trajectory_t tng_da * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add(tng_trajectory_t tng_data, - const int64_t id, - const char *block_name, - const tng_data_type datatype, - const tng_block_type block_type_flag, - int64_t n_frames, - const int64_t n_values_per_frame, - int64_t stride_length, - const int64_t first_particle_number, - const int64_t n_particles, - const int64_t codec_id, - void *new_data); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add + (tng_trajectory_t tng_data, + const int64_t id, + const char *block_name, + const tng_data_type datatype, + const tng_block_type block_type_flag, + int64_t n_frames, + const int64_t n_values_per_frame, + int64_t stride_length, + const int64_t first_particle_number, + const int64_t n_particles, + const int64_t codec_id, + void *new_data); /** * @brief Write data of one trajectory frame to the output_file of tng_data. @@ -1570,11 +1543,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add(tng_trajectory * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_data_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const int64_t block_id, - const void *data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_data_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const int64_t block_id, + const void *data, + const tng_hash_mode hash_mode); /** * @brief Write particle data of one trajectory frame to the output_file of @@ -1595,13 +1569,14 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write(tng_trajectory_t tng_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const int64_t block_id, - const int64_t val_first_particle, - const int64_t val_n_particles, - const void *data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const int64_t block_id, + const int64_t val_first_particle, + const int64_t val_n_particles, + const void *data, + const tng_hash_mode hash_mode); /** * @brief Free data of an array of values (2D). @@ -1612,11 +1587,12 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write(tng_trajecto * @param type is the data type of the data in the array (e.g. int/float/char). * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_data_values_free(const tng_trajectory_t tng_data, - union data_values **values, - const int64_t n_frames, - const int64_t n_values_per_frame, - const tng_data_type type); +tng_function_status DECLSPECDLLEXPORT tng_data_values_free + (const tng_trajectory_t tng_data, + union data_values **values, + const int64_t n_frames, + const int64_t n_values_per_frame, + const tng_data_type type); /** * @brief Free data of an array of values (3D). @@ -1628,12 +1604,13 @@ tng_function_status DECLSPECDLLEXPORT tng_data_values_free(const tng_trajectory_ * @param type is the data type of the data in the array (e.g. int/float/char). * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free(const tng_trajectory_t tng_data, - union data_values ***values, - const int64_t n_frames, - const int64_t n_particles, - const int64_t n_values_per_frame, - const tng_data_type type); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free + (const tng_trajectory_t tng_data, + union data_values ***values, + const int64_t n_frames, + const int64_t n_particles, + const int64_t n_values_per_frame, + const tng_data_type type); /** * @brief Retrieve non-particle data, from the last read frame set. @@ -1646,7 +1623,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free(const tng_tr * (n_frames * n_values_per_frame). * Since ***values is allocated in this function it is the callers * responsibility to free the memory. - * @param n_frames is set to the number of particles in the returned data. This is + * @param n_frames is set to the number of frames in the returned data. This is * needed to properly reach and/or free the data afterwards. * @param n_values_per_frame is set to the number of values per frame in the data. * This is needed to properly reach and/or free the data afterwards. @@ -1655,11 +1632,11 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free(const tng_tr * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, - const int64_t block_id, - union data_values ***values, - int64_t *n_frames, - int64_t *n_values_per_frame, - tng_data_type *type); + const int64_t block_id, + union data_values ***values, + int64_t *n_frames, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Retrieve a vector (1D array) of non-particle data, from the last read frame set. @@ -1673,6 +1650,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, * responsibility to free the memory. * @param n_frames is set to the number of particles in the returned data. This is * needed to properly reach and/or free the data afterwards. + * @param stride_length is set to the stride length of the returned data. * @param n_values_per_frame is set to the number of values per frame in the data. * This is needed to properly reach and/or free the data afterwards. * @param type is set to the data type of the data in the array. @@ -1680,12 +1658,14 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, - const int64_t block_id, - void **values, - int64_t *n_frames, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_data_vector_get + (tng_trajectory_t tng_data, + const int64_t block_id, + void **values, + int64_t *n_frames, + int64_t *stride_length, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Read and retrieve non-particle data, in a specific interval. @@ -1709,14 +1689,48 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_data_interval_get(tng_trajectory_t tng_data, - const int64_t block_id, - const int64_t start_frame_nr, - const int64_t end_frame_nr, - const tng_hash_mode hash_mode, - union data_values ***values, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_data_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ***values, + int64_t *n_values_per_frame, + tng_data_type *type); + +/** + * @brief Read and retrieve a vector (1D array) of non-particle data, + * in a specific interval. + * @param tng_data is a trajectory data container. tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param block_id is the id number of the particle data block to read. + * @param start_frame_nr is the index number of the first frame to read. + * @param end_frame_nr is the index number of the last frame to read. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @param values is a pointer to a 1-dimensional array (memory unallocated), which + * will be filled with data. The length of the array will be (n_frames * n_values_per_frame). + * Since **values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. + * @param type is set to the data type of the data in the array. + * @details This does only work for numerical (int, float, double) data. