diff options
Diffstat (limited to 'src/lib/trg_io.h')
| -rw-r--r-- | src/lib/trg_io.h | 152 |
1 files changed, 76 insertions, 76 deletions
diff --git a/src/lib/trg_io.h b/src/lib/trg_io.h index 7bdca5e..d321e6e 100644 --- a/src/lib/trg_io.h +++ b/src/lib/trg_io.h @@ -88,44 +88,44 @@ extern "C" #endif struct trg_bond { - uint64_t from_atom_id; /* One of the atoms of the bond */ - uint64_t to_atom_id; /* The other atom of the bond */ + int64_t from_atom_id; /* One of the atoms of the bond */ + int64_t to_atom_id; /* The other atom of the bond */ }; struct trg_atom { struct trg_residue *residue; /* The molecule containing this atom */ - uint64_t id; /* A unique (per molecule) ID number of the atom */ + int64_t id; /* A unique (per molecule) ID number of the atom */ char *atom_type; /* The atom_type (depending on the forcefield) */ char *name; /* The name of the atom */ }; struct trg_residue { struct trg_chain *chain; /* The chain containing this residue */ - uint64_t id; /* A unique (per chain) ID number of the residue */ + int64_t id; /* A unique (per chain) ID number of the residue */ char *name; /* The name of the residue */ - uint64_t n_atoms; /* The number of atoms in the residue */ + int64_t n_atoms; /* The number of atoms in the residue */ struct trg_atom *atoms; /* A list of atoms in the residue */ }; struct trg_chain { struct trg_molecule *molecule; /* The molecule containing this chain */ - uint64_t id; /* A unique (per molecule) ID number of the chain */ + int64_t id; /* A unique (per molecule) ID number of the chain */ char *name; /* The name of the chain */ - uint64_t n_residues; /* The number of residues in the chain */ + int64_t n_residues; /* The number of residues in the chain */ struct trg_residue *residues; /* A list of residues in the chain */ }; struct trg_molecule { - uint64_t id; /* A unique ID number of the molecule */ - uint64_t quaternary_str; /* Quaternary structure of the molecule. + int64_t id; /* A unique ID number of the molecule */ + int64_t quaternary_str; /* Quaternary structure of the molecule. 1 => monomeric 2 => dimeric 3 => trimeric etc */ - uint64_t n_chains; /* The number of chains in the molecule */ - uint64_t n_residues; /* The number of residues in the molecule */ - uint64_t n_atoms; /* The number of atoms in the molecule */ - uint64_t n_bonds; /* The number of bonds in the molecule. + int64_t n_chains; /* The number of chains in the molecule */ + int64_t n_residues; /* The number of residues in the molecule */ + int64_t n_atoms; /* The number of atoms in the molecule */ + int64_t n_bonds; /* The number of bonds in the molecule. If the bonds are not specified this value can be 0. */ char *name; /* The name of the molecule */ @@ -136,51 +136,51 @@ struct trg_molecule { }; struct trg_gen_block { - uint64_t header_contents_size; /* The size of the block header in bytes */ - uint64_t block_contents_size; /* The size of the block contents in bytes */ - uint64_t id; /* The ID of the block to determine its type */ + int64_t header_contents_size; /* The size of the block header in bytes */ + int64_t block_contents_size; /* The size of the block contents in bytes */ + int64_t id; /* The ID of the block to determine its type */ char hash[TRG_HASH_LEN]; /* The MD5 hash of the block to verify integrity */ char *name; /* The name of the block */ - uint64_t block_version; /* The library version used to write the block */ + int64_t block_version; /* The library version used to write the block */ char *header_contents; /* The full block header contents */ char *block_contents; /* The full block contents */ }; struct trg_frame_set_toc { - uint64_t n_blocks; /* The number of blocks listed in this + int64_t n_blocks; /* The number of blocks listed in this table of contents */ char **block_names; /* A list of block names */ }; struct trg_particle_mapping { - uint64_t num_first_particle; /* The index number of the first particle + int64_t num_first_particle; /* The