OOPSE/libBASS/MoleculeStamp.cpp

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <iostream>

#include "MoleculeStamp.hpp"

char MoleculeStamp::errMsg[500];

MoleculeStamp::MoleculeStamp(){
  
  n_atoms = 0;
  n_bonds = 0;
  n_bends = 0;
  n_torsions = 0;
  n_rigidbodies = 0;
  n_integrable = 0;

  unhandled = NULL;
  atoms = NULL;
  bonds = NULL;
  bends = NULL;
  torsions = NULL;
  rigidBodies = NULL;

  have_name = 0;
  have_atoms = 0;
  have_bonds = 0;
  have_bends = 0;
  have_torsions = 0;
  have_rigidbodies = 0;

}

MoleculeStamp::~MoleculeStamp(){
  int i;
  
  if( unhandled != NULL) delete unhandled;
  
  if( rigidBodies != NULL ) {
    for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i];
  }
  
  if( atoms != NULL ){
    for( i=0; i<n_atoms; i++ ) delete atoms[i];
  }
  
  if( bonds != NULL ){
    for( i=0; i<n_bonds; i++ ) delete bonds[i];
  }
  
  if( bends != NULL ){
    for( i=0; i<n_bends; i++ ) delete bends[i];
  }
  
  if( torsions != NULL ){
    for( i=0; i<n_torsions; i++ ) delete torsions[i];
  }
  
}

char* MoleculeStamp::assignString( char* lhs, char* rhs ){
  
  if( !strcmp( lhs, "name" ) ){
    strcpy( name, rhs );
    have_name = 1;
  }
  else{
    if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
    else unhandled->add( lhs, rhs );
    have_extras = 1;
  }
  return NULL;
}

char* MoleculeStamp::assignDouble( char* lhs, double rhs ){
  int i;

  if( !strcmp( lhs, "nAtoms" ) ){
    n_atoms = (int)rhs;
    
    if( have_atoms ){
      sprintf( errMsg,
               "MoleculeStamp error, n_atoms already declared"
               " for molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_atoms = 1;
    atoms = new AtomStamp*[n_atoms];
    for( i=0; i<n_atoms; i++ ) atoms[i] = NULL;
  }
  
  else if( !strcmp( lhs, "nBonds" ) ){
    n_bonds = (int)rhs;

    if( have_bonds ){
      sprintf( errMsg,  
               "MoleculeStamp error, n_bonds already declared for"
               " molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_bonds = 1;
    bonds = new BondStamp*[n_bonds];
    for( i=0; i<n_bonds; i++ ) bonds[i] = NULL;
  }
  
  else if( !strcmp( lhs, "nBends" ) ){
    n_bends = (int)rhs;

    if( have_bends ){
      sprintf( errMsg,
               "MoleculeStamp error, n_bends already declared for"
               " molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_bends = 1;
    bends = new BendStamp*[n_bends];
    for( i=0; i<n_bends; i++ ) bends[i] = NULL;
  }
  
  else if( !strcmp( lhs, "nTorsions" ) ){
    n_torsions = (int)rhs;

    if( have_torsions ){
      sprintf( errMsg,
               "MoleculeStamp error, n_torsions already declared for"
               " molecule: %s\n",
               name );
      return strdup( errMsg );
    }
    have_torsions = 1;
    torsions = new TorsionStamp*[n_torsions];
    for( i=0; i<n_torsions; i++ ) torsions[i] = NULL;
  }

  else if( !strcmp( lhs, "nRigidBodies" ) ){
    n_rigidbodies = (int)rhs;

    if( have_rigidbodies ){
      sprintf( errMsg,
               "MoleculeStamp error, n_rigidbodies already declared for"
               " molecule: %s\n",
               name );
      return strdup( errMsg );
    }
    have_rigidbodies = 1;
    rigidBodies = new RigidBodyStamp*[n_rigidbodies];
    for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
  }

  else{
    if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
    else unhandled->add( lhs, rhs );
    have_extras = 1;
  }
  return NULL;
}