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ***values, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Retrieve particle data, from the last read frame set. @@ -1732,7 +1746,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get(tng_trajectory_t tng * (n_frames * n_particles * n_values_per_frame). * Since ****values is allocated in this function it is the callers * responsibility to free the memory. - * @param n_frames is set to the number of particles in the returned data. This is + * @param n_frames is set to the number of frames in the returned data. This is * needed to properly reach and/or free the data afterwards. * @param n_particles is set to the number of particles in the returned data. This is * needed to properly reach and/or free the data afterwards. @@ -1742,13 +1756,50 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_particle_data_get(tng_trajectory_t tng_data, - const int64_t block_id, - union data_values ****values, - int64_t *n_frames, - int64_t *n_particles, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_get + (tng_trajectory_t tng_data, + const int64_t block_id, + union data_values ****values, + int64_t *n_frames, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); + +/** + * @brief Retrieve a vector (1D array) of particle data, from the last read frame set. + * @details The particle dimension of the returned values array is translated + * to real particle numbering, i.e. the numbering of the actual molecular + * system. + * @param tng_data is a trajectory data container. tng_data->input_file_path + * specifies which file to read from. If the file (input_file) is not open it + * will be opened. + * @param block_id is the id number of the particle data block to read. + * @param values is a pointer to a 1-dimensional array (memory unallocated), which + * will be filled with data. The length of the array will be + * (n_frames * n_particles * n_values_per_frame). + * Since **values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_frames is set to the number of frames in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param stride_length is set to the stride length of the returned data. + * @param n_particles is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. + * @param type is set to the data type of the data in the array. + * @details This does only work for numerical (int, float, double) data. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get + (tng_trajectory_t tng_data, + const int64_t block_id, + void **values, + int64_t *n_frames, + int64_t *stride_length, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Read and retrieve particle data, in a specific interval. @@ -1777,15 +1828,55 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get(tng_trajectory_t tng_data, - const int64_t block_id, - const int64_t start_frame_nr, - const int64_t end_frame_nr, - const tng_hash_mode hash_mode, - union data_values ****values, - int64_t *n_particles, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ****values, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); +/** + * @brief Read and retrieve a vector (1D array) particle data, in a + * specific interval. + * @details The particle dimension of the returned values array is translated + * to real particle numbering, i.e. the numbering of the actual molecular + * system. + * @param tng_data is a trajectory data container. tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param block_id is the id number of the particle data block to read. + * @param start_frame_nr is the index number of the first frame to read. + * @param end_frame_nr is the index number of the last frame to read. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @param values is a pointer to a 1-dimensional array (memory unallocated), which + * will be filled with data. The length of the array will be + * (n_frames * n_particles * n_values_per_frame). + * Since **values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_particles is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. + * @param type is set to the data type of the data in the array. + * @details This does only work for numerical (int, float, double) data. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + void **values, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); /** @brief Get the date and time of initial file creation in ISO format (string). * @param tng_data is a trajectory data container. @@ -1793,8 +1884,123 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get(tng_traject must be reserved beforehand. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_time_get_str(const tng_trajectory_t tng_data, - char *time); +tng_function_status DECLSPECDLLEXPORT tng_time_get_str + (const tng_trajectory_t tng_data, + char *time); + + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open + (const char *filename, + const char mode, + tng_trajectory_t *tng_data_p); + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close + (tng_trajectory_t *tng_data_p); + +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); + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add + (tng_trajectory_t tng_data, + const char *name, + const int64_t cnt, + tng_molecule_t *mol); + +tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get + (tng_trajectory_t tng_data, + const tng_molecule_t mol, + int64_t *n_particles, + char ***names, + char ***types, + char ***res_names, + int64_t **res_ids, + char ***chain_names, + int64_t **chain_ids); + +tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set + (tng_trajectory_t tng_data, + tng_molecule_t mol, + const int64_t n_particles, + const char **names, + const char **types, + const char **res_names, + const int64_t *res_ids, + const char **chain_names, + const int64_t *chain_ids); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_read + (tng_trajectory_t tng_data, + float *positions); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_read + (tng_trajectory_t tng_data, + float *velocities); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_read + (tng_trajectory_t tng_data, + float *forces); + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read + (tng_trajectory_t tng_data, + float *box_shape); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *positions); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *velocities); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *forces); + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *box_shape); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequence_set + (tng_trajectory_t tng_data, + const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequence_set + (tng_trajectory_t tng_data, + const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequence_set + (tng_trajectory_t tng_data, const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *positions); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *velocities); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *forces); + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *box_shape); |