1 /* vast2cn3d.c
2 *
3 * ===========================================================================
4 *
5 * PUBLIC DOMAIN NOTICE
6 * National Center for Biotechnology Information (NCBI)
7 *
8 * This software/database is a "United States Government Work" under the
9 * terms of the United States Copyright Act. It was written as part of
10 * the author's official duties as a United States Government employee and
11 * thus cannot be copyrighted. This software/database is freely available
12 * to the public for use. The National Library of Medicine and the U.S.
13 * Government do not place any restriction on its use or reproduction.
14 * We would, however, appreciate having the NCBI and the author cited in
15 * any work or product based on this material
16 *
17 * Although all reasonable efforts have been taken to ensure the accuracy
18 * and reliability of the software and data, the NLM and the U.S.
19 * Government do not and cannot warrant the performance or results that
20 * may be obtained by using this software or data. The NLM and the U.S.
21 * Government disclaim all warranties, express or implied, including
22 * warranties of performance, merchantability or fitness for any particular
23 * purpose.
24 *
25 * ===========================================================================
26 *
27 * File Name: vast2cn3d.c
28 *
29 * Author: Lewis Geer, Chris Hogue
30 *
31 * Version Creation Date: 03/18/98
32 *
33 * $Log: vast2cn3d.c,v $
34 * Revision 6.11 1999/10/13 20:19:35 zimmerma
35 * DZ: Removed use of temporary files - html output redirected to stdout
36 *
37 * Revision 6.10 1998/11/20 20:03:55 addess
38 * related to platform independence of VAST Search
39 *
40 * Revision 6.9 1998/10/14 17:16:35 addess
41 * sending aligned chains to Cn3D
42 *
43 * Revision 6.8 1998/07/17 18:46:30 madej
44 * Various changes, e.g. to support local IDs.
45 *
46 * Revision 6.7 1998/06/17 20:52:06 madej
47 * Fix for See File option in vastsrv.
48 *
49 *
50 */
51
52 #include <stdio.h>
53 #include <ncbi.h>
54 #include <accentr.h>
55 #include <objalign.h>
56 #include <objseq.h>
57 #include <objmgr.h>
58 #include <lsqfetch.h>
59 #include <netentr.h>
60 #include <www.h>
61 #include <sys/resource.h>
62 #include <mmdbapi.h>
63 #include <mmdbapi1.h>
64 #include "vastlocl.h"
65 #include "mmdblocl.h"
66 #include "mmdbdata.h"
67 #include "vast2mage.h"
68 #include "vastsrv.h"
69 #include "mkbioseq.h"
70 #include <asnmime.h>
71 #include <objmime.h>
72 #include <strimprt.h>
73
74
75
76 static char *BaseURL;
77 static FILE *OutputFile = NULL;
78 static char OutputName[200];
79 #define CPUTIME_MAX 120
80
81 /* Display a structural alignment in Cn3D. */
82
VastToCn3D(WWWInfoPtr www_info)83 Boolean LIBCALL VastToCn3D(WWWInfoPtr www_info)
84 {
85 FILE *pFile = NULL;
86 FILE *pIn = NULL;
87 Char pcBuf[100], pcLine[256], giBuf[20], URL[200];
88 CharPtr pcTest, pcL1 = NULL, Name, www_arg;
89 Int4 GetGi, Fid, Fsid, iFileExists = 0, indx;
90 BiostrucAnnotSetPtr pbsa = NULL;
91 BiostrucAnnotSetPtr pbsaShort = NULL;
92 BiostrucFeatureSetPtr pbsfs = NULL;
93 BiostrucFeaturePtr pbsf = NULL;
94 BiostrucResidueGraphSetPtr stdDictionary;