char*  MoleculeStamp::assignInt( char* lhs, int rhs ){
  int i;
  
  if( !strcmp( lhs, "nAtoms" ) ){
    n_atoms = rhs;
    
    if( have_atoms ){
      sprintf( errMsg,
               "MoleculeStamp error, n_atoms already declared for"
               " molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_atoms = 1;
    atoms = new AtomStamp*[n_atoms];
    for( i=0; i<n_atoms; i++ ) atoms[i] = NULL;
  }
  
  else if( !strcmp( lhs, "nBonds" ) ){
    n_bonds = rhs;

    if( have_bonds ){
      sprintf( errMsg,
               "MoleculeStamp error, n_bonds already declared for"
               " molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_bonds = 1;
    bonds = new BondStamp*[n_bonds];
    for( i=0; i<n_bonds; i++ ) bonds[i] = NULL;
  }
  
  else if( !strcmp( lhs, "nBends" ) ){
    n_bends = rhs;

    if( have_bends ){
      sprintf( errMsg,
               "MoleculeStamp error, n_bends already declared for"
               " molecule: %s\n",
               name );
      return strdup( errMsg );
    }
    have_bends = 1;
    bends = new BendStamp*[n_bends];
    for( i=0; i<n_bends; i++ ) bends[i] = NULL;
  }
  
  else if( !strcmp( lhs, "nTorsions" ) ){
    n_torsions = rhs;

    if( have_torsions ){
      sprintf( errMsg,
               "MoleculeStamp error, n_torsions already declared for"
               " molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_torsions = 1;
    torsions = new TorsionStamp*[n_torsions];
    for( i=0; i<n_torsions; i++ ) torsions[i] = NULL;
  }

  else if( !strcmp( lhs, "nRigidBodies" ) ){
    n_rigidbodies = rhs;

    if( have_rigidbodies ){
      sprintf( errMsg,
               "RigidBodyStamp error, n_rigidbodies already declared for"
               " molecule: %s\n",
               name);
      return strdup( errMsg );
    }
    have_rigidbodies = 1;
    rigidBodies = new RigidBodyStamp*[n_rigidbodies];
    for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
  }
  else{
    if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
    else unhandled->add( lhs, rhs );
    have_extras = 1;
  }
  return NULL;
}

char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){
  
  if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom;
  else {
    if( have_atoms ){
      sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", 
               atomIndex );
      return strdup( errMsg );
    }
    else return strdup("MoleculeStamp error, nAtoms not given before"
                       " first atom declaration." );
  }

  return NULL;
}

char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, 
                                   int rigidBodyIndex ){
  
  if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) 
    rigidBodies[rigidBodyIndex] = the_rigidbody;
  else {
    if( have_rigidbodies ){
      sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", 
               rigidBodyIndex );
      return strdup( errMsg );
    }
    else return strdup("MoleculeStamp error, nRigidBodies not given before"
                       " first rigidBody declaration." );
  }
  
  return NULL;
}

char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){
  
  
  if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond;
  else{
    if( have_bonds ){
      sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", 
               bondIndex );
      return strdup( errMsg );
    }
    else return strdup("MoleculeStamp error, nBonds not given before"
                       "first bond declaration." );
  }

  return NULL;
}

char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){
  
  
  if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend;
  else{
    if( have_bends ){
      sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", 
               bendIndex );
      return strdup( errMsg );
    }
    else return strdup("MoleculeStamp error, nBends not given before"
                       "first bend declaration." );
  }

  return NULL;
}

char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){
  
  
  if( have_torsions && torsionIndex < n_torsions ) 
    torsions[torsionIndex] = the_torsion;
  else{
    if( have_torsions ){
      sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", 
               torsionIndex );
      return strdup( errMsg );
    }
    else return strdup("MoleculeStamp error, nTorsions not given before"
                       "first torsion declaration." );
  }

  return NULL;
}

char* MoleculeStamp::checkMe( void ){
  
  int i;
  short int no_atom, no_rigidbody;

  if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name"
                                  " was not given.\n" );
  
