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1 /* mmdbapi.c
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information (NCBI)
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government do not place any restriction on its use or reproduction.
13 * We would, however, appreciate having the NCBI and the author cited in
14 * any work or product based on this material
15 *
16 * Although all reasonable efforts have been taken to ensure the accuracy
17 * and reliability of the software and data, the NLM and the U.S.
18 * Government do not and cannot warrant the performance or results that
19 * may be obtained by using this software or data. The NLM and the U.S.
20 * Government disclaim all warranties, express or implied, including
21 * warranties of performance, merchantability or fitness for any particular
22 * purpose.
23 *
24 * ===========================================================================
25 *
26 * File Name: mmdbapi1.c
27 *
28 * Author: Christopher Hogue
29 *
30 * Version Creation Date: 08/19/95
31 *
32 * $Revision: 6.12 $
33 *
34 * File Description: MMDBAPI wrappers.
35 *
36 * Modifications:
37 * --------------------------------------------------------------------------
38 * Date Name Description of modification
39 * ------- ---------- -----------------------------------------------------
40 *
41 *
42 *
43 * $Log: mmdbapi.c,v $
44 * Revision 6.12 1999/08/04 21:21:25 lewisg
45 * made ClearStructure turn off neighbor mode in non-cn3d mode
46 *
47 * Revision 6.11 1999/03/05 22:43:59 vakatov
48 * Made ClearStructures() function be NLM_EXTERN -- for the DLL build on PC
49 *
50 * Revision 6.10 1999/03/05 20:22:31 kans
51 * ClearStructures clears neighbor bit
52 *
53 * Revision 6.9 1998/08/26 18:02:38 kans
54 * fixed -v -fd warnings
55 *
56 * Revision 6.8 1998/08/12 21:54:37 lewisg
57 * pick correct master in SetNeighborOn
58 *
59 * Revision 6.7 1998/05/06 16:25:27 lewisg
60 * get rid of clear all structures bug
61 *
62 * Revision 6.6 1998/04/16 00:30:00 lewisg
63 * get rid of dead code
64 *
65 * Revision 6.5 1998/04/05 04:29:01 lewisg
66 * make SetNeighborOn set the right slaves in cn3d mode
67 *
68 * Revision 6.4 1998/04/04 00:57:52 lewisg
69 * corrected several functions to behave properly in neighbor mode
70 *
71 * Revision 6.3 1998/03/13 22:34:18 lewisg
72 * fix neighbor mode
73 *
74 * Revision 6.2 1998/03/06 01:16:00 lewisg
75 * merge
76 *
77 * Revision 6.0 1997/08/25 18:10:48 madden
78 * Revision changed to 6.0
79 *
80 * Revision 5.0 1996/05/28 14:02:09 ostell
81 * Set to revision 5.0
82 *
83 * Revision 1.6 1996/05/15 17:01:35 hogue
84 * Fixed compiler warnings.
85 *
86 * Revision 1.5 1996/04/18 17:05:49 hogue
87 * Added neighbor mode functionality, setting Master & Slave structures. GetFirstModelstruc gets first slave now when in neighbor mode. Backing out of neighbor mode resets pdnmsSelected to the Master.
88 *
89 * Revision 1.4 1996/01/31 21:30:49 hogue
90 * Major changes to accomodate multiple structures, added mmdbAPI
91 * data structure, list pointers for traversing structures,
92 * list pointers for PFB selection holders, etc.
93 *
94 * Revision 1.3 1995/10/07 15:24:19 hogue
95 * Counting biostrucs from 0 to n.
96 *
97 * Revision 1.2 1995/10/05 20:22:42 hogue
98 * Fixed some structure tracking bugs, added ClearStructures()
99 *
100 * Revision 1.1 1995/09/20 13:45:47 kans
101 * Initial revision
102 *
103 *
104 * ==========================================================================
105 */
106
107
108 /*
109
110 WARNING! The way some of these functions work is dependent on the setting of
111 pmmdbapi->fCn3D, which is set to TRUE when being run by Cn3D. This is to
112 eliminate the modality of those functions when running in Neighbor mode.
