Int2 Main()
{
PMSD pmsdRoot = NULL;
static char valfilein[PATH_MAX];
Int2 iDotLen = 0;
AsnIoPtr aip=NULL;
NcbiMimeAsn1Ptr nmap=NULL;
BiostrucPtr bsp=NULL;
BiostrucSeqPtr bssp=NULL;
PDNMS pdnmsModelstruc = NULL;
ErrSev esMsg,esLog,esFatal;
PDNML pdnmlModel;
PMLD pmldThis;
Boolean isMime = FALSE;
Int4 iModels = 0, iNCBImodel = 0, iPDBmodel = 0, iAscii = 0;
/* Initialize MMDB-API */
ErrSetLogfile("error_strSummary.log", ELOG_APPEND|ELOG_BANNER);
ErrSetOptFlags(EO_SHOW_SEVERITY|EO_SHOW_CODES|EO_LOG_FILELINE|EO_SHOW_USERSTR|EO_SHOW_ERRTEXT|EO_BEEP|EO_WAIT_KEY|EO_LOGTO_USRFILE);
if (!GetArgs("strSummary reports on what is inside .val or .cn3 or .prt file to stdout.\nCaution - will not work on Biounits downloaded from NCBI, use Asymmetric Units\n",3,Rargs))
return 1;
/* we use exact filenames and extensions to avoid confusion */
StringCpy(valfilein, Rargs[0].strvalue);
if (FileLength(valfilein) == 0)
{
ErrPostEx(SEV_FATAL,13,1,"Unable to find input file %s",Rargs[0].strvalue);
return 13;
}
if (!OpenMMDBAPI(0,NULL)) {
ErrPostEx(SEV_FATAL,12,1,"Unable to open MMDBAPI, check for missing bstdt.val dictionary file.");
return 12;
}
/* load an ASN.1 file *.val or *.c3d or *.prt write out Biostruc only */
aip=AsnIoOpen(valfilein,"rb");
if (aip==NULL) {
ErrPostEx(SEV_FATAL,11,1,"Unable open ASN.1 stream in file %s",valfilein);
return 11;
}
/* first try biostruc load */
/* printf("try biostruc\n"); */
esMsg=ErrGetMessageLevel();
esLog=ErrGetLogLevel();
esFatal=ErrGetFatalLevel();
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
bsp=BiostrucAsnRead(aip,NULL);
AsnIoClose(aip);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
if (bsp == NULL) { /* try ascii */
aip = AsnIoOpen(valfilein,"r");
if (aip==NULL) {
ErrPostEx(SEV_FATAL,10,1,"Unable open binary or ascii ASN.1 from file %s",valfilein);
return 10;
}
esMsg=ErrGetMessageLevel();
esLog=ErrGetLogLevel();
esFatal=ErrGetFatalLevel();
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
bsp=BiostrucAsnRead(aip,NULL);
AsnIoClose(aip);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
if (bsp) iAscii = 1;
}
if (bsp==NULL) {
/* printf("try mime binary\n"); */
/* then try NCBIMime load */
aip=NULL;
aip=AsnIoOpen(valfilein,"rb");
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
nmap=NcbiMimeAsn1AsnRead(aip,NULL);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
AsnIoClose(aip);
if (nmap == NULL) {
/* printf("try mime ascii\n"); */
aip=AsnIoOpen(valfilein,"r");
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
nmap=NcbiMimeAsn1AsnRead(aip,NULL);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
AsnIoClose(aip);
if (nmap) iAscii = 1;
}
if (nmap!=NULL) {
/* got an NCBI mime */
if (nmap->choice!=NcbiMimeAsn1_strucseq && nmap->choice!=NcbiMimeAsn1_strucseqs) {
/* wrong MIME type */
nmap=NcbiMimeAsn1Free(nmap);
ErrPostEx(SEV_ERROR,9,1,"MIME-type wrapper is not a strucseq or strucseqs - no Biostruc to report in: %s",valfilein);
return 9;
}
isMime = TRUE;
/* unwrap the mime and leave the bsp for PDB conversion */
bssp=(BiostrucSeqPtr)(nmap->data.ptrvalue);
bsp=bssp->structure;
bssp->structure = NULL;
/* may want to report on contents of wrapper ... */
nmap=NcbiMimeAsn1Free(nmap); /* discard the wrapper */
nmap = NULL;
bssp = NULL;
}
}
if (bsp == NULL) {
ErrPostEx(SEV_ERROR,8,1,"No Biostruc in files to report in: %s",valfilein);
