diff options
Diffstat (limited to 'src/lib/tng_io.h')
| -rw-r--r-- | src/lib/tng_io.h | 57 |
1 files changed, 31 insertions, 26 deletions
diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 23de289..cfb95d5 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -82,6 +82,11 @@ typedef enum {TNG_CHAR_DATA, typedef struct tng_trajectory *tng_trajectory_t; +typedef struct tng_molecule *tng_molecule_t; +typedef struct tng_chain *tng_chain_t; +typedef struct tng_residue *tng_residue_t; +typedef struct tng_atom *tng_atom_t; +typedef struct tng_bond *tng_bond_t; #ifdef __cplusplus extern "C" @@ -94,26 +99,26 @@ struct tng_bond { }; struct tng_atom { - struct tng_residue *residue; /* The molecule containing this atom */ + tng_residue_t residue; /* The molecule containing this 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 tng_residue { - struct tng_chain *chain; /* The chain containing this residue */ + tng_chain_t chain; /* The chain containing this residue */ int64_t id; /* A unique (per chain) ID number of the residue */ char *name; /* The name of the residue */ int64_t n_atoms; /* The number of atoms in the residue */ - struct tng_atom *atoms; /* A list of atoms in the residue */ + tng_atom_t atoms; /* A list of atoms in the residue */ }; struct tng_chain { - struct tng_molecule *molecule; /* The molecule containing this chain */ + tng_molecule_t molecule; /* The molecule containing this chain */ int64_t id; /* A unique (per molecule) ID number of the chain */ char *name; /* The name of the chain */ int64_t n_residues; /* The number of residues in the chain */ - struct tng_residue *residues; /* A list of residues in the chain */ + tng_residue_t residues; /* A list of residues in the chain */ }; struct tng_molecule { @@ -130,10 +135,10 @@ struct tng_molecule { If the bonds are not specified this value can be 0. */ char *name; /* The name of the molecule */ - struct tng_chain *chains; /* A list of chains in the molecule */ - struct tng_residue *residues; /* A list of residues in the molecule */ - struct tng_atom *atoms; /* A list of the atoms in the molecule */ - struct tng_bond *bonds; /* A list of the bonds in the molecule */ + tng_chain_t chains; /* A list of chains in the molecule */ + tng_residue_t residues; /* A list of residues in the molecule */ + tng_atom_t atoms; /* A list of the atoms in the molecule */ + tng_bond_t bonds; /* A list of the bonds in the molecule */ }; struct tng_gen_block { @@ -286,7 +291,7 @@ struct tng_trajectory { int64_t n_molecules; /* The number of different kinds of molecules in the trajectory */ - struct tng_molecule *molecules; /* A list of molecules in the trajectory */ + tng_molecule_t molecules; /* A list of molecules in the trajectory */ 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 */ @@ -412,14 +417,14 @@ tng_function_status tng_set_signature(tng_trajectory_t tng_data, *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(struct tng_molecule *molecule); +tng_function_status tng_init_molecule(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(struct tng_molecule *molecule); +tng_function_status tng_destroy_molecule(tng_molecule_t molecule); /* Setup a data block. *block is a pointer to pre-allocated memory. @@ -452,7 +457,7 @@ tng_function_status tng_set_block_name(tng_trajectory_t tng_data, has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_add_molecule(tng_trajectory_t tng_data, const char *name, - struct tng_molecule **molecule); + tng_molecule_t *molecule); /* Set the name of a molecule. tng_data is the trajectory data container containing the molecule.. @@ -461,7 +466,7 @@ tng_function_status tng_add_molecule(tng_trajectory_t tng_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_set_molecule_name(tng_trajectory_t tng_data, - struct tng_molecule *molecule, + tng_molecule_t molecule, const char *new_name); /* Set the count of a molecule. @@ -471,7 +476,7 @@ tng_function_status tng_set_molecule_name(tng_trajectory_t tng_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_get_molecule_cnt(tng_trajectory_t tng_data, - struct tng_molecule *molecule, + tng_molecule_t molecule, int64_t *cnt); /* Set the count of a molecule. @@ -481,7 +486,7 @@ tng_function_status tng_get_molecule_cnt(tng_trajectory_t tng_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_set_molecule_cnt(tng_trajectory_t tng_data, - struct tng_molecule *molecule, + tng_molecule_t molecule, int64_t cnt); /* Add a chain to a molecule. @@ -492,9 +497,9 @@ tng_function_status tng_set_molecule_cnt(tng_trajectory_t tng_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_add_chain_to_molecule(tng_trajectory_t tng_data, - struct tng_molecule *molecule, + tng_molecule_t molecule, const char *name, - struct tng_chain **chain); + tng_chain_t *chain); /* Set the name of a chain. tng_data is the trajectory data container containing the atom.. @@ -503,7 +508,7 @@ tng_function_status tng_add_chain_to_molecule(tng_trajectory_t tng_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_set_chain_name(tng_trajectory_t tng_data, - struct tng_chain *chain, + tng_chain_t chain, const char *new_name); /* Add a residue to a chain. @@ -514,9 +519,9 @@ tng_function_status tng_set_chain_name(tng_trajectory_t tng_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_add_residue_to_chain(tng_trajectory_t tng_data, - struct tng_chain *chain, + tng_chain_t chain, const char *name, - struct tng_residue **residue); + tng_residue_t *residue); /* Set the name of a residue. tng_data is the trajectory data container containing the residue.due. @@ -525,7 +530,7 @@ tng_function_status tng_add_residue_to_chain(tng_trajectory_t tng_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_set_residue_name(tng_trajectory_t tng_data, - struct tng_residue *residue, + tng_residue_t residue, const char *new_name); /* Add an atom to a residue. @@ -537,10 +542,10 @@ tng_function_status tng_set_residue_name(tng_trajectory_t tng_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_add_atom_to_residue(tng_trajectory_t tng_data, - struct tng_residue *residue, + tng_residue_t residue, const char *atom_name, const char *atom_type, - struct tng_atom **atom); + tng_atom_t *atom); /* Set the name of an atom. tng_data is the trajectory data container containing the atom.. @@ -549,7 +554,7 @@ tng_function_status tng_add_atom_to_residue(tng_trajectory_t tng_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_set_atom_name(tng_trajectory_t tng_data, - struct tng_atom *atom, + tng_atom_t atom, const char *new_name); /* Set the atom type of an atom. @@ -559,7 +564,7 @@ tng_function_status tng_set_atom_name(tng_trajectory_t tng_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_set_atom_type(tng_trajectory_t tng_data, - struct tng_atom *atom, + tng_atom_t atom, const char *new_type); /* Read the header blocks from the input_file of tng_data. |