  if( !have_atoms ){
    return strdup( "MoleculeStamp error. Molecule contains no atoms." );
  }
  
  no_rigidbody = 0;
  for( i=0; i<n_rigidbodies; i++ ){
    if( rigidBodies[i] == NULL ) no_rigidbody = 1;
  }

  if( no_rigidbody ){
    sprintf( errMsg, 
             "MoleculeStamp error. Not all of the RigidBodies were"
             " declared in molecule \"%s\".\n", name );
    return strdup( errMsg );
  }

  no_atom = 0;
  for( i=0; i<n_atoms; i++ ){
    if( atoms[i] == NULL ) no_atom = 1;
  }

  if( no_atom ){
    sprintf( errMsg, 
             "MoleculeStamp error. Not all of the atoms were"
             " declared in molecule \"%s\".\n", name );
    return strdup( errMsg );
  }


  n_integrable = n_atoms;
  for (i = 0; i < n_rigidbodies; i++) 
    n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object
  
  if (n_integrable <= 0 || n_integrable > n_atoms) {
    sprintf( errMsg, 
             "MoleculeStamp error. n_integrable is either <= 0 or"
             " greater than n_atoms in molecule \"%s\".\n", name );
    return strdup( errMsg );
  }

  return NULL;
}  
Revision:	1113
Committed:	Thu Apr 15 16:18:26 2004 UTC (20 years, 5 months ago) by tim
File size:	9184 byte(s)
Log Message:	fix whole bunch of bugs :-)
#	User	Rev	Content
1	gezelter	828	#include <stdlib.h>
2			#include <stdio.h>
3			#include <string.h>
4	mmeineke	377	#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	gezelter	957	n_rigidbodies = 0;
17	gezelter	1103	n_integrable = 0;
18	mmeineke	377
19			unhandled = NULL;
20			atoms = NULL;
21			bonds = NULL;
22			bends = NULL;
23			torsions = NULL;
24	gezelter	957	rigidBodies = NULL;
25	mmeineke	377
26			have_name = 0;
27			have_atoms = 0;
28			have_bonds = 0;
29			have_bends = 0;
30			have_torsions = 0;
31	gezelter	957	have_rigidbodies = 0;
32	mmeineke	377
33			}
34
35			MoleculeStamp::~MoleculeStamp(){
36			int i;
37
38			if( unhandled != NULL) delete unhandled;
39	gezelter	957
40			if( rigidBodies != NULL ) {
41			for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i];
42			}
43
44	mmeineke	377	if( atoms != NULL ){
45			for( i=0; i<n_atoms; i++ ) delete atoms[i];
46			}
47
48			if( bonds != NULL ){
49			for( i=0; i<n_bonds; i++ ) delete bonds[i];
50			}
51
52			if( bends != NULL ){
53			for( i=0; i<n_bends; i++ ) delete bends[i];
54			}
55
56			if( torsions != NULL ){
57			for( i=0; i<n_torsions; i++ ) delete torsions[i];
58			}
59
60			}
61
62			char* MoleculeStamp::assignString( char* lhs, char* rhs ){
63
64			if( !strcmp( lhs, "name" ) ){
65			strcpy( name, rhs );
66			have_name = 1;
67			}
68			else{
69			if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
70			else unhandled->add( lhs, rhs );
71			have_extras = 1;
72			}
73			return NULL;
74			}
75
76			char* MoleculeStamp::assignDouble( char* lhs, double rhs ){
77			int i;
78
79			if( !strcmp( lhs, "nAtoms" ) ){
80			n_atoms = (int)rhs;
81
82			if( have_atoms ){
83			sprintf( errMsg,
84			"MoleculeStamp error, n_atoms already declared"
85	gezelter	981	" for molecule: %s\n",
86	mmeineke	377	name);
87			return strdup( errMsg );
88			}
89			have_atoms = 1;
90			atoms = new AtomStamp*[n_atoms];
91			for( i=0; i<n_atoms; i++ ) atoms[i] = NULL;
92			}
93
94			else if( !strcmp( lhs, "nBonds" ) ){
95			n_bonds = (int)rhs;
96
97			if( have_bonds ){
98			sprintf( errMsg,
99			"MoleculeStamp error, n_bonds already declared for"
100			" molecule: %s\n",
101			name);
102			return strdup( errMsg );
103			}
104			have_bonds = 1;
105			bonds = new BondStamp*[n_bonds];
106			for( i=0; i<n_bonds; i++ ) bonds[i] = NULL;