return 8;
}
pdnmsModelstruc=MakeAModelstruc(bsp);
if (pdnmsModelstruc==NULL) {
ErrPostEx(SEV_ERROR,7,1,"Unable to convert Biostruc to Modelstruc");
return 7;
}
pmsdRoot=(PMSD)(pdnmsModelstruc->data.ptrvalue);
if (pmsdRoot==NULL) {
ErrPostEx(SEV_ERROR,6,1,"Internal error.");
return 6;
}
/* OK, Ready to Start Reporting */
printf("Filename: %s\n", valfilein);
if (Rargs[1].intvalue == FALSE) {
if (iAscii) printf("ASCII Asn.1 (.prt) ");
else printf("Binary Asn.1 (.val) ");
if (isMime) printf("Entry Point: NCBIMime\n");
else printf("Entry Point: Biostruc\n");
if (pmsdRoot->pcPDBName != NULL) printf("PDB code: %s\n",pmsdRoot->pcPDBName);
printf("MMDB Id: %d\n", (int) pmsdRoot->iMMDBid);
printf("Name: %s\n",GetStrucStrings(pdnmsModelstruc, LONG_NAME));
printf("PDB Class: %s\n",GetStrucStrings(pdnmsModelstruc, PDB_CLASS));
printf("PDB Source: %s\n",GetStrucStrings(pdnmsModelstruc, PDB_SOURCE));
pdnmlModel=pmsdRoot->pdnmlModels;
while (pdnmlModel) {
iModels++;
pmldThis=(PMLD)(pdnmlModel->data.ptrvalue);
if (pmldThis->iType==Model_type_ncbi_all_atom) {
iNCBImodel = pdnmlModel->choice;
}
if (pmldThis->iType==Model_type_pdb_model) {
iPDBmodel = pdnmlModel->choice;
}
pdnmlModel=pdnmlModel->next;
}
printf("Number of Models: %d\n",iModels);
if(iNCBImodel) printf("NCBI All Atom Model: %d\n",iNCBImodel);
if (iPDBmodel) printf("PDB All Atom Model: %d\n",iPDBmodel);
if (pmsdRoot->pDictLocal) printf("Has Local Chemical Graph Dictionary\n");
printf("Number of Molecules: %d\n", (int) pmsdRoot->iMolCount); /* number of molecules */
printf("Number of Objects: %d\n",(int) pmsdRoot->iObjCount); /* number of objects */
printf("Number of Density Sets: %d\n",(int) pmsdRoot->iDensCount); /* number of densities */
printf("Number of Inter-Molecule Bonds: %d\n", (int) pmsdRoot->iIMBCount);
if (Rargs[2].intvalue == TRUE) {
printf("\n\nRAMACHANDRAN Angles for all Proteins:\n");
if (iNCBImodel) {
printf("NCBI All Atom Coordinate Model Number %d\n\nChain, AA, Num, Phi, Psi\n",iNCBImodel);
WriteStdoutRamaOneModel(pmsdRoot, iNCBImodel );
}
else if (iPDBmodel) {
printf("PDB All Atom Coordinate Model Number %d:\n\nChain, AA, Num, Phi, Psi\n",iPDBmodel);
WriteStdoutRamaOneModel(pmsdRoot, iPDBmodel );
}
}
}
printf("\n\n");
/* Output FASTA for each chain and dump het list - oldie but goodie code ! */
WriteFASTASeqHet(pdnmsModelstruc, stdout);
/* Shut Down MMDB-API */
/* All Modelstrucs remaining are freed in CloseMMDB-API() */
CloseMMDBAPI();
return 0;
}
Boolean LIBCALL VastToCn3D(WWWInfoPtr www_info)
{
FILE *pFile = NULL;
FILE *pIn = NULL;
Char pcBuf[100], pcLine[256], giBuf[20], URL[200];
CharPtr pcTest, pcL1 = NULL, Name, www_arg;
Int4 GetGi, Fid, Fsid, iFileExists = 0, indx;
BiostrucAnnotSetPtr pbsa = NULL;
BiostrucAnnotSetPtr pbsaShort = NULL;
BiostrucFeatureSetPtr pbsfs = NULL;
BiostrucFeaturePtr pbsf = NULL;
BiostrucResidueGraphSetPtr stdDictionary;
ValNodePtr pvnFids = NULL, pvnFid = NULL;
Int2 iTest = 0, iPDB = 0, iColor;
AsnIoPtr aip = NULL;
Byte bRender;
Char *IPAddress = getenv("REMOTE_HOST");
Int4 NumLabels, iMMDBId;
ValNode * pbsidThis;
BiostrucPtr pbsMaster, pbsSlave, pbsSlaveHead = NULL, pbsSlaveTail, pbsTemp;
Char szName[5], chain[2];
Char * szTemp;
SeqAnnotPtr psaAlignHead = NULL, psaAlignTail;
SeqAlignPtr salpHead, salpTail;
SeqIdPtr sip;
DenseSegPtr dsp;
