diff options
Diffstat (limited to 'src/lib/tng_io.h')
| -rw-r--r-- | src/lib/tng_io.h | 144 |
1 files changed, 67 insertions, 77 deletions
diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 2c79c66..f7d6999 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -82,6 +82,9 @@ typedef enum {TRG_CHAR_DATA, + +typedef struct tng_trajectory *tng_trajectory_t; + #ifdef __cplusplus extern "C" { @@ -346,25 +349,25 @@ struct tng_trajectory { *tng_data is a pointer to pre-allocated memory. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_init_trajectory(struct tng_trajectory *tng_data); +tng_function_status tng_init_trajectory(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 TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_destroy_trajectory(struct tng_trajectory *tng_data); +tng_function_status tng_destroy_trajectory(tng_trajectory_t tng_data); /* Set the name of the input file. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_input_file(struct tng_trajectory *tng_data, +tng_function_status tng_set_input_file(tng_trajectory_t tng_data, const char *file_name); /* Set the name of the output file. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_output_file(struct tng_trajectory *tng_data, +tng_function_status tng_set_output_file(tng_trajectory_t tng_data, const char *file_name); /* Set the program name used when creating the trajectory. @@ -372,7 +375,7 @@ tng_function_status tng_set_output_file(struct tng_trajectory *tng_data, *new_name is a pointer to the string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_program_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_program_name(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the forcefield used in the trajectory. @@ -380,7 +383,7 @@ tng_function_status tng_set_program_name(struct tng_trajectory *tng_data, *new_name is a pointer to the string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_forcefield_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_forcefield_name(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the user creating the trajectory. @@ -388,7 +391,7 @@ tng_function_status tng_set_forcefield_name(struct tng_trajectory *tng_data, *new_name is a pointer to the string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_user_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_user_name(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the computer used when creating the trajectory. @@ -396,7 +399,7 @@ tng_function_status tng_set_user_name(struct tng_trajectory *tng_data, *new_name is a pointer to the string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_computer_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_computer_name(tng_trajectory_t tng_data, const char *new_name); /* Set the pgp_signature of the trajectory. @@ -404,7 +407,7 @@ tng_function_status tng_set_computer_name(struct tng_trajectory *tng_data, *signature is a pointer to the string containing the pgp_signature. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_signature(struct tng_trajectory *tng_data, +tng_function_status tng_set_signature(tng_trajectory_t tng_data, const char *signature); /* Setup a molecule container. @@ -434,96 +437,96 @@ tng_function_status tng_init_block(struct tng_gen_block *block); tng_function_status tng_destroy_block(struct tng_gen_block *block); /* Set the name of a data block. - *tng_data is a pointer to the trajectory containing the block. + tng_data is the trajectory data container containing the block. *block is a pointer to the block to rename. *new_name is a string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_block_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_block_name(tng_trajectory_t tng_data, struct tng_gen_block *block, const char *new_name); /* Add a molecule to the trajectory. - *tng_data is a pointer to the trajectory containing the block. + tng_data is the trajectory data container containing the block. *name is a pointer to the string containing the name of the new molecule. **molecule is a pointer to a pointer to the newly created molecule. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_add_molecule(struct tng_trajectory *tng_data, +tng_function_status tng_add_molecule(tng_trajectory_t tng_data, const char *name, struct tng_molecule **molecule); /* Set the name of a molecule. - *tng_data is a pointer to the trajectory containing the molecule. + tng_data is the trajectory data container containing the molecule. *molecule is a pointer to the molecule to rename. *new_name is a string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_molecule_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_molecule_name(tng_trajectory_t tng_data, struct tng_molecule *molecule, const char *new_name); /* Set the count of a molecule. - *tng_data is a pointer to the trajectory containing the molecule. + tng_data is the trajectory data container containing the molecule. *molecule is a pointer to the molecule to rename. *cnt is a pointer to the variable to be populated with the count. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_get_molecule_cnt(struct tng_trajectory *tng_data, +tng_function_status tng_get_molecule_cnt(tng_trajectory_t tng_data, struct tng_molecule *molecule, int64_t *cnt); /* Set the count of a molecule. - *tng_data is a pointer to the trajectory containing the molecule. + tng_data is the trajectory data container containing the molecule. *molecule is a pointer to the molecule to rename. cnt is the number of instances of this molecule. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_molecule_cnt(struct tng_trajectory *tng_data, +tng_function_status tng_set_molecule_cnt(tng_trajectory_t tng_data, struct tng_molecule *molecule, int64_t cnt); /* Add a chain to a molecule. - *tng_data is a pointer to the trajectory containing the molecule. + tng_data is the trajectory data container containing the molecule. *molecule is a pointer to the molecule to add a chain to. *name is a pointer to a string containing the name of the chain. **chain is a pointer to a pointer to the newly created chain. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_add_chain_to_molecule(struct tng_trajectory *tng_data, +tng_function_status tng_add_chain_to_molecule(tng_trajectory_t tng_data, struct tng_molecule *molecule, const char *name, struct tng_chain **chain); /* Set the name of a chain. - *tng_data is a pointer to the trajectory containing the atom. + tng_data is the trajectory data container containing the atom. *chain is a pointer to the chain to rename. *new_name is a string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_chain_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_chain_name(tng_trajectory_t tng_data, struct tng_chain *chain, const char *new_name); /* Add a residue to a chain. - *tng_data is a pointer to the trajectory containing the chain. + tng_data is the trajectory data container containing the chain. *chain is a pointer to the chain to add a residue to. *name is a pointer to a string containing the name of the residue. **residue is a pointer to a pointer to the newly created residue. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_add_residue_to_chain(struct tng_trajectory *tng_data, +tng_function_status tng_add_residue_to_chain(tng_trajectory_t tng_data, struct tng_chain *chain, const char *name, struct tng_residue **residue); /* Set the name of a residue. - *tng_data is a pointer to the trajectory containing the atom. + tng_data is the trajectory data container containing the residue. *residue is a pointer to the residue to rename. *new_name is a string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_residue_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_residue_name(tng_trajectory_t tng_data, struct tng_residue *residue, const char *new_name); @@ -535,57 +538,57 @@ tng_function_status tng_set_residue_name(struct tng_trajectory *tng_data, **atom is a pointer to a pointer to the newly created atom. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_add_atom_to_residue(struct tng_trajectory *tng_data, +tng_function_status tng_add_atom_to_residue(tng_trajectory_t tng_data, struct tng_residue *residue, const char *atom_name, const char *atom_type, struct tng_atom **atom); /* Set the name of an atom. - *tng_data is a pointer to the trajectory containing the atom. + tng_data is the trajectory data container containing the atom. *atom is a pointer to the atom to rename. *new_name is a string containing the wanted name. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_atom_name(struct tng_trajectory *tng_data, +tng_function_status tng_set_atom_name(tng_trajectory_t tng_data, struct tng_atom *atom, const char *new_name); /* Set the atom type of an atom. - *tng_data is a pointer to the trajectory containing the atom. + tng_data is the trajectory data container containing the atom. *atom is a pointer to the atom to change. *new_name is a string containing the atom type. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_set_atom_type(struct tng_trajectory *tng_data, +tng_function_status tng_set_atom_type(tng_trajectory_t tng_data, struct tng_atom *atom, const char *new_type); /* Read the header blocks from the input_file of tng_data. The trajectory blocks must be read separately and iteratively in chunks to fit in memory. - *tng_data is a pointer to trajectory data. tng_data->input_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_file_headers(struct tng_trajectory *tng_data, +tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, tng_close_file_flag close_file); /* Write the header blocks to the output_file of tng_data. The trajectory blocks must be written separately and iteratively in chunks to fit in memory. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the output_file will be closed after writing the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_write_file_headers(struct tng_trajectory *tng_data, +tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, tng_close_file_flag close_file); /* Read one (the next) block (of any kind) from the input_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->input_file_path specifies which + 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_data is a pointer to the struct which will be populated with the data. If block_data->input_file_pos > 0 it is the position from where the reading @@ -593,49 +596,36 @@ tng_function_status tng_write_file_headers(struct tng_trajectory *tng_data, If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_next_block(struct tng_trajectory *tng_data, +tng_function_status tng_read_next_block(tng_trajectory_t tng_data, struct tng_gen_block *block_data, tng_close_file_flag close_file); -/* Write one block (of any kind) to the output_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which - file to read from. If the file (output_file) is not open it will be opened. - *block_data is a pointer to the struct containing the - data. If block_data->output_file_pos > 0 it is the position from where the writing - starts otherwise it starts from the current position. - If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after writing the data. - Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error - has occurred or TRG_CRITICAL (2) if a major error has occured. */ -// tng_function_status tng_write_block(struct tng_trajectory *tng_data, -// struct tng_gen_block *block_data, -// tng_close_file_flag close_file); - /* Read