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Diffstat (limited to 'src/lib/tng_io.c')
-rw-r--r--src/lib/tng_io.c87
1 files changed, 43 insertions, 44 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index 51fa9c2..d6b6729 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -961,11 +961,11 @@ static tng_function_status tng_read_molecules_block
const tng_hash_mode hash_mode)
{
int i, j, k, l, len, offset = 0;
- struct tng_molecule *molecule;
- struct tng_chain *chain;
- struct tng_residue *residue;
- struct tng_atom *atom;
- struct tng_bond *bond;
+ tng_molecule_t molecule;
+ tng_chain_t chain;
+ tng_residue_t residue;
+ tng_atom_t atom;
+ tng_bond_t bond;
tng_bool same_hash;
if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS)
@@ -1035,7 +1035,7 @@ static tng_function_status tng_read_molecules_block
tng_data->n_particles = 0;
- tng_data->molecules = (struct tng_molecule *)
+ tng_data->molecules = (tng_molecule_t)
malloc(tng_data->n_molecules *
sizeof(struct tng_molecule));
if(!tng_data->molecules)
@@ -1160,7 +1160,7 @@ static tng_function_status tng_read_molecules_block
tng_data->n_particles += molecule->n_atoms *
tng_data->molecule_cnt_list[i];
- molecule->chains = (struct tng_chain *) malloc(molecule->n_chains *
+ molecule->chains = (tng_chain_t ) malloc(molecule->n_chains *
sizeof(struct tng_chain));
if(!molecule->chains)
{
@@ -1173,7 +1173,7 @@ static tng_function_status tng_read_molecules_block
chain = molecule->chains;
- molecule->residues = (struct tng_residue *)
+ molecule->residues = (tng_residue_t )
malloc(molecule->n_residues *
sizeof(struct tng_residue));
if(!molecule->residues)
@@ -1187,7 +1187,7 @@ static tng_function_status tng_read_molecules_block
residue = molecule->residues;
- molecule->atoms = (struct tng_atom *) malloc(molecule->n_atoms *
+ molecule->atoms = (tng_atom_t ) malloc(molecule->n_atoms *
sizeof(struct tng_atom));
if(!molecule->atoms)
{
@@ -1323,7 +1323,7 @@ static tng_function_status tng_read_molecules_block
}
offset += sizeof(molecule->n_bonds);
- molecule->bonds = (struct tng_bond *) malloc(molecule->n_bonds *
+ molecule->bonds = (tng_bond_t ) malloc(molecule->n_bonds *
sizeof(struct tng_bond));
if(!molecule->bonds)
{
@@ -1371,7 +1371,6 @@ static tng_function_status tng_read_molecules_block
return(TNG_SUCCESS);
}
-/* FIXME: Update this according to the new specs */
static tng_function_status tng_write_molecules_block
(tng_trajectory_t tng_data,
struct tng_gen_block *block,
@@ -1380,11 +1379,11 @@ static tng_function_status tng_write_molecules_block
{
int len = 0;
int i, j, k, l, offset = 0;
- struct tng_molecule *molecule;
- struct tng_chain *chain;
- struct tng_residue *residue;
- struct tng_atom *atom;
- struct tng_bond *bond;
+ tng_molecule_t molecule;
+ tng_chain_t chain;
+ tng_residue_t residue;
+ tng_atom_t atom;
+ tng_bond_t bond;
if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS)
{
@@ -4724,7 +4723,7 @@ tng_function_status tng_destroy_block(struct tng_gen_block *block)
}
tng_function_status tng_set_atom_name(tng_trajectory_t tng_data,
- struct tng_atom *atom,
+ tng_atom_t atom,
const char *new_name)
{
int len;
@@ -4753,7 +4752,7 @@ tng_function_status tng_set_atom_name(tng_trajectory_t tng_data,
}
tng_function_status tng_set_atom_type(tng_trajectory_t tng_data,
- struct tng_atom *atom,
+ tng_atom_t atom,
const char *new_type)
{
int len;
@@ -4781,7 +4780,7 @@ tng_function_status tng_set_atom_type(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
-tng_function_status tng_init_atom(struct tng_atom *atom)
+tng_function_status tng_init_atom(tng_atom_t atom)
{
atom->name = 0;
atom->atom_type = 0;
@@ -4789,7 +4788,7 @@ tng_function_status tng_init_atom(struct tng_atom *atom)
return(TNG_SUCCESS);
}
-tng_function_status tng_destroy_atom(struct tng_atom *atom)
+tng_function_status tng_destroy_atom(tng_atom_t atom)
{
if(atom->name)
{
@@ -4807,14 +4806,14 @@ tng_function_status tng_destroy_atom(struct tng_atom *atom)
tng_function_status tng_add_molecule(tng_trajectory_t tng_data,
const char *name,