107			}
108
109			else if( !strcmp( lhs, "nBends" ) ){
110			n_bends = (int)rhs;
111
112			if( have_bends ){
113			sprintf( errMsg,
114			"MoleculeStamp error, n_bends already declared for"
115			" molecule: %s\n",
116			name);
117			return strdup( errMsg );
118			}
119			have_bends = 1;
120			bends = new BendStamp*[n_bends];
121			for( i=0; i<n_bends; i++ ) bends[i] = NULL;
122			}
123
124			else if( !strcmp( lhs, "nTorsions" ) ){
125			n_torsions = (int)rhs;
126
127			if( have_torsions ){
128			sprintf( errMsg,
129			"MoleculeStamp error, n_torsions already declared for"
130			" molecule: %s\n",
131			name );
132			return strdup( errMsg );
133			}
134			have_torsions = 1;
135			torsions = new TorsionStamp*[n_torsions];
136			for( i=0; i<n_torsions; i++ ) torsions[i] = NULL;
137			}
138	gezelter	957
139			else if( !strcmp( lhs, "nRigidBodies" ) ){
140			n_rigidbodies = (int)rhs;
141
142			if( have_rigidbodies ){
143			sprintf( errMsg,
144			"MoleculeStamp error, n_rigidbodies already declared for"
145			" molecule: %s\n",
146			name );
147			return strdup( errMsg );
148			}
149			have_rigidbodies = 1;
150			rigidBodies = new RigidBodyStamp*[n_rigidbodies];
151			for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
152			}
153
154	mmeineke	377	else{
155			if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
156			else unhandled->add( lhs, rhs );
157			have_extras = 1;
158			}
159			return NULL;
160			}
161
162			char* MoleculeStamp::assignInt( char* lhs, int rhs ){
163			int i;
164
165			if( !strcmp( lhs, "nAtoms" ) ){
166			n_atoms = rhs;
167
168			if( have_atoms ){
169			sprintf( errMsg,
170			"MoleculeStamp error, n_atoms already declared for"
171			" molecule: %s\n",
172			name);
173			return strdup( errMsg );
174			}
175			have_atoms = 1;
176			atoms = new AtomStamp*[n_atoms];
177			for( i=0; i<n_atoms; i++ ) atoms[i] = NULL;
178			}
179
180			else if( !strcmp( lhs, "nBonds" ) ){
181			n_bonds = rhs;
182
183			if( have_bonds ){
184			sprintf( errMsg,
185			"MoleculeStamp error, n_bonds already declared for"
186			" molecule: %s\n",
187			name);
188			return strdup( errMsg );
189			}
190			have_bonds = 1;
191			bonds = new BondStamp*[n_bonds];
192			for( i=0; i<n_bonds; i++ ) bonds[i] = NULL;
193			}
194
195			else if( !strcmp( lhs, "nBends" ) ){
196			n_bends = rhs;
197
198			if( have_bends ){
199			sprintf( errMsg,
200			"MoleculeStamp error, n_bends already declared for"
201			" molecule: %s\n",
202			name );
203			return strdup( errMsg );
204			}
205			have_bends = 1;
206			bends = new BendStamp*[n_bends];
207			for( i=0; i<n_bends; i++ ) bends[i] = NULL;
208			}
209
210			else if( !strcmp( lhs, "nTorsions" ) ){
211			n_torsions = rhs;
212
213			if( have_torsions ){
214			sprintf( errMsg,
215			"MoleculeStamp error, n_torsions already declared for"
216			" molecule: %s\n",
217			name);
218			return strdup( errMsg );
219			}
220			have_torsions = 1;
221			torsions = new TorsionStamp*[n_torsions];
222			for( i=0; i<n_torsions; i++ ) torsions[i] = NULL;
223			}
224	gezelter	957
225			else if( !strcmp( lhs, "nRigidBodies" ) ){
226			n_rigidbodies = rhs;
227
228			if( have_rigidbodies ){
229			sprintf( errMsg,
230			"RigidBodyStamp error, n_rigidbodies already declared for"
231			" molecule: %s\n",
232			name);
233			return strdup( errMsg );
234			}
235			have_rigidbodies = 1;
236			rigidBodies = new RigidBodyStamp*[n_rigidbodies];
237			for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
238			}
239	mmeineke	377	else{
240			if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
