1 |
#include <stdlib.h> |
2 |
#include <stdio.h> |
3 |
#include <string.h> |
4 |
#include <iostream> |
5 |
|
6 |
#include "MoleculeStamp.hpp" |
7 |
|
8 |
char MoleculeStamp::errMsg[500]; |
9 |
|
10 |
MoleculeStamp::MoleculeStamp(){ |
11 |
|
12 |
n_atoms = 0; |
13 |
n_bonds = 0; |
14 |
n_bends = 0; |
15 |
n_torsions = 0; |
16 |
n_rigidbodies = 0; |
17 |
n_cutoffgroups = 0; |
18 |
n_integrable = 0; |
19 |
|
20 |
unhandled = NULL; |
21 |
atoms = NULL; |
22 |
bonds = NULL; |
23 |
bends = NULL; |
24 |
torsions = NULL; |
25 |
rigidBodies = NULL; |
26 |
cutoffGroups = NULL; |
27 |
|
28 |
have_name = 0; |
29 |
have_atoms = 0; |
30 |
have_bonds = 0; |
31 |
have_bends = 0; |
32 |
have_torsions = 0; |
33 |
have_rigidbodies = 0; |
34 |
have_cutoffgroups = 0; |
35 |
|
36 |
} |
37 |
|
38 |
MoleculeStamp::~MoleculeStamp(){ |
39 |
int i; |
40 |
|
41 |
if( unhandled != NULL) delete unhandled; |
42 |
|
43 |
if( rigidBodies != NULL ) { |
44 |
for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i]; |
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} |
46 |
delete[] rigidBodies; |
47 |
|
48 |
if( cutoffGroups != NULL ) { |
49 |
for( i=0; i<n_cutoffgroups; i++ ) delete cutoffGroups[i]; |
50 |
} |
51 |
delete[] cutoffGroups; |
52 |
|
53 |
if( atoms != NULL ){ |
54 |
for( i=0; i<n_atoms; i++ ) delete atoms[i]; |
55 |
} |
56 |
delete[] atoms; |
57 |
|
58 |
if( bonds != NULL ){ |
59 |
for( i=0; i<n_bonds; i++ ) delete bonds[i]; |
60 |
} |
61 |
delete[] bonds; |
62 |
|
63 |
if( bends != NULL ){ |
64 |
for( i=0; i<n_bends; i++ ) delete bends[i]; |
65 |
} |
66 |
delete[] bends; |
67 |
|
68 |
if( torsions != NULL ){ |
69 |
for( i=0; i<n_torsions; i++ ) delete torsions[i]; |
70 |
} |
71 |
delete[] torsions; |
72 |
|
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|
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|
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|
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} |
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|
78 |
char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
79 |
|
80 |
if( !strcmp( lhs, "name" ) ){ |
81 |
strcpy( name, rhs ); |
82 |
have_name = 1; |
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} |
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else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
86 |
else unhandled->add( lhs, rhs ); |
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have_extras = 1; |
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} |
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return NULL; |
90 |
} |
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|
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char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
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int i; |
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|
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = (int)rhs; |
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|
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if( have_atoms ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_atoms already declared" |
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" for molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_atoms = 1; |
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atoms = new AtomStamp*[n_atoms]; |
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for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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} |
109 |
|
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else if( !strcmp( lhs, "nBonds" ) ){ |
111 |
n_bonds = (int)rhs; |
112 |
|
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if( have_bonds ){ |
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sprintf( errMsg, |
115 |
"MoleculeStamp error, n_bonds already declared for" |
116 |
" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_bonds = 1; |
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bonds = new BondStamp*[n_bonds]; |
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for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
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} |
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|
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = (int)rhs; |
127 |
|
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if( have_bends ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bends already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_bends = 1; |