BioseqPtr bsp;
SeqEntryPtr sep;
char str [52];
NcbiMimeAsn1Ptr pvnNcbi;
BiostrucAlignPtr pbsaStruct;
AsnIoPtr paiFile, aipr;
Boolean is_network;
Int4 uid, uidmaster = 0;
Int2 retcode = 3;
CharPtr JobID = NULL, pcPass;
Char AsnPath[PATH_MAX];
Char AsnName[10];
Int2 ret, complexity;
Int4 iFidCount = 0;
Boolean Chain;
/* SeqAsnLoad();
objmmdb1AsnLoad();
objmmdb2AsnLoad();
objmmdb3AsnLoad();
SeqAlignAsnLoad();
objmimeAsnLoad();
*/
if ((indx = WWWFindName(www_info, "uid")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h3>No accession (PDB ID) was input - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
GetGi = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric MMDB-id input - no results.</h3>\n");
return 0;
}
/* vsid and pass are to look at alignments from VAST Search */
if ((indx = WWWFindName(www_info, "vsid")) >= 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
JobID = StringSave(www_arg);
if ((indx = WWWFindName(www_info, "pass")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Password required.</h3>\n");
return 0;
}
else {
www_arg = WWWGetValueByIndex(www_info, indx);
pcPass = StringSave(www_arg);
if ((ret = Check_VastSearch_Password(pcPass, JobID)) != 1) {
if (ret == 2) return 0;
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Incorrect password.</h3>\n");
return 0;
}
}
}
if ((indx = WWWFindName(www_info, "hit")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<br>\n<h2>No alignment was selected!</h2>\n");
printf("<h3>Please click on up to 5 boxes in the leftmost column of the table.</h3>\n");
return 0;
}
/* loop over all the "hit" values in the list */
NumLabels = WWWGetNumEntries(www_info);
for (indx = 0; indx < NumLabels; indx++) {
Name = WWWGetNameByIndex(www_info, indx);
if (StrICmp(Name, "hit") == 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fid = (Int4) atol(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric slave alignment code - no results.</h3>\n");
return 0;
}
if (++iFidCount > 5) break;
pvnFid = ValNodeAddInt(&pvnFids, 0, Fid);
}
}
if ((indx = WWWFindName(www_info, "chaindom")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>No feature set ID (master alignment code) - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fsid = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric master alignment code - no results.</h3>\n");
return 0;
}
if ((indx = WWWFindName(www_info, "chn_complexity")) < 0)
Chain = TRUE;
else
{
www_arg = WWWGetValueByIndex(www_info, indx);
complexity =(Int2)atoi(www_arg);
if (complexity) Chain = TRUE;
else Chain = FALSE;
}
if ((indx = WWWFindName(www_info, "atm_complexity")) < 0)
/* select alpha Carbons only by default */
complexity = ONECOORDRES;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
complexity = (Int2) atoi(www_arg);
else
complexity = ONECOORDRES;
}
if ((complexity != ONECOORDRES) && (complexity != ONECOORDATOM))
/* bizarre value, but default to alpha-Carbons only */
complexity = ONECOORDRES;
/* action == 0 indicates MIME; action == 1 is text; action == 2 is save */
if ((indx = WWWFindName(www_info, "action")) < 0)
iPDB = 0;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
iPDB = (Int4) atoi(www_arg);
else
iPDB = 0;
}
if (VASTInit() != TRUE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find VAST data on server.\n");
printf("Contact [email protected]</h3>\n");
