diff options
Diffstat (limited to 'src/lib/tng_io.h')
| -rw-r--r-- | src/lib/tng_io.h | 106 |
1 files changed, 37 insertions, 69 deletions
diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index cfb95d5..59b8265 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -352,25 +352,25 @@ struct tng_trajectory { *tng_data is a pointer to pre-allocated memory. Returns 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_init_trajectory(tng_trajectory_t tng_data); +tng_function_status tng_trajectory_init(tng_trajectory_t tng_data); /* Clean up a trajectory data container. *tng_data is a pointer to pre-allocated memory containing trajectory data. All allocated memory in the data structure is freed. Returns 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_destroy_trajectory(tng_trajectory_t tng_data); +tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data); /* Set the name of the input file. Returns 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_set_input_file(tng_trajectory_t tng_data, +tng_function_status tng_input_file_set(tng_trajectory_t tng_data, const char *file_name); /* Set the name of the output file. Returns 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_set_output_file(tng_trajectory_t tng_data, +tng_function_status tng_output_file_set(tng_trajectory_t tng_data, const char *file_name); /* Set the program name used when creating the trajectory. @@ -378,7 +378,7 @@ tng_function_status tng_set_output_file(tng_trajectory_t tng_data, *new_name is a pointer to the string containing the wanted name. Returns 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_set_program_name(tng_trajectory_t tng_data, +tng_function_status tng_program_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the forcefield used in the trajectory. @@ -386,7 +386,7 @@ tng_function_status tng_set_program_name(tng_trajectory_t tng_data, *new_name is a pointer to the string containing the wanted name. Returns 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_set_forcefield_name(tng_trajectory_t tng_data, +tng_function_status tng_forcefield_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the user creating the trajectory. @@ -394,7 +394,7 @@ tng_function_status tng_set_forcefield_name(tng_trajectory_t tng_data, *new_name is a pointer to the string containing the wanted name. Returns 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_set_user_name(tng_trajectory_t tng_data, +tng_function_status tng_user_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the computer used when creating the trajectory. @@ -402,7 +402,7 @@ tng_function_status tng_set_user_name(tng_trajectory_t tng_data, *new_name is a pointer to the string containing the wanted name. Returns 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_set_computer_name(tng_trajectory_t tng_data, +tng_function_status tng_computer_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the pgp_signature of the trajectory. @@ -410,34 +410,34 @@ tng_function_status tng_set_computer_name(tng_trajectory_t tng_data, *signature is a pointer to the string containing the pgp_signature. Returns 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_set_signature(tng_trajectory_t tng_data, +tng_function_status tng_signature_set(tng_trajectory_t tng_data, const char *signature); /* Setup a molecule container. *molecule is a pointer to pre-allocated memory. Returns 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_init_molecule(tng_molecule_t molecule); +tng_function_status tng_molecule_init(tng_molecule_t molecule); /* Clean up a molecule container. *molecule is a pointer to pre-allocated memory containing a molecule. All allocated memory in the data structure is freed. Returns 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_destroy_molecule(tng_molecule_t molecule); +tng_function_status tng_molecule_destroy(tng_molecule_t molecule); /* Setup a data block. *block is a pointer to pre-allocated memory. Returns 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_init_block(struct tng_gen_block *block); +tng_function_status tng_block_init(struct tng_gen_block *block); /* Clean up a data block. *block is a pointer to pre-allocated memory. All allocated memory in the data structure is freed. Returns 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_destroy_block(struct tng_gen_block *block); +tng_function_status tng_block_destroy(struct tng_gen_block *block); /* Set the name of a data block. tng_data is the trajectory data container containing the block.. @@ -445,7 +445,7 @@ tng_function_status tng_destroy_block(struct tng_gen_block *block); *new_name is a string containing the wanted name. Returns 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_set_block_name(tng_trajectory_t