one (the next) frame set, including toc, mapping and related data blocks from the input_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->input_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_next_frame_set(struct tng_trajectory *tng_data, +tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, tng_close_file_flag close_file); /* Write one (the next) frame set, including toc, mapping and related data blocks to the output_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the output_file will be closed after writing the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_write_frame_set(struct tng_trajectory *tng_data, +tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, tng_close_file_flag close_file); -tng_function_status tng_new_frame_set(struct tng_trajectory *tng_data, +tng_function_status tng_new_frame_set(tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames); -tng_function_status tng_add_particle_data_block(struct tng_trajectory *tng_data, +tng_function_status tng_add_particle_data_block(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, @@ -649,109 +639,109 @@ tng_function_status tng_add_particle_data_block(struct tng_trajectory *tng_data, /* Read one (the next) trajectory block from the input_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->input_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_next_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_read_next_traj_block(tng_trajectory_t tng_data, tng_close_file_flag close_file); /* Write one (the next) trajectory block to the output_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the output_file will be closed after writing the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_write_next_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_write_next_traj_block(tng_trajectory_t tng_data, tng_close_file_flag close_file); /* Read one trajectory block from the input_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->input_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_read_traj_block(tng_trajectory_t tng_data, int64_t block_id, tng_close_file_flag close_file); /* Write one trajectory block to the output_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which + 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. block_id is the ID of the block to write. If close_file == TRG_CLOSE_FILE (1) the output_file will be closed after writing the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_write_traj_block(struct tng_trajectory *tng_data, +tng_function_status tng_write_traj_block(tng_trajectory_t tng_data, int64_t block_id, tng_close_file_flag close_file); /* Read a requested frame set. - *tng_data is a pointer to trajectory data. tng_data->current_trajectory_frame_set + tng_data is a trajectory data container. tng_data->current_trajectory_frame_set will be the read frame set. frame_set_nr is the number of the frame set to return (starting from 0). Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_frame_set_nr(struct tng_trajectory *tng_data, +tng_function_status tng_read_frame_set_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 pointer to trajectory data. tng_data->input_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_frame_nr(struct tng_trajectory *tng_data, +tng_function_status tng_read_frame_nr(tng_trajectory_t tng_data, int64_t frame_nr, tng_close_file_flag close_file); /* Write one trajectory frame to the output_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which + 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. If close_file == TRG_CLOSE_FILE (1) the output_file will be closed after writing the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_write_frame_nr(struct tng_trajectory *tng_data, +tng_function_status tng_write_frame_nr(tng_trajectory_t tng_data, int64_t frame_nr, tng_close_file_flag close_file); /* Read a number of consecutive trajectory frames from the input_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->input_file_path specifies which + 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. start_frame_nr is the index number of the first frame to read. end_frame_nr is the index number of the last frame to read. If close_file == TRG_CLOSE_FILE (1) the input_file will be closed after reading the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_read_frame_nrs(struct tng_trajectory *tng_data, +tng_function_status tng_read_frame_nrs(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr, tng_close_file_flag close_file); /* Write a number of consecutive trajectory frames to the output_file of tng_data. - *tng_data is a pointer to trajectory data. tng_data->output_file_path specifies which + tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (input_file) is not open it will be opened. start_frame_nr is the index number of the first frame to write. end_frame_nr is the index number of the last frame to write. If close_file == TRG_CLOSE_FILE (1) the output_file will be closed after writing the data. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_write_frame_nrs(struct tng_trajectory *tng_data, +tng_function_status tng_write_frame_nrs(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr, tng_close_file_flag close_file); /* Get the date and time of initial file creation in ISO format (string). - *tng_data is a pointer to trajectory data. + tng_data is a trajectory data container. *time is a pointer to the string in which the date will be stored. Memory must be reserved beforehand. Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_get_time_str(struct tng_trajectory *tng_data, char *time); +tng_function_status tng_get_time_str(tng_trajectory_t tng_data, char *time); #ifdef __cplusplus } /* end extern "C" */ |