index number of the first particle in this mapping block */ - uint64_t n_particles; /* The number of particles list in this + int64_t n_particles; /* The number of particles list in this mapping block */ - uint64_t *real_particle_numbers; /* the mapping of index numbers to the + int64_t *real_particle_numbers; /* the mapping of index numbers to the real particle numbers in the trajectory */ }; struct trg_trajectory_frame_set { struct trg_frame_set_toc contents; /* The table of contents of this frame set */ - uint64_t n_mapping_blocks; /* The number of different particle + int64_t n_mapping_blocks; /* The number of different particle mapping blocks present. */ struct trg_particle_mapping *mappings; /* The atom mappings of this frame set */ - uint64_t first_frame; /* The first frame of this frame set */ - uint64_t n_frames; /* The number of frames in this frame set */ - uint64_t *molecule_cnt_list; /* A list of the number of each molecule + int64_t first_frame; /* The first frame of this frame set */ + int64_t n_frames; /* The number of frames in this frame set */ + int64_t *molecule_cnt_list; /* A list of the number of each molecule type - only used when using variable number of atoms */ - uint64_t n_particles; /* The number of particles/atoms - only + int64_t n_particles; /* The number of particles/atoms - only used when using variable number of atoms */ - uint64_t next_frame_set_file_pos; /* The file position of the next frame set */ - uint64_t prev_frame_set_file_pos; /* The file position of the previous + int64_t next_frame_set_file_pos; /* The file position of the next frame set */ + int64_t prev_frame_set_file_pos; /* The file position of the previous frame set */ - uint64_t long_stride_next_frame_set_file_pos; /* The file position of the frame + int64_t long_stride_next_frame_set_file_pos; /* The file position of the frame set one stride step ahead */ - uint64_t long_stride_prev_frame_set_file_pos; /* The file position of the frame + int64_t long_stride_prev_frame_set_file_pos; /* The file position of the frame set one stride step behind */ /* The data blocks in a frame set are trajectory data blocks */ @@ -203,7 +203,7 @@ union data_values { /* FIXME: Should there be a pointer to a trg_gen_block from each data block? */ struct trg_particle_data { - uint64_t block_id; /* The block ID of the data block + int64_t block_id; /* The block ID of the data block containing this particle data. This is used to determine the kind of data that is stored */ @@ -211,16 +211,16 @@ struct trg_particle_data { This is used to determine the kind of data that is stored */ trg_data_type datatype; /* The type of data stored. */ - uint64_t first_frame_with_data; /* The first frame number of the + int64_t first_frame_with_data; /* The first frame number of the first data point */ - uint64_t n_frames; /* The number of frames in this + int64_t n_frames; /* The number of frames in this frame set */ - uint64_t n_values_per_frame; /* The number of values stored per + int64_t n_values_per_frame; /* The number of values stored per frame */ - uint64_t stride_length; /* The number of frames between + int64_t stride_length; /* The number of frames between each data point - e.g. when storing sparse data. */ - uint64_t codec_id; /* ID of the CODEC used for compression + int64_t codec_id; /* ID of the CODEC used for compression 0 == no compression. */ double compression_multiplier; /* The multiplier used for getting integer values for compression */ @@ -230,16 +230,16 @@ struct trg_particle_data { }; struct trg_data { - uint64_t block_id; + int64_t block_id; char *block_name; /* The name of the data block. This is used to determine the kind of data that is stored */ trg_data_type datatype; /* The type of data stored. */ - uint64_t first_frame_with_data; - uint64_t n_frames; - uint64_t n_values_per_frame; - uint64_t stride_length; - uint64_t codec_id; /* ID of the CODEC used for compression + int64_t