| 14 |
|
n_bends = 0; |
| 15 |
|
n_torsions = 0; |
| 16 |
|
n_rigidbodies = 0; |
| 17 |
+ |
n_integrable = 0; |
| 18 |
|
|
| 19 |
|
unhandled = NULL; |
| 20 |
|
atoms = NULL; |
| 82 |
|
if( have_atoms ){ |
| 83 |
|
sprintf( errMsg, |
| 84 |
|
"MoleculeStamp error, n_atoms already declared" |
| 85 |
< |
"for molecule: %s\n", |
| 85 |
> |
" for molecule: %s\n", |
| 86 |
|
name); |
| 87 |
|
return strdup( errMsg ); |
| 88 |
|
} |
| 247 |
|
char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
| 248 |
|
|
| 249 |
|
if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
| 250 |
< |
else{ |
| 250 |
> |
else { |
| 251 |
|
if( have_atoms ){ |
| 252 |
|
sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
| 253 |
|
atomIndex ); |
| 254 |
|
return strdup( errMsg ); |
| 255 |
|
} |
| 256 |
|
else return strdup("MoleculeStamp error, nAtoms not given before" |
| 257 |
< |
"first atom declaration." ); |
| 257 |
> |
" first atom declaration." ); |
| 258 |
|
} |
| 259 |
|
|
| 260 |
|
return NULL; |
| 265 |
|
|
| 266 |
|
if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
| 267 |
|
rigidBodies[rigidBodyIndex] = the_rigidbody; |
| 268 |
< |
else{ |
| 268 |
> |
else { |
| 269 |
|
if( have_rigidbodies ){ |
| 270 |
|
sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
| 271 |
|
rigidBodyIndex ); |
| 272 |
|
return strdup( errMsg ); |
| 273 |
|
} |
| 274 |
|
else return strdup("MoleculeStamp error, nRigidBodies not given before" |
| 275 |
< |
"first rigidBody declaration." ); |
| 275 |
> |
" first rigidBody declaration." ); |
| 276 |
|
} |
| 277 |
|
|
| 278 |
|
return NULL; |
| 334 |
|
|
| 335 |
|
int i; |
| 336 |
|
short int no_atom, no_rigidbody; |
| 336 |
– |
|
| 337 |
– |
// Fix for Rigid Bodies!!! Molecules may not have any atoms that |
| 338 |
– |
// they know about. They might have only rigid bodies (which then |
| 339 |
– |
// know about the atoms! |
| 340 |
– |
|
| 337 |
|
|
| 338 |
|
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
| 339 |
|
" was not given.\n" ); |
| 340 |
< |
|
| 341 |
< |
if( !have_rigidbodies && !have_atoms ){ |
| 342 |
< |
return strdup( "MoleculeStamp error. Molecule contains no atoms or RigidBodies." ); |
| 340 |
> |
|
| 341 |
> |
if( !have_atoms ){ |
| 342 |
> |
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
| 343 |
|
} |
| 344 |
|
|
| 345 |
|
no_rigidbody = 0; |
| 365 |
|
" declared in molecule \"%s\".\n", name ); |
| 366 |
|
return strdup( errMsg ); |
| 367 |
|
} |
| 372 |
– |
|
| 373 |
– |
return NULL; |
| 374 |
– |
} |
| 368 |
|
|
| 369 |
|
|
| 370 |
< |
int MoleculeStamp::getTotAtoms() { |
| 371 |
< |
int total_atoms; |
| 372 |
< |
int i; |
| 373 |
< |
|
| 374 |
< |
total_atoms = n_atoms; |
| 375 |
< |
|
| 376 |
< |
if( rigidBodies != NULL ) { |
| 377 |
< |
for( i=0; i<n_rigidbodies; i++ ) |
| 378 |
< |
total_atoms += rigidBodies[i]->getNAtoms(); |
| 370 |
> |
n_integrable = n_atoms; |
| 371 |
> |
for (i = 0; i < n_rigidbodies; i++) |
| 372 |
> |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
| 373 |
> |
|
| 374 |
> |
if (n_integrable <= 0 || n_integrable > n_atoms) { |
| 375 |
> |
sprintf( errMsg, |
| 376 |
> |
"MoleculeStamp error. n_integrable is either <= 0 or" |
| 377 |
> |
" greater than n_atoms in molecule \"%s\".\n", name ); |
| 378 |
> |
return strdup( errMsg ); |
| 379 |
|
} |
| 380 |
|
|
| 381 |
< |
return total_atoms; |
| 382 |
< |
} |
| 390 |
< |
|
| 381 |
> |
return NULL; |
| 382 |
> |
} |
