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-rw-r--r--src/lib/tng_io.c329
1 files changed, 232 insertions, 97 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index c7f5c10..9dc065f 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -1744,6 +1744,54 @@ static tng_function_status tng_chain_data_read(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
+/** Write the chain data of a molecules block.
+ * @param tng_data is a trajectory data container.
+ * @param block is a general block container.
+ * @param chain is the chain data container.
+ * @param offset is the offset of the block output and is updated when writing.
+ * @return TNG_SUCCESS(0) is successful.
+ */
+static tng_function_status tng_chain_data_write(tng_trajectory_t tng_data,
+ tng_gen_block_t block,
+ tng_chain_t chain,
+ int *offset)
+{
+ int len;
+
+ memcpy(block->block_contents+*offset, &chain->id, sizeof(chain->id));
+ if(tng_data->output_endianness_swap_func_64)
+ {
+ if(tng_data->output_endianness_swap_func_64(tng_data,
+ (int64_t *)block->header_contents+*offset)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(chain->id);
+
+ len = tng_min(strlen(chain->name) + 1, TNG_MAX_STR_LEN);
+ strncpy(block->block_contents + *offset, chain->name, len);
+ *offset += len;
+
+ memcpy(block->block_contents+*offset, &chain->n_residues,
+ sizeof(chain->n_residues));
+ if(tng_data->output_endianness_swap_func_64)
+ {
+ if(tng_data->output_endianness_swap_func_64(tng_data,
+ (int64_t *)block->header_contents+*offset)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(chain->n_residues);
+
+ return(TNG_SUCCESS);
+}
+
/** Read the residue data of a molecules block.
* @param tng_data is a trajectory data container.
* @param block is a general block container.
@@ -1796,6 +1844,54 @@ static tng_function_status tng_residue_data_read(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
+/** Write the residue data of a molecules block.
+ * @param tng_data is a trajectory data container.
+ * @param block is a general block container.
+ * @param residue is the residue data container.
+ * @param offset is the offset of the block output and is updated when writing.
+ * @return TNG_SUCCESS(0) is successful.
+ */
+static tng_function_status tng_residue_data_write(tng_trajectory_t tng_data,
+ tng_gen_block_t block,
+ tng_residue_t residue,
+ int *offset)
+{
+ int len;
+
+ memcpy(block->block_contents+*offset, &residue->id, sizeof(residue->id));
+ if(tng_data->output_endianness_swap_func_64)
+ {
+ if(tng_data->output_endianness_swap_func_64(tng_data,
+ (int64_t *)block->header_contents+*offset)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(residue->id);
+
+ len = tng_min(strlen(residue->name) + 1, TNG_MAX_STR_LEN);
+ strncpy(block->block_contents + *offset, residue->name, len);
+ *offset += len;
+
+ memcpy(block->block_contents+*offset, &residue->n_atoms,
+ sizeof(residue->n_atoms));
+ if(tng_data->output_endianness_swap_func_64)
+ {
+ if(tng_data->output_endianness_swap_func_64(tng_data,
+ (int64_t *)block->header_contents+*offset)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(residue->n_atoms);
+
+ return(TNG_SUCCESS);
+}
+
/** Read the atom data of a molecules block.
* @param tng_data is a trajectory data container.
* @param block is a general block container.
@@ -1841,6 +1937,45 @@ static tng_function_status tng_atom_data_read(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
+/** Write the atom data of a molecules block.
+ * @param tng_data is a trajectory data container.
+ * @param block is a general block container.
+ * @param atom is the atom data container.
+ * @param offset is the offset of the block output and is updated when writing.
+ * @return TNG_SUCCESS(0) is successful.
+ */
+static tng_function_status tng_atom_data_write(tng_trajectory_t tng_data,
+ tng_gen_block_t block,
+ tng_atom_t atom,
+ int *offset)
+{
+ int len;
+
+ memcpy(block->block_contents+*offset, &atom->id,
+ sizeof(atom->id));
+ if(tng_data->output_endianness_swap_func_64)
+ {
+ if(tng_data->output_endianness_swap_func_64(tng_data,
+ (int64_t *)block->header_contents+*offset)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(atom->id);
+
+ len = tng_min(strlen(atom->name) + 1, TNG_MAX_STR_LEN);
+ strncpy(block->block_contents + *offset, atom->name, len);
+ *offset += len;
+
+ len = tng_min(strlen(atom->atom_type) + 1, TNG_MAX_STR_LEN);
+ strncpy(block->block_contents + *offset, atom->atom_type, len);
+ *offset += len;
+
+ return(TNG_SUCCESS);
+}
+
/** Read a molecules block. Contains chain, residue and atom data
* @param tng_data is a trajectory data container.
* @param block is a general block container.