113
114 */
115
116 #include <mmdbapi.h>
117
118
119
120 static pmmdbAPI pmmdbapi = NULL;
121
122 Boolean LIBCALL IsMMDBAPIOpen(void)
123 {
124 return (Boolean) (pmmdbapi != NULL);
125 }
126
127 void LIBCALL fnMMDBCn3Dmode (void) /* may I never live this down */
128 {
129 pmmdbapi->fCn3D = TRUE;
130 }
131
132 pmmdbAPI LIBCALL NewMMDBAPI(void)
133 {
134 pmmdbAPI papi = NULL;
135
136 papi = (pmmdbAPI)MemNew((size_t)(sizeof(mmdbAPI)));
137 return papi;
138 }
139
140 Int2 LIBCALL OpenMMDBAPI(Byte bExtent, CharPtr pcDictName)
141 {
142
143 if (pmmdbapi != NULL) return 1;
144 else pmmdbapi = NewMMDBAPI();
145 if (bExtent == 0)
146 pmmdbapi->bExtent = (Byte) POWER_VIEW;
147 else
148 pmmdbapi->bExtent = (Byte) bExtent;
149 if (pcDictName == NULL)
150 pmmdbapi->prgdDict = LoadDict(DICT_DEFAULT);
151 else
152 pmmdbapi->prgdDict = LoadDict(pcDictName);
153 if (!pmmdbapi->prgdDict)
154 {
155 ErrClear();
156 ErrPostEx(SEV_FATAL,0,0, "Unable to Load Residue Dictionary");
157 ErrShow();
158 return 0;
159 }
160 if (! (objmmdb1AsnLoad() && objmmdb2AsnLoad() && objmmdb3AsnLoad() ))
161 {
162 ErrClear();
163 ErrPostEx(SEV_FATAL,0,0, "Internal objmmdbNAsnLoad() Failure");
164 ErrShow();
165 return 0;
166 }
167 pmmdbapi->iLocalCount = 0;
168 pmmdbapi->iFeatureSet = 0;
169 pmmdbapi->iFeatureId = 0;
170 pmmdbapi->pvnsffHead = NULL;
171 pmmdbapi->pColorFunc = NULL;
172 pmmdbapi->Neighbor = FALSE;
173 pmmdbapi->fCn3D = FALSE;
174 return 1;
175 }
176
177
178 BiostrucPtr LIBCALL FetchBiostrucPDB(CharPtr pcAcession, Int4 iModelLevel, Int4 iMaxModels)
179 {
180 BiostrucPtr pbsTemp;
181 pbsTemp = FetchBS(pcAcession, INP_PDB_ACCESSION, iModelLevel,
182 iMaxModels, pmmdbapi->bExtent);
183 return pbsTemp;
184 }
185
186 PDNMS LIBCALL MakeAModelstruc(BiostrucPtr pbsThis)
187 {
188 PDNMS pdnmsTemp = NULL;
189 PDNMS pdnmsCount = NULL;
190 PMSD pmsdThis = NULL;
191 PMSD pmsdMaster = NULL;
192 Int4 iCount = 0;
193
194 if (!pmmdbapi)
195 {
196 ErrClear();
197 ErrPostEx(SEV_FATAL,0,0, "MMDBAPI Not Initialized\n Use InitMMDBAPI() \n");
198 ErrShow();
199 return pdnmsTemp;
200 }
201
202 if (!pbsThis) return pdnmsTemp;
203 if (pmmdbapi->Neighbor && pmmdbapi->pdnmsMaster)
204 {
205 pmsdMaster = (PMSD) pmmdbapi->pdnmsMaster->data.ptrvalue;
206 pmmdbapi->iLocalCount++;
207 pdnmsTemp = Biostruc2Modelstruc(&pmsdMaster->pdnmsSlaves, pbsThis, pmmdbapi->prgdDict,
208 pmmdbapi->bExtent, pmmdbapi->iLocalCount, NULL, (Int2)0);
209 }
210 else
211 {
212 pmmdbapi->iLocalCount++;
213 pdnmsTemp = Biostruc2Modelstruc(&pmmdbapi->pdnmsMain, pbsThis, pmmdbapi->prgdDict,
214 pmmdbapi->bExtent, pmmdbapi->iLocalCount, NULL, (Int2)0);
215 }
216 if (!pdnmsTemp)
217 {
218 pmmdbapi->iLocalCount--; /* back it off the counter */
219 return pdnmsTemp; /* NOTE THE BIOSTRUC pbsThis is FREED if this fails!!*/
220 }
221
222 if (pmmdbapi->Neighbor)
223 {
224 pmmdbapi->pdnmsSlave = pdnmsTemp;
225 pmmdbapi->pdnmsSelected = pmmdbapi->pdnmsMaster;
226 }
227 else pmmdbapi->pdnmsSelected = pdnmsTemp;
228
229 pmsdThis = (PMSD) pdnmsTemp->data.ptrvalue;