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bends = new BendStamp*[n_bends]; |
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for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
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} |
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|
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = (int)rhs; |
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|
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if( have_torsions ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_torsions already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_torsions = 1; |
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torsions = new TorsionStamp*[n_torsions]; |
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for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
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} |
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|
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = (int)rhs; |
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|
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if( have_rigidbodies ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_rigidbodies already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_rigidbodies = 1; |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
167 |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
168 |
} |
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|
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else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
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n_cutoffgroups = (int)rhs; |
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|
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if( have_cutoffgroups ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_cutoffgroups already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_cutoffgroups = 1; |
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cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
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for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
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} |
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|
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else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
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else unhandled->add( lhs, rhs ); |
188 |
have_extras = 1; |
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} |
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return NULL; |
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} |
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|
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char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
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int i; |
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|
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = rhs; |
198 |
|
199 |
if( have_atoms ){ |
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sprintf( errMsg, |
201 |
"MoleculeStamp error, n_atoms already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_atoms = 1; |
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atoms = new AtomStamp*[n_atoms]; |
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for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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} |
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|
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = rhs; |
213 |
|
214 |
if( have_bonds ){ |
215 |
sprintf( errMsg, |
216 |
"MoleculeStamp error, n_bonds already declared for" |
217 |
" molecule: %s\n", |
218 |
name); |
219 |
return strdup( errMsg ); |
220 |
} |
221 |
have_bonds = 1; |
222 |
bonds = new BondStamp*[n_bonds]; |
223 |
for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
224 |
} |
225 |
|
226 |
else if( !strcmp( lhs, "nBends" ) ){ |
227 |
n_bends = rhs; |
228 |
|
229 |
if( have_bends ){ |
230 |
sprintf( errMsg, |
231 |
"MoleculeStamp error, n_bends already declared for" |
232 |
" molecule: %s\n", |
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name ); |
234 |
return strdup( errMsg ); |
235 |
} |
236 |
have_bends = 1; |
237 |
bends = new BendStamp*[n_bends]; |
238 |
for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
239 |
} |
240 |
|
241 |
else if( !strcmp( lhs, "nTorsions" ) ){ |
