diff options
Diffstat (limited to 'include')
| -rw-r--r-- | include/tng_io.h | 122 |
1 files changed, 95 insertions, 27 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 0bd15a0..c7cb9ba 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1,6 +1,6 @@ /* This code is part of the tng binary trajectory format. * - * VERSION 1.0 + * VERSION 1.1 * * Written by Magnus Lundborg * Copyright (c) 2012, The GROMACS development team. @@ -25,7 +25,7 @@ * Each block can contain MD5 hashes to verify data integrity and the file * can be signed by the user to ensure that the origin is correct. * - * This is version 1.0 of the TNG API. The intention is that this version of + * This is version 1.1 of the TNG API. The intention is that this version of * the API and ABI should be stable, but it is still possible that future * changes might make that impossible, in which case that will be clarified. * @@ -124,7 +124,7 @@ * for ( step = 1; step < step_num; step++ ) * { * compute ( np, nd, pos, vel, mass, force, &potential, &kinetic ); - * + * * if(step % step_save == 0) * { * // Write positions, velocities and forces @@ -153,7 +153,7 @@ * #include <stdlib.h> * #include <stdio.h> * #include <tng_io.h> - * + * * int main(int argc, char **argv) * { * tng_trajectory_t traj; @@ -164,31 +164,31 @@ * // Set a default frame range * int64_t first_frame = 0, last_frame = 5000; * int k; - * + * * // A reference must be passed to allocate memory * tng_util_trajectory_open(argv[1], 'r', &traj); - * + * * if(tng_num_frames_get(traj, &tot_n_frames) != TNG_SUCCESS) * { * printf("Cannot determine the number of frames in the file\n"); * tng_util_trajectory_close(&traj); * exit(1); * } - * + * * if(tng_num_particles_get(traj, &n_particles) != TNG_SUCCESS) * { * printf("Cannot determine the number of particles in the file\n"); * tng_util_trajectory_close(&traj); * exit(1); * } - * + * * printf("%"PRId64" frames in file\n", tot_n_frames); - * + * * if(last_frame > tot_n_frames - 1) * { * last_frame = tot_n_frames - 1; * } - * + * * if(tng_util_box_shape_read(traj, &box_shape, &stride_length) == * TNG_SUCCESS) * { @@ -203,10 +203,10 @@ * { * printf("Simulation box shape not set in the file (or could not be read)\n"); * } - * + * * n_frames = last_frame - first_frame + 1; - * - * + * + * * // Get the positions of all particles in the requested frame range. * // The positions are stored in the positions array. * // N.B. No proper error checks. @@ -233,14 +233,14 @@ * { * printf("Cannot read positions\n"); * } - * + * * // Free memory * if(positions) * { * free(positions); * } * tng_util_trajectory_close(&traj); - * + * * return(0); * } * @@ -1064,8 +1064,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy * @param tng_data is the trajectory data container containing the block.. * @param name is a pointer to the string containing the name of the new molecule. * @param molecule is a pointer to the newly created molecule. - * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major - * error has occured. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_add (tng_trajectory_t tng_data, @@ -1073,6 +1073,21 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add tng_molecule_t *molecule); /** + * @brief Add a molecule with a specific ID to the trajectory. + * @param tng_data is the trajectory data container containing the block.. + * @param name is a pointer to the string containing the name of the new molecule. + * @param id is the ID of the created molecule. + * @param molecule is a pointer to the newly created molecule. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add + (tng_trajectory_t tng_data, + const char *name, + const int64_t id, + tng_molecule_t *molecule); + +/** * @brief Set the name of a molecule. * @param tng_data is the trajectory data container containing the molecule.. * @param molecule is the molecule to rename. @@ -1138,8 +1153,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find * @param molecule is the molecule to add a chain to. * @param name is a string containing the name of the chain. * @param chain is a pointer to the newly created chain. - * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major - * error has occured. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add (tng_trajectory_t tng_data, @@ -1148,6 +1163,23 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add tng_chain_t *chain); /** + * @brief Add a chain with a specific id to a molecule. + * @param tng_data is the trajectory data container containing the molecule.. + * @param molecule is the molecule to add a chain to. + * @param name is a string containing the name of the chain. + * @param id is the ID of the created chain. + * @param chain is a pointer to the newly created chain. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *name, + const int64_t id, + tng_chain_t *chain); + +/** * @brief Set the name of a chain. * @param tng_data is the trajectory data container containing the atom.. * @param chain is the chain to rename. @@ -1185,8 +1217,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find * @param chain is the chain to add a residue to. * @param name is a string containing the name of the residue. * @param residue is a pointer to the newly created residue. - * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major - * error has occured. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add (tng_trajectory_t tng_data, @@ -1195,6 +1227,23 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add tng_residue_t *residue); /** + * @brief Add a residue with a specific ID to a chain. + * @param tng_data is the trajectory data container containing the chain.. + * @param chain is the chain to add a residue to. + * @param name is a string containing the name of the residue. + * @param id is the ID of the created residue. + * @param residue is a pointer to the newly created residue. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *name, + const int64_t id, + tng_residue_t *residue); + +/** * @brief Set the name of a residue. * @param tng_data is the trajectory data container containing the residue. * @param residue is the residue to rename. @@ -1214,8 +1263,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set * @param atom_name is a string containing the name of the atom. * @param atom_type is a string containing the atom type of the atom. * @param atom is a pointer to the newly created atom. - * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major - * error has occured. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add (tng_trajectory_t tng_data, @@ -1225,6 +1274,25 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add tng_atom_t *atom); /** + * @brief Add an atom with a specific ID to a residue. + * @param tng_data is the trajectory containing the residue. + * @param residue is the residue to add an atom to. + * @param atom_name is a string containing the name of the atom. + * @param atom_type is a string containing the atom type of the atom. + * @param id is the ID of the created atom. + * @param atom is a pointer to the newly created atom. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could + * not be set properly or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add + (tng_trajectory_t tng_data, + tng_residue_t residue, + const char *atom_name, + const char *atom_type, + const int64_t id, + tng_atom_t *atom); + +/** * @brief Set the name of an atom. * @param tng_data is the trajectory data container containing the atom. * @param atom is the atom to rename. @@ -1941,13 +2009,13 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close // 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, @@ -1958,7 +2026,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close // 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, @@ -1969,7 +2037,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close // const int64_t *res_ids, // const char **chain_names, // const int64_t *chain_ids); - + /** * @brief High-level function for reading the positions of all particles * from all frames. |