tng_data, +tng_function_status tng_block_name_set(tng_trajectory_t tng_data, struct tng_gen_block *block, const char *new_name); @@ -455,7 +455,7 @@ tng_function_status tng_set_block_name(tng_trajectory_t tng_data, **molecule is a pointer to a pointer to the newly created molecule. Returns 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_add_molecule(tng_trajectory_t tng_data, +tng_function_status tng_molecule_add(tng_trajectory_t tng_data, const char *name, tng_molecule_t *molecule); @@ -465,7 +465,7 @@ tng_function_status tng_add_molecule(tng_trajectory_t tng_data, *new_name is a string containing the wanted name. Returns 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_set_molecule_name(tng_trajectory_t tng_data, +tng_function_status tng_molecule_name_set(tng_trajectory_t tng_data, tng_molecule_t molecule, const char *new_name); @@ -475,7 +475,7 @@ tng_function_status tng_set_molecule_name(tng_trajectory_t tng_data, *cnt is a pointer to the variable to be populated with the count. Returns 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_get_molecule_cnt(tng_trajectory_t tng_data, +tng_function_status tng_molecule_cnt_get(tng_trajectory_t tng_data, tng_molecule_t molecule, int64_t *cnt); @@ -485,7 +485,7 @@ tng_function_status tng_get_molecule_cnt(tng_trajectory_t tng_data, cnt is the number of instances of this molecule. Returns 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_set_molecule_cnt(tng_trajectory_t tng_data, +tng_function_status tng_molecule_cnt_set(tng_trajectory_t tng_data, tng_molecule_t molecule, int64_t cnt); @@ -496,7 +496,7 @@ tng_function_status tng_set_molecule_cnt(tng_trajectory_t tng_data, **chain is a pointer to a pointer to the newly created chain. Returns 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_add_chain_to_molecule(tng_trajectory_t tng_data, +tng_function_status tng_molecule_chain_add(tng_trajectory_t tng_data, tng_molecule_t molecule, const char *name, tng_chain_t *chain); @@ -507,7 +507,7 @@ tng_function_status tng_add_chain_to_molecule(tng_trajectory_t tng_data, *new_name is a string containing the wanted name. Returns 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_set_chain_name(tng_trajectory_t tng_data, +tng_function_status tng_chain_name_set(tng_trajectory_t tng_data, tng_chain_t chain, const char *new_name); @@ -518,7 +518,7 @@ tng_function_status tng_set_chain_name(tng_trajectory_t tng_data, **residue is a pointer to a pointer to the newly created residue. Returns 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_add_residue_to_chain(tng_trajectory_t tng_data, +tng_function_status tng_chain_residue_add(tng_trajectory_t tng_data, tng_chain_t chain, const char *name, tng_residue_t *residue); @@ -529,7 +529,7 @@ tng_function_status tng_add_residue_to_chain(tng_trajectory_t tng_data, *new_name is a string containing the wanted name. Returns 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_set_residue_name(tng_trajectory_t tng_data, +tng_function_status tng_residue_name_set(tng_trajectory_t tng_data, tng_residue_t residue, const char *new_name); @@ -541,7 +541,7 @@ tng_function_status tng_set_residue_name(tng_trajectory_t tng_data, **atom is a pointer to a pointer to the newly created atom. Returns 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_add_atom_to_residue(tng_trajectory_t tng_data, +tng_function_status tng_residue_atom_add(tng_trajectory_t tng_data, tng_residue_t residue, const char *atom_name, const char *atom_type, @@ -553,7 +553,7 @@ tng_function_status tng_add_atom_to_residue(tng_trajectory_t tng_data, *new_name is a string containing the wanted name. Returns 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_set_atom_name(tng_trajectory_t tng_data, +tng_function_status tng_atom_name_set(tng_trajectory_t tng_data, tng_atom_t atom, const char *new_name); @@ -563,7 +563,7 @@ tng_function_status tng_set_atom_name(tng_trajectory_t tng_data, *new_name is a string containing the atom type. Returns 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_set_atom_type(tng_trajectory_t tng_data, +tng_function_status tng_atom_type_set(tng_trajectory_t tng_data, tng_atom_t atom, const char *new_type); @@ -576,7 +576,7 @@ tng_function_status tng_set_atom_type(tng_trajectory_t tng_data, compared to the md5 hash of the read contents to ensure valid data. Returns 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_read_file_headers(tng_trajectory_t tng_data, +tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); /* Write the header blocks to the output_file of tng_data. @@ -587,7 +587,7 @@ tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated. Returns 