first_frame_with_data; + int64_t n_frames; + int64_t n_values_per_frame; + int64_t stride_length; + int64_t codec_id; /* ID of the CODEC used for compression 0 == no compression. */ double compression_multiplier; union data_values **values; /* A 2-dimensional array of values, @@ -267,7 +267,7 @@ struct trg_trajectory { char *forcefield_name; /* The forcefield used in the simulations */ char *user_name; /* The name of the user running the simulations */ - uint64_t time; /* The time (n seconds since 1970) when + int64_t time; /* The time (n seconds since 1970) when the file was created */ char *computer_name; /* The name of the computer on which the simulations were performed */ @@ -276,38 +276,38 @@ struct trg_trajectory { char var_num_atoms_flag; /* A flag indicating if the number of atoms can vary throughout the simulation, e.g. using a grand canonical ensemble */ - uint64_t frame_set_n_frames; /* The number of frames in a frame set. + int64_t frame_set_n_frames; /* The number of frames in a frame set. It is allowed to have frame sets with fewer frames, but this will help searching for specific frames */ - uint64_t stride_length; /* The number of frame sets in a long stride + int64_t stride_length; /* The number of frame sets in a long stride step */ - uint64_t n_molecules; /* The number of different kinds of + int64_t n_molecules; /* The number of different kinds of molecules in the trajectory */ struct trg_molecule *molecules; /* A list of molecules in the trajectory */ - uint64_t *molecule_cnt_list; /* A list of the count of each molecule - + int64_t *molecule_cnt_list; /* A list of the count of each molecule - if using variable number of particles this will be specified in each frame set */ - uint64_t n_particles; /* The total number of particles/atoms. If + int64_t n_particles; /* The total number of particles/atoms. If using variable number of particles this will be specified in each frame set */ - uint64_t n_id_name_pairs; /* The number of ID-name + int64_t n_id_name_pairs; /* The number of ID-name pairs */ struct trg_block_id_name_pair *id_name_pairs; /* A list of ID-name pairs */ - uint64_t first_trajectory_frame_set_input_file_pos; /* The pos in the src + int64_t first_trajectory_frame_set_input_file_pos; /* The pos in the src file of the first frame set */ - uint64_t first_trajectory_frame_set_output_file_pos; /* The pos in the dest + int64_t first_trajectory_frame_set_output_file_pos; /* The pos in the dest file of the first frame set */ - uint64_t last_trajectory_frame_set_input_file_pos; /* The pos in the src + int64_t last_trajectory_frame_set_input_file_pos; /* The pos in the src file of the last frame set */ - uint64_t last_trajectory_frame_set_output_file_pos; /* The pos in the dest + int64_t last_trajectory_frame_set_output_file_pos; /* The pos in the dest file of the last frame set */ struct trg_trajectory_frame_set current_trajectory_frame_set; /* The currently @@ -319,12 +319,12 @@ struct trg_trajectory { long int current_trajectory_frame_set_output_file_pos;/* The pos in the dest file of the current frame set */ - uint64_t n_trajectory_frame_sets; /* The number of frame sets + int64_t n_trajectory_frame_sets; /* The number of frame sets in the trajectory */ - uint64_t n_trajectory_blocks; /* The number of trajectory blocks + int64_t n_trajectory_blocks; /* The number of trajectory blocks in the file */ - uint64_t n_non_trajectory_blocks; /* The number of non-trajectory blocks + int64_t n_non_trajectory_blocks; /* The number of non-trajectory blocks in the file */ struct trg_gen_block non_trajectory_blocks[32]; /* A list of non-trajectory blocks */ @@ -471,7 +471,7 @@ trg_function_status trg_set_molecule_name(struct trg_trajectory *trg_data, has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_get_molecule_cnt(struct trg_trajectory *trg_data, struct trg_molecule *molecule, - uint64_t *cnt); + int64_t *cnt); /* Set the count of a molecule. *trg_data is a