230 pmsdThis->iHashChange = MakeHashChange(pdnmsTemp);
231 AssignBackBone(pdnmsTemp);
232 AssignVirtual(pdnmsTemp);
233 AssignIons(pdnmsTemp);
234
235 return pdnmsTemp;
236 }
237
238
239 PDNMS LIBCALL GetPDNMSMain(void)
240 {
241 return pmmdbapi->pdnmsMain;
242 }
243
244 PRGD LIBCALL GetPRGDDictionary(void)
245 {
246 return pmmdbapi->prgdDict;
247 }
248
249
250 void LIBCALL ChangeMMDBAPIbExtent(Byte bExtent)
251 {
252 pmmdbapi->bExtent = bExtent;
253 }
254
255
256 Byte LIBCALL GetMMDBAPIbExtent(void)
257 {
258 return pmmdbapi->bExtent;
259 }
260
261
262
263
264 Int4 LIBCALL MakeHashChange(PDNMS pdnmsThis)
265 {
266 PMSD pmsdThis = NULL;
267 Int4 iHashCalc = 0;
268 Int4 iAtomLocs = 0;
269
270 if (!pdnmsThis) return iHashCalc;
271 pmsdThis = (PMSD) pdnmsThis->data.ptrvalue;
272 iAtomLocs = AssignAtomLocId(pdnmsThis);
273 if (!(pmsdThis->bUpdate & (Byte) AM_CHANGED))
274 return pmsdThis->iMMDBid;
275
276 /* only changed if dirty bit set ... */
277 iHashCalc = pmsdThis->iMMDBid + pmsdThis->iModels + pmsdThis->iFeatures +
278 pmsdThis->iObjCount + pmsdThis->iDensCount + 100000 + iAtomLocs;
279 iHashCalc++; /* inc by one... for incremental changes (eg transform'ns) */
280 return iHashCalc;
281
282 }
283
284 Int4 LIBCALL CountModelstrucs(void)
285 {
286 Int4 iCount = 0;
287 PDNMS pdnmsCount = NULL;
288
289 if (!pmmdbapi) return iCount;
290 pdnmsCount = pmmdbapi->pdnmsMain;
291 while (pdnmsCount)
292 {
293 iCount++;
294 pdnmsCount = pdnmsCount->next;
295 }
296 return iCount;
297 }
298
299
300 void LIBCALL FreeAModelstruc(PDNMS pdnmsThis)
301 {
302 Int2 iLocalId;
303 ValNodePtr pvnKillSelectList = NULL;
304
305
306 iLocalId = (Int2) pdnmsThis->choice;
307 pvnKillSelectList = ValNodeExtractList(&pmmdbapi->pvnPFBSelect, iLocalId);
308 ValNodeFree(pvnKillSelectList); /* selection list purged for this Modelstruc */
309 if (pdnmsThis == pmmdbapi->pdnmsSelected)
310 pmmdbapi->pdnmsSelected = NULL;
311 if (pdnmsThis == pmmdbapi->pdnmsPrevious)
312 pmmdbapi->pdnmsPrevious = NULL;
313 if (pdnmsThis == pmmdbapi->pdnmsSlave)
314 pmmdbapi->pdnmsSlave = NULL;
315 if (pdnmsThis == pmmdbapi->pdnmsHolder)
316 pmmdbapi->pdnmsHolder = pdnmsThis->last;
317 if(AreNeighborsOn() && pdnmsThis != pmmdbapi->pdnmsMaster)
318 FreeDNMS(((PMSD)(pmmdbapi->pdnmsMaster->data.ptrvalue))->pdnmsSlaves, pdnmsThis);
319 else
320 {
321 if (pdnmsThis == pmmdbapi->pdnmsMaster) pmmdbapi->pdnmsMaster = NULL;
322 pmmdbapi->pdnmsMain = FreeDNMS(pmmdbapi->pdnmsMain, pdnmsThis);
323 }
324 }
325
326
327 NLM_EXTERN void LIBCALL ClearStructures(void)
328 {
329 PDNMS pdnmsThis = NULL;
330
331 if (!pmmdbapi) return;
332 pdnmsThis = GetFirstModelstruc();
333 if (!pdnmsThis) return;
334 FreeListDNMS(pdnmsThis);
335 if (!pmmdbapi->Neighbor || pmmdbapi->fCn3D)
336 {
337 pmmdbapi->pdnmsMain = NULL;
338 pmmdbapi->pdnmsMaster = NULL;
339 }
340 pmmdbapi->Neighbor = 0;
341 pmmdbapi->pdnmsSlave = NULL;
342 pmmdbapi->pdnmsHolder = NULL;
343 pmmdbapi->pdnmsSelected = NULL;
344 pmmdbapi->pdnmsPrevious = NULL;
345 ValNodeFree(pmmdbapi->pvnPFBSelect);