95 ValNodePtr pvnFids = NULL, pvnFid = NULL;
96 Int2 iTest = 0, iPDB = 0, iColor;
97 AsnIoPtr aip = NULL;
98 Byte bRender;
99 Char *IPAddress = getenv("REMOTE_HOST");
100 Int4 NumLabels, iMMDBId;
101 ValNode * pbsidThis;
102 BiostrucPtr pbsMaster, pbsSlave, pbsSlaveHead = NULL, pbsSlaveTail, pbsTemp;
103 Char szName[5], chain[2];
104 Char * szTemp;
105 SeqAnnotPtr psaAlignHead = NULL, psaAlignTail;
106 SeqAlignPtr salpHead, salpTail;
107 SeqIdPtr sip;
108 DenseSegPtr dsp;
109 BioseqPtr bsp;
110 SeqEntryPtr sep;
111 char str [52];
112 NcbiMimeAsn1Ptr pvnNcbi;
113 BiostrucAlignPtr pbsaStruct;
114 AsnIoPtr paiFile, aipr;
115 Boolean is_network;
116 Int4 uid, uidmaster = 0;
117 Int2 retcode = 3;
118 CharPtr JobID = NULL, pcPass;
119 Char AsnPath[PATH_MAX];
120 Char AsnName[10];
121 Int2 ret, complexity;
122 Int4 iFidCount = 0;
123 Boolean Chain;
124
125 /* SeqAsnLoad();
126
127
128 objmmdb1AsnLoad();
129 objmmdb2AsnLoad();
130 objmmdb3AsnLoad();
131 SeqAlignAsnLoad();
132 objmimeAsnLoad();
133 */
134
135
136 if ((indx = WWWFindName(www_info, "uid")) < 0) {
137 printf("Content-type: text/html\n\n");
138 printf("<h3>No accession (PDB ID) was input - nothing to report.</h3>\n");
139 return 0;
140 }
141
142 www_arg = WWWGetValueByIndex(www_info, indx);
143
144 if (isdigit(www_arg[0]))
145 GetGi = (Int4) atoi(www_arg);
146 else {
147 printf("Content-type: text/html\n\n");
148 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
149 printf("<h3>Non-numeric MMDB-id input - no results.</h3>\n");
150 return 0;
151 }
152
153 /* vsid and pass are to look at alignments from VAST Search */
154 if ((indx = WWWFindName(www_info, "vsid")) >= 0) {
155 www_arg = WWWGetValueByIndex(www_info, indx);
156 JobID = StringSave(www_arg);
157
158 if ((indx = WWWFindName(www_info, "pass")) < 0) {
159 printf("Content-type: text/html\n\n");
160 printf("<body bgcolor = \"#f0f0f0\">\n");
161 printf("<h2>VAST SEARCH</h2>\n");
162 printf("<h3>Password required.</h3>\n");
163 return 0;
164 }
165 else {
166 www_arg = WWWGetValueByIndex(www_info, indx);
167 pcPass = StringSave(www_arg);
168
169 if ((ret = Check_VastSearch_Password(pcPass, JobID)) != 1) {
170 if (ret == 2) return 0;
171 printf("Content-type: text/html\n\n");
172 printf("<body bgcolor = \"#f0f0f0\">\n");
173 printf("<h2>VAST SEARCH</h2>\n");
174 printf("<h3>Incorrect password.</h3>\n");
175 return 0;
176 }
177 }
178 }
179
180 if ((indx = WWWFindName(www_info, "hit")) < 0) {
181 printf("Content-type: text/html\n\n");
182 printf("<body bgcolor = \"#f0f0f0\">\n");
183 printf("<br>\n<h2>No alignment was selected!</h2>\n");
184 printf("<h3>Please click on up to 5 boxes in the leftmost column of the table.</h3>\n");
185 return 0;
186 }
187
188 /* loop over all the "hit" values in the list */
189 NumLabels = WWWGetNumEntries(www_info);
190
191 for (indx = 0; indx < NumLabels; indx++) {
192 Name = WWWGetNameByIndex(www_info, indx);
193
194 if (StrICmp(Name, "hit") == 0) {
195 www_arg = WWWGetValueByIndex(www_info, indx);
196
197 if (isdigit(www_arg[0]))
198 Fid = (Int4) atol(www_arg);
199 else {
200 printf("Content-type: text/html\n\n");
201 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
