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-rw-r--r--src/lib/tng_io.c290
1 files changed, 177 insertions, 113 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index ef4d14a..c7f5c10 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -1692,6 +1692,155 @@ static tng_function_status tng_general_info_block_write
return(TNG_SUCCESS);
}
+/** Read 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 input and is updated when reading.
+ * @return TNG_SUCCESS(0) is successful.
+ */
+static tng_function_status tng_chain_data_read(tng_trajectory_t tng_data,
+ tng_gen_block_t block,
+ tng_chain_t chain,
+ int *offset)
+{
+ int len;
+
+ memcpy(&chain->id, block->block_contents+*offset,
+ sizeof(chain->id));
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &chain->id)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(chain->id);
+
+ len = tng_min(strlen(block->block_contents+*offset) + 1,
+ TNG_MAX_STR_LEN);
+ chain->name = malloc(len);
+ strncpy(chain->name,
+ block->block_contents+*offset, len);
+ *offset += len;
+
+ memcpy(&chain->n_residues, block->block_contents+*offset,
+ sizeof(chain->n_residues));
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &chain->n_residues)
+ != 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.
+ * @param residue is the residue data container.
+ * @param offset is the offset of the block input and is updated when reading.
+ * @return TNG_SUCCESS(0) is successful.
+ */
+static tng_function_status tng_residue_data_read(tng_trajectory_t tng_data,
+ tng_gen_block_t block,
+ tng_residue_t residue,
+ int *offset)
+{
+ int len;
+
+ memcpy(&residue->id, block->block_contents+*offset,
+ sizeof(residue->id));
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &residue->id)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(residue->id);
+
+ len = tng_min(strlen(block->block_contents+*offset) + 1,
+ TNG_MAX_STR_LEN);
+ residue->name = malloc(len);
+ strncpy(residue->name,
+ block->block_contents+*offset, len);
+ *offset += len;
+
+ memcpy(&residue->n_atoms, block->block_contents+*offset,
+ sizeof(residue->n_atoms));
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &residue->n_atoms)
+ != 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.
+ * @param atom is the atom data container.
+ * @param offset is the offset of the block input and is updated when reading.
+ * @return TNG_SUCCESS(0) is successful.
+ */
+static tng_function_status tng_atom_data_read(tng_trajectory_t tng_data,
+ tng_gen_block_t block,
+ tng_atom_t atom,
+ int *offset)
+{
+ int len;
+
+ memcpy(&atom->id, block->block_contents+*offset,
+ sizeof(atom->id));
+ if(tng_data->input_endianness_swap_func_64)
+ {
+ if(tng_data->input_endianness_swap_func_64(tng_data,
+ &atom->id)
+ != TNG_SUCCESS)
+ {
+ printf("Cannot swap byte order. %s: %d\n",
+ __FILE__, __LINE__);
+ }
+ }
+ *offset += sizeof(atom->id);
+
+ len = tng_min(strlen(block->block_contents+*offset) + 1,
+ TNG_MAX_STR_LEN);
+ atom->name = malloc(len);
+ strncpy(atom->name,
+ block->block_contents+*offset, len);
+ *offset += len;
+
+ len = tng_min(strlen(block->block_contents+*offset) + 1,
+ TNG_MAX_STR_LEN);
+ atom->atom_type = malloc(len);
+ strncpy(atom->atom_type,
+ block->block_contents+*offset, 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.