346 pmmdbapi->pvnPFBSelect = NULL;
347 pmmdbapi->pvnUndoMark = NULL;
348 /* lyg. no freeing of feature data in pmmdbapi. Is this a good idea? */
349 }
350
351
352 void LIBCALL CloseMMDBAPI(void)
353 {
354 if (!pmmdbapi) return;
355 if (pmmdbapi->pdnmsMain) FreeListDNMS(pmmdbapi->pdnmsMain);
356 if (pmmdbapi->pvnPFBSelect) ValNodeFree(pmmdbapi->pvnPFBSelect);
357 if (pmmdbapi->prgdDict) BiostrucResidueGraphSetFree(pmmdbapi->prgdDict);
358 if (pmmdbapi->pvnsffHead) FreeListVNSFF(pmmdbapi->pvnsffHead);
359 if (pmmdbapi) MemFree(pmmdbapi);
360 return;
361 }
362
363
364
365 CharPtr LIBCALL GetStrucStrings(PDNMS pdnmsThis, Int4 iPickType)
366 {
367 PMSD pmsdThis;
368
369 if (!pdnmsThis) pdnmsThis = pmmdbapi->pdnmsMain;
370 if (!pdnmsThis) return NULL;
371 pmsdThis = (PMSD) pdnmsThis->data.ptrvalue;
372 if (pmsdThis->bMe != (Byte) AM_MSD) return NULL;
373 if (iPickType == LONG_NAME) return (pmsdThis->pcChemName);
374 if (iPickType == PDB_ACC) return (pmsdThis->pcPDBName);
375 if (iPickType == PDB_CLASS) return (pmsdThis->pcPdbClass);
376 if (iPickType == PDB_SOURCE) return (pmsdThis->pcPdbSource);
377 return NULL;
378 }
379
380
381
382 void LIBCALL SetSelectedModelstruc(PDNMS pdnmsThis)
383 {
384
385 /* doesn't check to see if structure is a really a slave if Neighbor mode on */
386
387 if (pmmdbapi->Neighbor == TRUE && !(pmmdbapi->fCn3D))
388 {
389 pmmdbapi->pdnmsSlave = pdnmsThis;
390 pmmdbapi->pdnmsSelected = pdnmsThis;
391 }
392 else
393 pmmdbapi->pdnmsSelected = pdnmsThis;
394 }
395
396 void LIBCALL SetNeighborOn(void)
397 {
398
399 if (!pmmdbapi->pdnmsMaster)
400 pmmdbapi->pdnmsMaster = GetSelectedModelstruc();
401
402 if ( pmmdbapi->pdnmsMaster && !(pmmdbapi->fCn3D))
403 {
404 pmmdbapi->Neighbor = TRUE;
405 if (!pmmdbapi->pdnmsSlave)
406 {
407 pmmdbapi->pdnmsSlave = GetFirstModelstruc(); /* NULL if none loaded */
408 }
409 else pmmdbapi->Neighbor = FALSE;
410 }
411 else
412 {
413 pmmdbapi->pdnmsMaster = GetSelectedModelstruc();
414 if (pmmdbapi->pdnmsMaster)
415 {
416 pmmdbapi->pdnmsSlave = ((PMSD)(pmmdbapi->pdnmsMaster->data.ptrvalue))->pdnmsSlaves;
417 pmmdbapi->Neighbor = TRUE;
418 }
419 }
420 }
421
422
423 Boolean LIBCALL AreNeighborsOn(void)
424 {
425 return pmmdbapi->Neighbor;
426 }
427
428 void LIBCALL SetNeighborOff(void)
429 {
430 pmmdbapi->pdnmsSelected = pmmdbapi->pdnmsMaster;
431 pmmdbapi->Neighbor = FALSE;
432 pmmdbapi->pdnmsSlave = NULL;
433 }
434
435 PDNMS LIBCALL GetSelectedModelstruc(void)
436 {
437 if (pmmdbapi->Neighbor == TRUE && !(pmmdbapi->fCn3D))
438 return pmmdbapi->pdnmsSlave;
439 else
440 return pmmdbapi->pdnmsSelected;
441 }
442
443 PDNMS LIBCALL SwapModelstruc(void)
444 {
445 PDNMS pdnmsTemp;
446 pdnmsTemp = pmmdbapi->pdnmsSelected;
447 pmmdbapi->pdnmsSelected = pmmdbapi->pdnmsPrevious;
448 pmmdbapi->pdnmsPrevious = pdnmsTemp;
449 return pmmdbapi->pdnmsSelected;
450 }
451
452
453 void LIBCALL SetMasterModelstruc(PDNMS pdnmsThis)
454 {
455 pmmdbapi->pdnmsMaster = pdnmsThis;
456 }
457
458 PDNMS LIBCALL GetMasterModelstruc(void)