- struct tng_molecule **molecule)
+ tng_molecule_t *molecule)
{
- struct tng_molecule *new_molecules;
+ tng_molecule_t new_molecules;
int64_t *new_molecule_cnt_list;
int id, i;
tng_bool found_id = TRUE;
- new_molecules = (struct tng_molecule *)realloc(tng_data->molecules,
+ new_molecules = (tng_molecule_t)realloc(tng_data->molecules,
sizeof(struct tng_molecule) *
(tng_data->n_molecules + 1));
@@ -4876,7 +4875,7 @@ tng_function_status tng_add_molecule(tng_trajectory_t tng_data,
}
tng_function_status tng_set_molecule_name(tng_trajectory_t tng_data,
- struct tng_molecule *molecule,
+ tng_molecule_t molecule,
const char *new_name)
{
int len;
@@ -4905,7 +4904,7 @@ tng_function_status tng_set_molecule_name(tng_trajectory_t tng_data,
}
tng_function_status tng_get_molecule_cnt(tng_trajectory_t tng_data,
- struct tng_molecule *molecule,
+ tng_molecule_t molecule,
int64_t *cnt)
{
int i, index = -1;
@@ -4928,7 +4927,7 @@ tng_function_status tng_get_molecule_cnt(tng_trajectory_t tng_data,
}
tng_function_status tng_set_molecule_cnt(tng_trajectory_t tng_data,
- struct tng_molecule *molecule,
+ tng_molecule_t molecule,
const int64_t cnt)
{
int i, index = -1, old_cnt;
@@ -4955,13 +4954,13 @@ tng_function_status tng_set_molecule_cnt(tng_trajectory_t tng_data,
}
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)
{
- struct tng_chain *new_chains;
+ tng_chain_t new_chains;
- new_chains = (struct tng_chain *) realloc(molecule->chains,
+ new_chains = (tng_chain_t ) realloc(molecule->chains,
sizeof(struct tng_chain) *
(molecule->n_chains + 1));
@@ -4990,7 +4989,7 @@ tng_function_status tng_add_chain_to_molecule(tng_trajectory_t tng_data,
}
tng_function_status tng_set_chain_name(tng_trajectory_t tng_data,
- struct tng_chain *chain,
+ tng_chain_t chain,
const char *new_name)
{
int len;
@@ -5019,13 +5018,13 @@ tng_function_status tng_set_chain_name(tng_trajectory_t tng_data,
}
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)
{
int curr_index;
- struct tng_residue *new_residues, *temp_residue, *last_residue;
- struct tng_molecule *molecule = chain->molecule;
+ tng_residue_t new_residues, temp_residue, last_residue;
+ tng_molecule_t molecule = chain->molecule;
if(chain->n_residues)
{
@@ -5037,7 +5036,7 @@ tng_function_status tng_add_residue_to_chain(tng_trajectory_t tng_data,
curr_index = -1;
}
- new_residues = (struct tng_residue *) realloc(molecule->residues,
+ new_residues = (tng_residue_t ) realloc(molecule->residues,
sizeof(struct tng_residue) *
(molecule->n_residues + 1));
@@ -5096,7 +5095,7 @@ tng_function_status tng_add_residue_to_chain(tng_trajectory_t tng_data,
}
tng_function_status tng_set_residue_name(tng_trajectory_t tng_data,
- struct tng_residue *residue,
+ tng_residue_t residue,
const char *new_name)
{
int len;
@@ -5125,14 +5124,14 @@ tng_function_status tng_set_residue_name(tng_trajectory_t tng_data,
}
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)
{
int curr_index;
- struct tng_atom *new_atoms, *temp_atom, *last_atom;
- struct tng_molecule *molecule = residue->chain->molecule;
+ tng_atom_t new_atoms, temp_atom, last_atom;
+ tng_molecule_t molecule = residue->chain->molecule;
if(residue->n_atoms)
{
@@ -5144,7 +5143,7 @@ tng_function_status tng_add_atom_to_residue(tng_trajectory_t tng_data,
curr_index = -1;
}
- new_atoms = (struct tng_atom *) realloc(molecule->atoms,
+ new_atoms = (tng_atom_t ) realloc(molecule->atoms,
sizeof(struct tng_atom) *
(molecule->n_atoms + 1));
@@ -5202,7 +5201,7 @@ tng_function_status tng_add_atom_to_residue(tng_trajectory_t tng_data,
}
-tng_function_status tng_init_molecule(struct tng_molecule *molecule)
+tng_function_status tng_init_molecule(tng_molecule_t molecule)
{
molecule->name = 0;
molecule->n_chains = 0;
@@ -5217,7 +5216,7 @@ tng_function_status tng_init_molecule(struct tng_molecule *molecule)
return(TNG_SUCCESS);
}
-tng_function_status tng_destroy_molecule(struct tng_molecule *molecule)
+tng_function_status tng_destroy_molecule(tng_molecule_t molecule)
{
int i;
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