202 printf("<h3>Non-numeric slave alignment code - no results.</h3>\n");
203 return 0;
204 }
205
206 if (++iFidCount > 5) break;
207 pvnFid = ValNodeAddInt(&pvnFids, 0, Fid);
208 }
209 }
210
211 if ((indx = WWWFindName(www_info, "chaindom")) < 0) {
212 printf("Content-type: text/html\n\n");
213 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
214 printf("<h3>No feature set ID (master alignment code) - nothing to report.</h3>\n");
215 return 0;
216 }
217
218 www_arg = WWWGetValueByIndex(www_info, indx);
219
220 if (isdigit(www_arg[0]))
221 Fsid = (Int4) atoi(www_arg);
222 else {
223 printf("Content-type: text/html\n\n");
224 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
225 printf("<h3>Non-numeric master alignment code - no results.</h3>\n");
226 return 0;
227 }
228
229 if ((indx = WWWFindName(www_info, "chn_complexity")) < 0)
230 Chain = TRUE;
231 else
232 {
233 www_arg = WWWGetValueByIndex(www_info, indx);
234 complexity =(Int2)atoi(www_arg);
235
236 if (complexity) Chain = TRUE;
237 else Chain = FALSE;
238 }
239
240 if ((indx = WWWFindName(www_info, "atm_complexity")) < 0)
241 /* select alpha Carbons only by default */
242 complexity = ONECOORDRES;
243 else {
244 www_arg = WWWGetValueByIndex(www_info, indx);
245
246 if (isdigit(www_arg[0]))
247 complexity = (Int2) atoi(www_arg);
248 else
249 complexity = ONECOORDRES;
250 }
251
252 if ((complexity != ONECOORDRES) && (complexity != ONECOORDATOM))
253 /* bizarre value, but default to alpha-Carbons only */
254 complexity = ONECOORDRES;
255
256 /* action == 0 indicates MIME; action == 1 is text; action == 2 is save */
257 if ((indx = WWWFindName(www_info, "action")) < 0)
258 iPDB = 0;
259 else {
260 www_arg = WWWGetValueByIndex(www_info, indx);
261
262 if (isdigit(www_arg[0]))
263 iPDB = (Int4) atoi(www_arg);
264 else
265 iPDB = 0;
266 }
267
268 if (VASTInit() != TRUE) {
269 printf("Content-type: text/html\n\n");
270 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
271 printf("<h3>Can't find VAST data on server.\n");
272 printf("Contact info@ncbi.nlm.nih.gov</h3>\n");
273 return 0;
274 }
275
276 OpenMMDBAPI((POWER_VIEW /* ^ FETCH_ENTREZ */), NULL);
277 pbsa = LocalGetFeatureSet(GetGi, Fsid, JobID);
278
279 if (pbsa == NULL) {
280 printf("Content-type: text/html\n\n");
281 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
282 printf("<h3>No master alignment record exists for %ld.</h3>\n", (long) GetGi);
283 return 0;
284 }
285
286 if (iFidCount == 1)
287 pbsaShort = BiostrucAnnotSetGetByFid(pbsa, Fid, Fsid);
288 else
289 pbsaShort = PruneBiostrucAnnotHits(pbsa, Fsid, pvnFids);
290
291 if (pbsaShort == NULL) {
292 printf("Content-type: text/html\n\n");
293 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
294 printf("<h3>Can't find alignment record.</h3>\n");
295 return 0;
296 }
297
298 if (MMDBInit() == FALSE) {
299 printf("Content-type: text/html\n\n");
300 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
301 printf("<h3>MMDBInit failed.</h3>\n");
302 return 0;
303 }
304
305 pbsfs = pbsaShort->features;
306
307 pbsaStruct = BiostrucAlignNew();
308
309 if (pbsfs)
310 {