@@ -1916,29 +2065,35 @@ static tng_function_status tng_molecules_block_read
tng_data->n_particles += molecule->n_atoms *
tng_data->molecule_cnt_list[i];
- molecule->chains = malloc(molecule->n_chains *
- sizeof(struct tng_chain));
- if(!molecule->chains)
+ if(molecule->n_chains > 0)
{
- printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- molecule->n_chains * sizeof(struct tng_chain),
- __FILE__, __LINE__);
- return(TNG_CRITICAL);
- }
+ molecule->chains = malloc(molecule->n_chains *
+ sizeof(struct tng_chain));
+ if(!molecule->chains)
+ {
+ printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ molecule->n_chains * sizeof(struct tng_chain),
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
- chain = molecule->chains;
+ chain = molecule->chains;
+ }
- molecule->residues = malloc(molecule->n_residues *
- sizeof(struct tng_residue));
- if(!molecule->residues)
+ if(molecule->n_residues > 0)
{
- printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- molecule->n_residues * sizeof(struct tng_residue),
- __FILE__, __LINE__);
- return(TNG_CRITICAL);
- }
+ molecule->residues = malloc(molecule->n_residues *
+ sizeof(struct tng_residue));
+ if(!molecule->residues)
+ {
+ printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ molecule->n_residues * sizeof(struct tng_residue),
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
- residue = molecule->residues;
+ residue = molecule->residues;
+ }
molecule->atoms = malloc(molecule->n_atoms *
sizeof(struct tng_atom));
@@ -1952,119 +2107,28 @@ static tng_function_status tng_molecules_block_read
atom = molecule->atoms;
- /* Each molecule contains chains - read them */
+ /* Each molecule can contain chains - read them */
for(j=molecule->n_chains; j--;)
{
chain->molecule = molecule;
-
- memcpy(&chain->id, block->block_contents+offset,
- sizeof(chain->id));
- if(tng_data->input_endianness_swap_func_64)
- {
- if(tng_data->input_endianness_swap_func_64(tng_data,
- &chain->id)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(chain->id);
- len = tng_min(strlen(block->block_contents+offset) + 1,
- TNG_MAX_STR_LEN);
- chain->name = malloc(len);
- strncpy(chain->name,
- block->block_contents+offset, len);
- offset += len;
-
- memcpy(&chain->n_residues, block->block_contents+offset,
- sizeof(chain->n_residues));
- if(tng_data->input_endianness_swap_func_64)
- {
- if(tng_data->input_endianness_swap_func_64(tng_data,
- &chain->n_residues)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(chain->n_residues);
+ 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;
- memcpy(&residue->id, block->block_contents+offset,
- sizeof(residue->id));
- if(tng_data->input_endianness_swap_func_64)
- {
- if(tng_data->input_endianness_swap_func_64(tng_data,
- &residue->id)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(residue->id);
-
- len = tng_min(strlen(block->block_contents+offset) + 1,
- TNG_MAX_STR_LEN);
- residue->name = malloc(len);
- strncpy(residue->name,
- block->block_contents+offset, len);
- offset += len;
- memcpy(&residue->n_atoms, block->block_contents+offset,
- sizeof(residue->n_atoms));
- if(tng_data->input_endianness_swap_func_64)
- {
- if(tng_data->input_endianness_swap_func_64(tng_data,
- &residue->n_atoms)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(residue->n_atoms);
+ 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;
-
- memcpy(&atom->id, block->block_contents+offset,
- sizeof(atom->id));
- if(tng_data->input_endianness_swap_func_64)
- {
- if(tng_data->input_endianness_swap_func_64(tng_data,
- &atom->id)
- != TNG_SUCCESS)
- {
- printf("Cannot swap byte order. %s: %d\n",
- __FILE__, __LINE__);
- }
- }
- offset += sizeof(atom->id);
- len = tng_min(strlen(block->block_contents+offset) + 1,
- TNG_MAX_STR_LEN);
- atom->name = malloc(len);
- strncpy(atom->name,
- block->block_contents+offset, len);
- offset += len;
-
- len = tng_min(strlen(block->block_contents+offset) + 1,
- TNG_MAX_STR_LEN);
- atom->atom_type = malloc(len);
- strncpy(atom->atom_type,
- block->block_contents+offset, len);
- offset += len;
+ tng_atom_data_read(tng_data, block, atom, &offset);
atom++;
}
contact: Jan Huwald // Impressum