return 0;
}
OpenMMDBAPI((POWER_VIEW /* ^ FETCH_ENTREZ */), NULL);
pbsa = LocalGetFeatureSet(GetGi, Fsid, JobID);
if (pbsa == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>No master alignment record exists for %ld.</h3>\n", (long) GetGi);
return 0;
}
if (iFidCount == 1)
pbsaShort = BiostrucAnnotSetGetByFid(pbsa, Fid, Fsid);
else
pbsaShort = PruneBiostrucAnnotHits(pbsa, Fsid, pvnFids);
if (pbsaShort == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find alignment record.</h3>\n");
return 0;
}
if (MMDBInit() == FALSE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>MMDBInit failed.</h3>\n");
return 0;
}
pbsfs = pbsaShort->features;
pbsaStruct = BiostrucAlignNew();
if (pbsfs)
{
pbsf = pbsfs->features;
szTemp = pbsf->name;
szName[0] = szTemp[0];
szName[1] = szTemp[1];
szName[2] = szTemp[2];
szName[3] = szTemp[3];
szName[4] = '\0';
}
if (JobID == NULL)
pbsMaster = FetchBiostrucPDB(szName, complexity, 1);
else
{
AsnName[0]='\0';
StringCpy(AsnName, "/b");
StringCat(AsnName, szName);
AsnPath[0]='\0';
StringCpy(AsnPath, VSPATH);
StringCat(AsnPath, JobID);
StringCat(AsnPath, AsnName);
pbsMaster = FetchBS(AsnPath, 0, complexity, 1, POWER_VIEW);
}
if (pbsMaster == NULL)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load master structure.</h3>\n");
return 0;
}
/* Load in Standard Dictionary to make sequences - Ken */
aipr = NULL;
aipr = AsnIoOpen("bstdt", "rb");
if (aipr == NULL)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find standard dictionary.</h3>\n");
return 0;
}
stdDictionary = BiostrucResidueGraphSetAsnRead(aipr, NULL);
AsnIoFlush(aipr);
aipr = AsnIoClose(aipr);
/* retrieve the bioseq for master and put in ValNode */
sep = (SeqEntryPtr) MakeBioseqs(pbsMaster, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[4] != ' ')
{
chain[0] = szTemp[4];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsMaster, chain);
pbsMaster = NULL;
pbsMaster = pbsTemp;
}
}
/* Make a linked list of Biostrucs of the slave structures*/
while (pbsf)
{
szTemp = pbsf->name;
szName[0] = szTemp[7];
szName[1] = szTemp[8];
szName[2] = szTemp[9];
szName[3] = szTemp[10];
szName[4] = '\0';
if (!pbsSlaveHead)
{
pbsSlaveHead = FetchBiostrucPDB(szName, complexity, 1);
if (!pbsSlaveHead)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load slave structure.</h3>\n");
return 0;
}
/* Make Bioseq for Slaves */
sep = (SeqEntryPtr) MakeBioseqs(pbsSlaveHead, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[11] != ' ')
{
chain[0] = szTemp[11];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlaveHead, chain);
pbsSlaveHead = NULL;
pbsSlaveHead = pbsTemp;
}
}
pbsSlaveTail = pbsSlaveHead;
}
else
{
pbsSlave = FetchBiostrucPDB(szName, complexity, 1);
if (!pbsSlave)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load slave structure.</h3>\n");
return 0;
}
/* Make Bioseq for Slaves */
sep = (SeqEntryPtr) MakeBioseqs(pbsSlave, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[11] != ' ')
{
chain[0] = szTemp[11];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlave, chain);
pbsSlave = NULL;
pbsSlave = pbsTemp;
}
}
pbsSlaveTail->next = pbsSlave;
pbsSlaveTail = pbsSlaveTail->next;
pbsSlaveTail->next = NULL;
}
pbsf = pbsf->next;
}
/* Make a linked list of sequence alignments of master and slaves */
pbsf=pbsfs->features;
while (pbsf) {