311 pbsf = pbsfs->features;
312 szTemp = pbsf->name;
313 szName[0] = szTemp[0];
314 szName[1] = szTemp[1];
315 szName[2] = szTemp[2];
316 szName[3] = szTemp[3];
317 szName[4] = '\0';
318 }
319
320 if (JobID == NULL)
321 pbsMaster = FetchBiostrucPDB(szName, complexity, 1);
322 else
323 {
324 AsnName[0]='\0';
325 StringCpy(AsnName, "/b");
326 StringCat(AsnName, szName);
327
328 AsnPath[0]='\0';
329 StringCpy(AsnPath, VSPATH);
330 StringCat(AsnPath, JobID);
331 StringCat(AsnPath, AsnName);
332
333 pbsMaster = FetchBS(AsnPath, 0, complexity, 1, POWER_VIEW);
334 }
335
336 if (pbsMaster == NULL)
337 {
338 printf("Content-type: text/html\n\n");
339 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
340 printf("<h3> Unable to load master structure.</h3>\n");
341 return 0;
342 }
343
344 /* Load in Standard Dictionary to make sequences - Ken */
345 aipr = NULL;
346 aipr = AsnIoOpen("bstdt", "rb");
347
348 if (aipr == NULL)
349 {
350 printf("Content-type: text/html\n\n");
351 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
352 printf("<h3>Can't find standard dictionary.</h3>\n");
353 return 0;
354 }
355
356 stdDictionary = BiostrucResidueGraphSetAsnRead(aipr, NULL);
357 AsnIoFlush(aipr);
358 aipr = AsnIoClose(aipr);
359
360 /* retrieve the bioseq for master and put in ValNode */
361 sep = (SeqEntryPtr) MakeBioseqs(pbsMaster, stdDictionary);
362 if ( sep == NULL )
363 {
364 printf("Content-type: text/html\n\n");
365 printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
366 printf("<h3>Unable to get SeqEntry.</h3>\n");
367 return 0;
368 }
369 ValNodeLink(&(pbsaStruct->sequences), sep);
370 /* PruneBiostruc if Aligned Chain Options has been chosen */
371 if (Chain)
372 {
373 if (szTemp[4] != ' ')
374 {
375 chain[0] = szTemp[4];
376 chain[1] = '\0';
377 pbsTemp = (BiostrucPtr)PruneBiostruc(pbsMaster, chain);
378 pbsMaster = NULL;
379 pbsMaster = pbsTemp;
380 }
381 }
382
383 /* Make a linked list of Biostrucs of the slave structures*/
384 while (pbsf)
385 {
386 szTemp = pbsf->name;
387 szName[0] = szTemp[7];
388 szName[1] = szTemp[8];
389 szName[2] = szTemp[9];
390 szName[3] = szTemp[10];
391 szName[4] = '\0';
392
393 if (!pbsSlaveHead)
394 {
395 pbsSlaveHead = FetchBiostrucPDB(szName, complexity, 1);
396 if (!pbsSlaveHead)
397 {
398 printf("Content-type: text/html\n\n");
399 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
400 printf("<h3> Unable to load slave structure.</h3>\n");
401 return 0;
402 }
403 /* Make Bioseq for Slaves */
404 sep = (SeqEntryPtr) MakeBioseqs(pbsSlaveHead, stdDictionary);
405 if ( sep == NULL )
406 {
407 printf("Content-type: text/html\n\n");
408 printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
409 printf("<h3>Unable to get SeqEntry.</h3>\n");
410 return 0;
411 }
412 ValNodeLink(&(pbsaStruct->sequences), sep);
413 /* PruneBiostruc if Aligned Chain Options has been chosen */
414 if (Chain)
415 {
416 if (szTemp[11] != ' ')
417 {
418 chain[0] = szTemp[11];
419 chain[1] = '\0';
420 pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlaveHead, chain);
421 pbsSlaveHead = NULL;
422 pbsSlaveHead = pbsTemp;
423 }
424 }
425 pbsSlaveTail = pbsSlaveHead;
426 }
427 else