242 |
n_torsions = rhs; |
243 |
|
244 |
if( have_torsions ){ |
245 |
sprintf( errMsg, |
246 |
"MoleculeStamp error, n_torsions already declared for" |
247 |
" molecule: %s\n", |
248 |
name); |
249 |
return strdup( errMsg ); |
250 |
} |
251 |
have_torsions = 1; |
252 |
torsions = new TorsionStamp*[n_torsions]; |
253 |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
254 |
} |
255 |
|
256 |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
257 |
n_rigidbodies = rhs; |
258 |
|
259 |
if( have_rigidbodies ){ |
260 |
sprintf( errMsg, |
261 |
"MoleculeStamp error, n_rigidbodies already declared for" |
262 |
" molecule: %s\n", |
263 |
name); |
264 |
return strdup( errMsg ); |
265 |
} |
266 |
have_rigidbodies = 1; |
267 |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
268 |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
269 |
} |
270 |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
271 |
n_cutoffgroups = rhs; |
272 |
|
273 |
if( have_cutoffgroups ){ |
274 |
sprintf( errMsg, |
275 |
"MoleculeStamp error, n_cutoffgroups already declared for" |
276 |
" molecule: %s\n", |
277 |
name); |
278 |
return strdup( errMsg ); |
279 |
} |
280 |
have_cutoffgroups = 1; |
281 |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
282 |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
283 |
} |
284 |
else{ |
285 |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
286 |
else unhandled->add( lhs, rhs ); |
287 |
have_extras = 1; |
288 |
} |
289 |
return NULL; |
290 |
} |
291 |
|
292 |
char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
293 |
|
294 |
if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
295 |
else { |
296 |
if( have_atoms ){ |
297 |
sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
298 |
atomIndex ); |
299 |
return strdup( errMsg ); |
300 |
} |
301 |
else return strdup("MoleculeStamp error, nAtoms not given before" |
302 |
" first atom declaration." ); |
303 |
} |
304 |
|
305 |
return NULL; |
306 |
} |
307 |
|
308 |
char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
309 |
int rigidBodyIndex ){ |
310 |
|
311 |
if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
312 |
rigidBodies[rigidBodyIndex] = the_rigidbody; |
313 |
else { |
314 |
if( have_rigidbodies ){ |
315 |
sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
316 |
rigidBodyIndex ); |
317 |
return strdup( errMsg ); |
318 |
} |
319 |
else return strdup("MoleculeStamp error, nRigidBodies not given before" |
320 |
" first rigidBody declaration." ); |
321 |
} |
322 |
|
323 |
return NULL; |
324 |
} |
325 |
|
326 |
char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, |
327 |
int cutoffGroupIndex ){ |
328 |
|
329 |
if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) |
330 |
cutoffGroups[cutoffGroupIndex] = the_cutoffgroup; |
331 |
else { |
332 |
if( have_cutoffgroups ){ |
333 |
sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", |
334 |
cutoffGroupIndex ); |
335 |
return strdup( errMsg ); |
336 |
} |
337 |
else return strdup("MoleculeStamp error, nCutoffGroups not given before" |
338 |
" first CutoffGroup declaration." ); |
339 |
} |
340 |
|
341 |
return NULL; |
342 |
} |
343 |
|
344 |
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
345 |
|
346 |
|
347 |
if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
348 |
else{ |
349 |
if( have_bonds ){ |
350 |
sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
351 |
bondIndex ); |
352 |
return strdup( errMsg ); |
353 |
} |
354 |
else return strdup("MoleculeStamp error, nBonds not given before" |
355 |
"first bond declaration." ); |
356 |
} |
357 |
|
358 |
return NULL; |
359 |
} |
360 |
|
361 |
char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
362 |
|
363 |
|
364 |
if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
365 |
else{ |
366 |
if( have_bends ){ |
367 |
sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
368 |
bendIndex ); |
369 |
return strdup( errMsg ); |
370 |
} |
371 |
else return strdup("MoleculeStamp error, nBends not given before" |
372 |
"first bend declaration." ); |
373 |
} |
374 |
|
375 |
return NULL; |
376 |
} |
377 |
|
378 |
char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
379 |
|
380 |
|
381 |
if( have_torsions && torsionIndex < n_torsions ) |
382 |
torsions[torsionIndex] = the_torsion; |
383 |
else{ |
384 |
if( have_torsions ){ |
385 |
sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
386 |
torsionIndex ); |
387 |
return strdup( errMsg ); |
388 |
} |
389 |
else return strdup("MoleculeStamp error, nTorsions not given before" |