pointer to the trajectory containing the molecule. @@ -481,7 +481,7 @@ trg_function_status trg_get_molecule_cnt(struct trg_trajectory *trg_data, has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_set_molecule_cnt(struct trg_trajectory *trg_data, struct trg_molecule *molecule, - uint64_t cnt); + int64_t cnt); /* Add a chain to a molecule. *trg_data is a pointer to the trajectory containing the molecule. @@ -632,19 +632,19 @@ trg_function_status trg_write_frame_set(struct trg_trajectory *trg_data, trg_close_file_flag close_file); trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, - const uint64_t first_frame, - const uint64_t n_frames); + const int64_t first_frame, + const int64_t n_frames); trg_function_status trg_add_particle_data_block(struct trg_trajectory *trg_data, - const uint64_t id, + const int64_t id, const char *block_name, const char datatype, - const uint64_t n_frames, - const uint64_t n_values_per_frame, - const uint64_t stride_length, - const uint64_t first_particle_number, - const uint64_t n_particles, - uint64_t codec_id, + const int64_t n_frames, + const int64_t n_values_per_frame, + const int64_t stride_length, + const int64_t first_particle_number, + const int64_t n_particles, + int64_t codec_id, void *new_data); @@ -674,7 +674,7 @@ trg_function_status trg_write_next_traj_block(struct trg_trajectory *trg_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. */ trg_function_status trg_read_traj_block(struct trg_trajectory *trg_data, - uint64_t block_id, + int64_t block_id, trg_close_file_flag close_file); /* Write one trajectory block to the output_file of trg_data. @@ -685,7 +685,7 @@ trg_function_status trg_read_traj_block(struct trg_trajectory *trg_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. */ trg_function_status trg_write_traj_block(struct trg_trajectory *trg_data, - uint64_t block_id, + int64_t block_id, trg_close_file_flag close_file); /* Read a requested frame set. @@ -695,7 +695,7 @@ trg_function_status trg_write_traj_block(struct trg_trajectory *trg_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. */ trg_function_status trg_read_frame_set_nr(struct trg_trajectory *trg_data, - uint64_t frame_set_nr); + int64_t frame_set_nr); /* Read one trajectory frame from the input_file of trg_data. *trg_data is a pointer to trajectory data. trg_data->input_file_path specifies which @@ -705,7 +705,7 @@ trg_function_status trg_read_frame_set_nr(struct trg_trajectory *trg_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. */ trg_function_status trg_read_frame_nr(struct trg_trajectory *trg_data, - uint64_t frame_nr, + int64_t frame_nr, trg_close_file_flag close_file); /* Write one trajectory frame to the output_file of trg_data. @@ -716,7 +716,7 @@ trg_function_status trg_read_frame_nr(struct trg_trajectory *trg_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. */ trg_function_status trg_write_frame_nr(struct trg_trajectory *trg_data, - uint64_t frame_nr, + int64_t frame_nr, trg_close_file_flag close_file); /* Read a number of consecutive trajectory frames from the input_file of trg_data. @@ -728,8 +728,8 @@ trg_function_status trg_write_frame_nr(struct trg_trajectory *trg_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. */ trg_function_status trg_read_frame_nrs(struct trg_trajectory *trg_data, - uint64_t start_frame_nr, - uint64_t end_frame_nr, + int64_t start_frame_nr, + int64_t end_frame_nr, trg_close_file_flag close_file); /* Write a number of consecutive trajectory frames to the output_file of trg_data. @@ -741,8 +741,8 @@ trg_function_status trg_read_frame_nrs(struct trg_trajectory *trg_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. */ trg_function_status trg_write_frame_nrs(struct trg_trajectory *trg_data, - uint64_t start_frame_nr, - uint64_t end_frame_nr, + int64_t start_frame_nr, + int64_t end_frame_nr, trg_close_file_flag close_file); /* Get the date and time of initial file creation in ISO format (string). |