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_write_file_headers(tng_trajectory_t tng_data, +tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); @@ -601,7 +601,7 @@ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, compared to the md5 hash of the read contents to ensure valid data. Returns 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_read_next_block(tng_trajectory_t tng_data, +tng_function_status tng_block_read_next(tng_trajectory_t tng_data, struct tng_gen_block *block_data, const tng_hash_mode hash_mode); @@ -614,7 +614,7 @@ tng_function_status tng_read_next_block(tng_trajectory_t tng_data, compared to the md5 hash of the read contents to ensure valid data. Returns 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_read_next_frame_set(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); /* Write one frame set, including toc, mapping and related data blocks @@ -624,14 +624,14 @@ tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, If hash_mode == TNG_USE_HASH an md5 hash for each block will be generated. Returns 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_write_frame_set(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); -tng_function_status tng_new_frame_set(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames); -tng_function_status tng_add_particle_data_block(tng_trajectory_t tng_data, +tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -644,27 +644,13 @@ tng_function_status tng_add_particle_data_block(tng_trajectory_t tng_data, void *new_data); -/* Read one (the next) trajectory block from the input_file of tng_data. - 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. - Returns 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_read_next_traj_block(tng_trajectory_t tng_data); - -/* Write one trajectory block to the output_file of tng_data. - tng_data is a trajectory data container. tng_data->output_file_path specifies which - file to write to. If the file (output_file) is not open it will be opened. - Returns 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_write_next_traj_block(tng_trajectory_t tng_data); - /* Read one trajectory block from the input_file of tng_data. 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. block_id is the ID of the block to read. Returns 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_read_traj_block(tng_trajectory_t tng_data, +tng_function_status tng_traj_block_read(tng_trajectory_t tng_data, int64_t block_id); /* Write one trajectory block to the output_file of tng_data. @@ -673,7 +659,7 @@ tng_function_status tng_read_traj_block(tng_trajectory_t tng_data, block_id is the ID of the block to write. Returns 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_write_traj_block(tng_trajectory_t tng_data, +tng_function_status tng_traj_block_write(tng_trajectory_t tng_data, int64_t block_id); /* Read a requested frame set. @@ -682,27 +668,9 @@ tng_function_status tng_write_traj_block(tng_trajectory_t tng_data, frame_set_nr is the number of the frame set to return (starting from 0). Returns 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_read_frame_set_nr(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_read_nr(tng_trajectory_t tng_data, int64_t frame_set_nr); -/* Read one trajectory frame from the input_file of tng_data. - 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. - frame_nr is the index number of the frame to read. - Returns 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_read_frame_nr(tng_trajectory_t tng_data, - int64_t frame_nr); - -/* Write one trajectory frame to the output_file of tng_data. - tng_data is a trajectory data container. tng_data->output_file_path specifies which - file to write to. If the file (output_file) is not open it will be opened. - frame_nr is the index number of the frame to write. - Returns 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_write_frame_nr(tng_trajectory_t tng_data, - int64_t frame_nr); - /* Read a number of consecutive trajectory frames from the input_file of tng_data. 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. @@ -710,7 +678,7 @@ tng_function_status tng_write_frame_nr(tng_trajectory_t tng_data, end_frame_nr is the index number of the last frame to read. Returns 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_read_frame_nrs(tng_trajectory_t tng_data, +tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr); @@ -721,7 +689,7 @@ tng_function_status tng_read_frame_nrs(tng_trajectory_t tng_data, end_frame_nr is the index number of the last frame to write. Returns 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_write_frame_nrs(tng_trajectory_t tng_data, +tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr); |