459 {
460 return pmmdbapi->pdnmsMaster;
461 }
462
463 void LIBCALL SetSlaveModelstruc(PDNMS pdnmsThis)
464 {
465 pmmdbapi->pdnmsSlave = pdnmsThis;
466 }
467
468 PDNMS LIBCALL GetSlaveModelstruc(void)
469 {
470 return pmmdbapi->pdnmsSlave;
471 }
472
473 /**************************************************/
474 /* GetFirstModelstruc, GetNextModelstruc and */
475 /* GetPreviousModelstruc are provided to walk */
476 /* the doubly-linked list of structures that */
477 /* MMDBAPI has in memory... */
478 /* SetHolderModelstruc allows one to set the */
479 /* pointer to any of the structures */
480 /**************************************************/
481
482 PDNMS LIBCALL GetFirstModelstruc(void)
483 {
484
485 PMSD pmsdThis = NULL;
486 PDNMS pdnmsThis = NULL;
487
488 if (pmmdbapi->Neighbor && !(pmmdbapi->fCn3D))
489 {
490 pdnmsThis = GetMasterModelstruc();
491 if (pdnmsThis)
492 {
493 pmsdThis = (PMSD) pdnmsThis->data.ptrvalue;
494 pmmdbapi->pdnmsHolder = pmsdThis->pdnmsSlaves;
495 return pmsdThis->pdnmsSlaves;
496 }
497 else return NULL;
498 }
499 pmmdbapi->pdnmsHolder = pmmdbapi->pdnmsMain;
500 return pmmdbapi->pdnmsMain;
501 }
502
503
504 void LIBCALL SetHolderModelstruc(PDNMS pdnmsThis)
505 {
506 pmmdbapi->pdnmsHolder = pdnmsThis;
507 }
508
509 PDNMS LIBCALL GetNextModelstruc(void)
510 {
511 if (pmmdbapi->pdnmsHolder)
512 {
513 pmmdbapi->pdnmsHolder = pmmdbapi->pdnmsHolder->next;
514 return pmmdbapi->pdnmsHolder;
515 }
516 return NULL;
517 }
518
519 PDNMS LIBCALL GetPreviousModelstruc(void)
520 { /* node which came before this one */
521 if (pmmdbapi->pdnmsHolder)
522 {
523 pmmdbapi->pdnmsHolder = pmmdbapi->pdnmsHolder->last;
524 return pmmdbapi->pdnmsHolder;
525 }
526 return NULL;
527 }
528
529 ValNodePtr LIBCALL AddPFBSelect(PFB pfbThis)
530 {
531 PDNMS pdnmsStruc = NULL;
532 PMSD pmsdStruc = NULL;
533
534 if (!pfbThis) return NULL;
535 pdnmsStruc = DNFromPFB((PFB)ToMSDParent(pfbThis));
536 pmmdbapi->pvnUndoMark = ValNodeAddPointer(&pmmdbapi->pvnPFBSelect,
537 pdnmsStruc->choice, (VoidPtr) pfbThis);
538 /* the choice field allows us to extract pointers
539 * to different structures from the list, esp. when freeing
540 * specific structures.
541 */
542 return pmmdbapi->pvnUndoMark;
543 }
544
545
546 void LIBCALL ClearPFBSelectList(void)
547 {
548 ValNodeFree(pmmdbapi->pvnPFBSelect);
549 pmmdbapi->pvnPFBSelect = NULL;
550 return;
551 }
552
553 void LIBCALL UndoPFBSelectList(void)
554 {
555 ValNodeFree(pmmdbapi->pvnUndoMark);
556 return;
557 }
558
559
560
561 PSFF LIBCALL DoesFeatureTypeHaveFuncs(Uint1 iCode)
562 {
563 ValNodePtr pvn = NULL;
564 PSFF psffThis = NULL;
565
566 ValNodeFindNext(pmmdbapi->pvnsffHead, NULL, iCode);
567 if (pvn)
568 {
569 psffThis = (PSFF) pvn->data.ptrvalue;
570 return psffThis;
571 }
572 return NULL;
573 }
574
575 Uint1 LIBCALL Call3DColorProc(ColorPropPtr pcpThis)
576 {
577 Uint1 i = 0;
578 if (pmmdbapi->pColorFunc)
579 (*(pmmdbapi->pColorFunc)) (pcpThis, &i);
580 return i;
581 }
582
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