428 {
429 pbsSlave = FetchBiostrucPDB(szName, complexity, 1);
430 if (!pbsSlave)
431 {
432 printf("Content-type: text/html\n\n");
433 printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
434 printf("<h3> Unable to load slave structure.</h3>\n");
435 return 0;
436 }
437 /* Make Bioseq for Slaves */
438 sep = (SeqEntryPtr) MakeBioseqs(pbsSlave, stdDictionary);
439 if ( sep == NULL )
440 {
441 printf("Content-type: text/html\n\n");
442 printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
443 printf("<h3>Unable to get SeqEntry.</h3>\n");
444 return 0;
445 }
446 ValNodeLink(&(pbsaStruct->sequences), sep);
447 /* PruneBiostruc if Aligned Chain Options has been chosen */
448 if (Chain)
449 {
450 if (szTemp[11] != ' ')
451 {
452 chain[0] = szTemp[11];
453 chain[1] = '\0';
454 pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlave, chain);
455 pbsSlave = NULL;
456 pbsSlave = pbsTemp;
457 }
458 }
459 pbsSlaveTail->next = pbsSlave;
460 pbsSlaveTail = pbsSlaveTail->next;
461 pbsSlaveTail->next = NULL;
462 }
463
464 pbsf = pbsf->next;
465 }
466 /* Make a linked list of sequence alignments of master and slaves */
467 pbsf=pbsfs->features;
468 while (pbsf) {
469 if (!psaAlignHead) {
470 psaAlignHead = fnPBSFtoPSA (pbsf); /* get the sequence alignments */
471 if (psaAlignHead == NULL || psaAlignHead->data == NULL) {
472 printf("Content-type: text/html\n\n");
473 printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
474 printf("<h3>Unable to create SeqAnnot.</h3>\n");
475 return 0;
476 }
477 salpHead = (SeqAlignPtr)(psaAlignHead->data);
478 salpTail = salpHead;
479 }
480 else {
481 psaAlignTail = fnPBSFtoPSA (pbsf);
482 salpTail->next = (SeqAlignPtr)(psaAlignTail->data);
483 if (psaAlignTail == NULL || psaAlignTail->data == NULL) {
484 printf("Content-type: text/html\n\n");
485 printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
486 printf("<h3>Unable to create SeqAnnot.</h3>\n");
487 return 0;
488 }
489 salpTail = salpTail->next;
490 salpTail->next = NULL;
491 }
492 pbsf = pbsf->next;
493 }
494
495 pbsaStruct->master = pbsMaster;
496 pbsaStruct->slaves = pbsSlaveHead;
497 pbsaStruct->alignments = pbsaShort;
498 pbsaStruct->seqalign = psaAlignHead;
499
500 pvnNcbi = ValNodeNew(NULL);
501 pvnNcbi->choice = NcbiMimeAsn1_alignstruc;
502 pvnNcbi->data.ptrvalue = pbsaStruct;
503 pvnNcbi = (NcbiMimeAsn1Ptr) CheckId(pvnNcbi, JobID); /* to check identity, yanli */
504
505 OutputFile = stdout;
506
507 if (iPDB == 0) /* cn3d MIME */
508 printf ("Content-type: chemical/ncbi-asn1-binary\n\n");
509
510 else if (iPDB == 1) { /* "See File" */
511 printf ("Content-type: text/html\n\n");
512 printf ("<HTML><body><pre>\n");
513 }
514
515 else /* "Save File" */
516 printf ("Content-type: application/octet-stream\n\n");
517
518 if (iPDB != 1)
519 paiFile = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
520
521 else
522 paiFile = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
523
524 NcbiMimeAsn1AsnWrite(pvnNcbi, paiFile, NULL);
525 AsnIoFlush(paiFile);
526 AsnIoClose(paiFile);
527
528 CloseMMDBAPI();
529 MMDBFini();
530 VASTFini();
531 return 0;
532
533 } /* end of VastToCn3D */
534