@@ -2079,6 +2214,10 @@ static tng_function_status tng_molecules_block_read
chain = molecule->chains;
}
+ else
+ {
+ chain = 0;
+ }
if(molecule->n_residues > 0)
{
@@ -2094,6 +2233,10 @@ static tng_function_status tng_molecules_block_read
residue = molecule->residues;
}
+ else
+ {
+ residue = 0;
+ }
molecule->atoms = malloc(molecule->n_atoms *
sizeof(struct tng_atom));
@@ -2107,34 +2250,73 @@ static tng_function_status tng_molecules_block_read
atom = molecule->atoms;
- /* Each molecule can contain chains - read them */
- for(j=molecule->n_chains; j--;)
+ if(molecule->n_chains > 0)
{
- chain->molecule = molecule;
+ /* Read the chains of the molecule */
+ for(j=molecule->n_chains; j--;)
+ {
+ chain->molecule = molecule;
- tng_chain_data_read(tng_data, block, chain, &offset);
+ tng_chain_data_read(tng_data, block, chain, &offset);
+
+ chain->residues = residue;
+
+ /* Read the residues of the chain */
+ for(k=chain->n_residues; k--;)
+ {
+ residue->chain = chain;
- chain->residues = residue;
- /* Read the residues of the chain */
- for(k=chain->n_residues; k--;)
+ tng_residue_data_read(tng_data, block, residue, &offset);
+
+ residue->atoms = atom;
+ /* Read the atoms of the residue */
+ for(l=residue->n_atoms; l--;)
+ {
+ atom->residue = residue;
+
+ tng_atom_data_read(tng_data, block, atom, &offset);
+
+ atom++;
+ }
+ residue++;
+ }
+ chain++;
+ }
+ }
+ else
+ {
+ if(molecule->n_residues > 0)
{
- residue->chain = chain;
+ for(k=molecule->n_residues; k--;)
+ {
+ residue->chain = 0;
- tng_residue_data_read(tng_data, block, residue, &offset);
+ tng_residue_data_read(tng_data, block, residue, &offset);
- residue->atoms = atom;
- /* Read the atoms of the residue */
- for(l=residue->n_atoms; l--;)
+ residue->atoms = atom;
+ /* Read the atoms of the residue */
+ for(l=residue->n_atoms; l--;)
+ {
+ atom->residue = residue;
+
+ tng_atom_data_read(tng_data, block, atom, &offset);
+
+ atom++;
+ }
+ residue++;
+ }
+ }
+ else
+ {
+ for(l=molecule->n_atoms; l--;)
{
- atom->residue = residue;
+ atom->residue = 0;
tng_atom_data_read(tng_data, block, atom, &offset);
atom++;
}
- residue++;
}
- chain++;
}
memcpy(&molecule->n_bonds, block->block_contents+offset,
@@ -2478,105 +2660,58 @@ static tng_function_status tng_molecules_block_write
}
offset += sizeof(molecule->n_atoms);
- chain = molecule->chains;
- for(j = molecule->n_chains; j--;)
+ if(molecule->n_chains > 0)
{
- memcpy(block->block_contents+offset, &chain->id, sizeof(chain->id));
- if(tng_data->output_endianness_swap_func_64)
+ chain = molecule->chains;
+ for(j = molecule->n_chains; j--;)
{
- if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)block->header_contents+offset)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(chain->id);
+ tng_chain_data_write(tng_data, block, chain, &offset);
- len = tng_min(strlen(chain->name) + 1, TNG_MAX_STR_LEN);
- strncpy(block->block_contents + offset, chain->name, len);
- offset += len;
-
- memcpy(block->block_contents+offset, &chain->n_residues,
- sizeof(chain->n_residues));
- if(tng_data->output_endianness_swap_func_64)
- {
- if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)block->header_contents+offset)
- != TNG_SUCCESS)
+ residue = chain->residues;
+ for(k = chain->n_residues; k--;)
{
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(chain->n_residues);
+ tng_residue_data_write(tng_data, block, residue, &offset);
- residue = chain->residues;
- for(k = chain->n_residues; k--;)
- {
- memcpy(block->block_contents+offset, &residue->id, sizeof(residue->id));
- if(tng_data->output_endianness_swap_func_64)
- {
- if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)block->header_contents+offset)
- != TNG_SUCCESS)
+ atom = residue->atoms;
+ for(l = residue->n_atoms; l--;)
{
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
+ tng_atom_data_write(tng_data, block, atom, &offset);
+
+ atom++;
}
+ residue++;
}
- offset += sizeof(residue->id);
-
- len = tng_min(strlen(residue->name) + 1, TNG_MAX_STR_LEN);
- strncpy(block->block_contents + offset, residue->name, len);
- offset += len;
-
- memcpy(block->block_contents+offset, &residue->n_atoms,
- sizeof(residue->n_atoms));
- if(tng_data->output_endianness_swap_func_64)
+ chain++;
+ }
+ }
+ else
+ {
+ if(molecule->n_residues > 0)
+ {
+ for(k = chain->n_residues; k--;)
{
- if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)block->header_contents+offset)
- != TNG_SUCCESS)
+ tng_residue_data_write(tng_data, block, residue, &offset);
+
+ atom = residue->atoms;
+ for(l = residue->n_atoms; l--;)
{
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(residue->n_atoms);
+ tng_atom_data_write(tng_data, block, atom, &offset);
- atom = residue->atoms;
+ atom++;
+ }
+ residue++;
+ }
+ }
+ else
+ {
+ atom = molecule->atoms;
for(l = residue->n_atoms; l--;)
{
- // printf("j=%d\n", j);
- memcpy(block->block_contents+offset, &atom->id,
- sizeof(atom->id));
- if(tng_data->output_endianness_swap_func_64)
- {
- if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)block->header_contents+offset)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(atom->id);
-
- len = tng_min(strlen(atom->name) + 1, TNG_MAX_STR_LEN);
- strncpy(block->block_contents + offset, atom->name, len);
- offset += len;
-
- len = tng_min(strlen(atom->atom_type) + 1, TNG_MAX_STR_LEN);
- strncpy(block->block_contents + offset, atom->atom_type, len);
- offset += len;
+ tng_atom_data_write(tng_data, block, atom, &offset);
atom++;
}
- residue++;
}
- chain++;
}
memcpy(block->block_contents+offset, &molecule->n_bonds,
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