390 |
"first torsion declaration." ); |
391 |
} |
392 |
|
393 |
return NULL; |
394 |
} |
395 |
|
396 |
char* MoleculeStamp::checkMe( void ){ |
397 |
|
398 |
int i; |
399 |
short int no_atom, no_rigidbody, no_cutoffgroup; |
400 |
|
401 |
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
402 |
" was not given.\n" ); |
403 |
|
404 |
if( !have_atoms ){ |
405 |
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
406 |
} |
407 |
|
408 |
no_rigidbody = 0; |
409 |
for( i=0; i<n_rigidbodies; i++ ){ |
410 |
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
411 |
} |
412 |
|
413 |
if( no_rigidbody ){ |
414 |
sprintf( errMsg, |
415 |
"MoleculeStamp error. Not all of the RigidBodies were" |
416 |
" declared in molecule \"%s\".\n", name ); |
417 |
return strdup( errMsg ); |
418 |
} |
419 |
|
420 |
no_cutoffgroup = 0; |
421 |
for( i=0; i<n_cutoffgroups; i++ ){ |
422 |
if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1; |
423 |
} |
424 |
|
425 |
if( no_cutoffgroup ){ |
426 |
sprintf( errMsg, |
427 |
"MoleculeStamp error. Not all of the CutoffGroups were" |
428 |
" declared in molecule \"%s\".\n", name ); |
429 |
return strdup( errMsg ); |
430 |
} |
431 |
|
432 |
no_atom = 0; |
433 |
for( i=0; i<n_atoms; i++ ){ |
434 |
if( atoms[i] == NULL ) no_atom = 1; |
435 |
} |
436 |
|
437 |
if( no_atom ){ |
438 |
sprintf( errMsg, |
439 |
"MoleculeStamp error. Not all of the atoms were" |
440 |
" declared in molecule \"%s\".\n", name ); |
441 |
return strdup( errMsg ); |
442 |
} |
443 |
|
444 |
n_integrable = n_atoms; |
445 |
for (i = 0; i < n_rigidbodies; i++) |
446 |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
447 |
|
448 |
if (n_integrable <= 0 || n_integrable > n_atoms) { |
449 |
sprintf( errMsg, |
450 |
"MoleculeStamp error. n_integrable is either <= 0 or" |
451 |
" greater than n_atoms in molecule \"%s\".\n", name ); |
452 |
return strdup( errMsg ); |
453 |
} |
454 |
|
455 |
return NULL; |
456 |
} |
457 |
|
458 |
|
459 |
//Function Name: isBondInSameRigidBody |
460 |
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
461 |
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
462 |
int rbA; |
463 |
int rbB; |
464 |
int consAtomA; |
465 |
int consAtomB; |
466 |
|
467 |
if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
468 |
return false; |
469 |
|
470 |
if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
471 |
return false; |
472 |
|
473 |
if(rbB == rbA) |
474 |
return true; |
475 |
else |
476 |
return false; |
477 |
} |
478 |
|
479 |
|
480 |
// Function Name isAtomInRigidBody |
481 |
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
482 |
//and consAtomIndex |
483 |
//atomIndex : the index of atom in component |
484 |
//whichRigidBody: the index of rigidbody in component |
485 |
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
486 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
487 |
RigidBodyStamp* rbStamp; |
488 |
int numRb; |
489 |
int numAtom; |
490 |
|
491 |
numRb = this->getNRigidBodies(); |
492 |
|
493 |
for(int i = 0 ; i < numRb; i++){ |
494 |
rbStamp = this->getRigidBody(i); |
495 |
numAtom = rbStamp->getNMembers(); |
496 |
for(int j = 0; j < numAtom; j++) |
497 |
if (rbStamp->getMember(j) == atomIndex){ |
498 |
whichRigidBody = i; |
499 |
consAtomIndex = j; |
500 |
return true; |
501 |
} |
502 |
} |
503 |
|
504 |
return false; |
505 |
|
506 |
} |
507 |
|
508 |
//return the position of joint atom apears in rigidbody's definition |
509 |
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
510 |
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
511 |
vector<pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
512 |
RigidBodyStamp* rbStamp1; |
513 |
RigidBodyStamp* rbStamp2; |
514 |
int natomInRb1; |
515 |
int natomInRb2; |
516 |
int atomIndex1; |
517 |
int atomIndex2; |
518 |
vector<pair<int, int> > jointAtomIndexPair; |
519 |
|
520 |
rbStamp1 = this->getRigidBody(rb1); |
521 |
natomInRb1 =rbStamp1->getNMembers(); |
522 |
|
523 |
rbStamp2 = this->getRigidBody(rb2); |
524 |
natomInRb2 =rbStamp2->getNMembers(); |
525 |
|
526 |
for(int i = 0; i < natomInRb1; i++){ |
527 |
atomIndex1 = rbStamp1->getMember(i); |
528 |
|
529 |
for(int j= 0; j < natomInRb1; j++){ |
530 |
atomIndex2 = rbStamp2->getMember(j); |
531 |
|
532 |
if(atomIndex1 == atomIndex2){ |
533 |
jointAtomIndexPair.push_back(make_pair(i, j)); |
534 |
break; |
535 |
} |
536 |
|
537 |
}//end for(j =0) |
538 |
|
539 |
}//end for (i = 0) |
540 |
|
541 |
return jointAtomIndexPair; |
542 |
} |