241			else unhandled->add( lhs, rhs );
242			have_extras = 1;
243			}
244			return NULL;
245			}
246
247			char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){
248
249			if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom;
250	gezelter	1103	else {
251	mmeineke	377	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	gezelter	981	" first atom declaration." );
258	mmeineke	377	}
259
260			return NULL;
261			}
262
263	gezelter	957	char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody,
264			int rigidBodyIndex ){
265
266			if( have_rigidbodies && rigidBodyIndex < n_rigidbodies )
267			rigidBodies[rigidBodyIndex] = the_rigidbody;
268	gezelter	1103	else {
269	gezelter	957	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	gezelter	981	" first rigidBody declaration." );
276	gezelter	957	}
277
278			return NULL;
279			}
280
281	mmeineke	377	char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){
282
283
284			if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond;
285			else{
286			if( have_bonds ){
287			sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range",
288			bondIndex );
289			return strdup( errMsg );
290			}
291			else return strdup("MoleculeStamp error, nBonds not given before"
292			"first bond declaration." );
293			}
294
295			return NULL;
296			}
297
298			char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){
299
300
301			if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend;
302			else{
303			if( have_bends ){
304			sprintf( errMsg, "MoleculeStamp error, %d out of nBends range",
305			bendIndex );
306			return strdup( errMsg );
307			}
308			else return strdup("MoleculeStamp error, nBends not given before"
309			"first bend declaration." );
310			}
311
312			return NULL;
313			}
314
315			char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){
316
317
318			if( have_torsions && torsionIndex < n_torsions )
319			torsions[torsionIndex] = the_torsion;
320			else{
321			if( have_torsions ){
322			sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range",
323			torsionIndex );
324			return strdup( errMsg );
325			}
326			else return strdup("MoleculeStamp error, nTorsions not given before"
327			"first torsion declaration." );
328			}
329
330			return NULL;
331			}
332
333			char* MoleculeStamp::checkMe( void ){
334
335			int i;
336	gezelter	957	short int no_atom, no_rigidbody;
337
338			if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name"
339			" was not given.\n" );
340	gezelter	988
341			if( !have_atoms ){
342			return strdup( "MoleculeStamp error. Molecule contains no atoms." );
343	mmeineke	377	}
344
345	gezelter	957	no_rigidbody = 0;
346			for( i=0; i<n_rigidbodies; i++ ){
347			if( rigidBodies[i] == NULL ) no_rigidbody = 1;
348			}
349
350			if( no_rigidbody ){
351			sprintf( errMsg,
352			"MoleculeStamp error. Not all of the RigidBodies were"
353			" declared in molecule \"%s\".\n", name );
354			return strdup( errMsg );
355			}
356
357	mmeineke	377	no_atom = 0;
358			for( i=0; i<n_atoms; i++ ){
359			if( atoms[i] == NULL ) no_atom = 1;
360			}
361
362			if( no_atom ){
363			sprintf( errMsg,
364			"MoleculeStamp error. Not all of the atoms were"
365			" declared in molecule \"%s\".\n", name );
366			return strdup( errMsg );
367			}
368
369	gezelter	1103
370			n_integrable = n_atoms;
371			for (i = 0; i < n_rigidbodies; i++)
372	tim	1113	n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object
373	gezelter	1103
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	mmeineke	377	return NULL;
382	gezelter	988	}