if (!psaAlignHead) {
psaAlignHead = fnPBSFtoPSA (pbsf); /* get the sequence alignments */
if (psaAlignHead == NULL || psaAlignHead->data == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to create SeqAnnot.</h3>\n");
return 0;
}
salpHead = (SeqAlignPtr)(psaAlignHead->data);
salpTail = salpHead;
}
else {
psaAlignTail = fnPBSFtoPSA (pbsf);
salpTail->next = (SeqAlignPtr)(psaAlignTail->data);
if (psaAlignTail == NULL || psaAlignTail->data == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to create SeqAnnot.</h3>\n");
return 0;
}
salpTail = salpTail->next;
salpTail->next = NULL;
}
pbsf = pbsf->next;
}
pbsaStruct->master = pbsMaster;
pbsaStruct->slaves = pbsSlaveHead;
pbsaStruct->alignments = pbsaShort;
pbsaStruct->seqalign = psaAlignHead;
pvnNcbi = ValNodeNew(NULL);
pvnNcbi->choice = NcbiMimeAsn1_alignstruc;
pvnNcbi->data.ptrvalue = pbsaStruct;
pvnNcbi = (NcbiMimeAsn1Ptr) CheckId(pvnNcbi, JobID); /* to check identity, yanli */
OutputFile = stdout;
if (iPDB == 0) /* cn3d MIME */
printf ("Content-type: chemical/ncbi-asn1-binary\n\n");
else if (iPDB == 1) { /* "See File" */
printf ("Content-type: text/html\n\n");
printf ("<HTML><body><pre>\n");
}
else /* "Save File" */
printf ("Content-type: application/octet-stream\n\n");
if (iPDB != 1)
paiFile = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
else
paiFile = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
NcbiMimeAsn1AsnWrite(pvnNcbi, paiFile, NULL);
AsnIoFlush(paiFile);
AsnIoClose(paiFile);
CloseMMDBAPI();
MMDBFini();
VASTFini();
return 0;
} /* end of VastToCn3D */
Nlm_Int2 Main ()
{
Int2 iTest;
Byte bRender;
Int2 iColor;
PDNMS pdnmsModelstruc;
BiostrucPtr pbsBiostruc;
Char cOut[254];
FILE *pFile;
ErrSetFatalLevel(SEV_MAX);
if (! GetArgs("GetMMDB",NUMARGS,myargs))
return 1;
/* Initialize MMDBAPI */
if (! OpenMMDBAPI(0, NULL))
{
printf("Have not opened mmdbapi");
return 2;
}
/* load an ASN.1 Biostruc */
/* Any other method of obtaining a Biostruc is fine... */
/* This one does a built-in lookup of PDB accesion numbers */
/* then fetches the file using the Entrez clinet-server interface */
pbsBiostruc = FetchBiostrucPDB(myargs[0].strvalue, myargs[3].intvalue, 100);
if (pbsBiostruc == NULL)
{
printf("Have not fetched Biostruc");
return 3;
}
/* convert it into a Modelstruc pointed to by pdnmsModelstruc */
pdnmsModelstruc= MakeAModelstruc(pbsBiostruc);
if ( pdnmsModelstruc == NULL )
{
printf("Have not converted Biostruc");
return 4;
}
if (myargs[1].intvalue == 0) /* Summary */
{
if (!myargs[2].strvalue)
{
sprintf(cOut,"%s.sum", myargs[0].strvalue);
pFile = fopen(cOut, "w");
}
else
pFile = fopen(myargs[2].strvalue,"w");
iTest = WriteStructSummary(pdnmsModelstruc,pFile);
}
if (myargs[1].intvalue == 2) /* Kinemage */
{
bRender = (Byte) myargs[5].intvalue;
iColor = (Int2) myargs[4].intvalue;
if (!myargs[2].strvalue)
{
sprintf(cOut,"%s.kin", myargs[0].strvalue);
pFile = fopen(cOut, "w");
}
else
pFile = fopen(myargs[2].strvalue,"w");
iTest = WriteKinAllModel(pdnmsModelstruc,pFile,
iColor,bRender);
}
if (myargs[1].intvalue == 1) /* PDB */
{
if (!myargs[2].strvalue)
{
sprintf(cOut,"%s.pdb", myargs[0].strvalue);
pFile = fopen(cOut, "w");
}
else
pFile = fopen(myargs[2].strvalue,"w");
iTest = WritePDBAllModel(pdnmsModelstruc,pFile);
}
/* Free the Modelstruc (and its enclosed Biostruc) */
/* FreeAModelstruc(PDNMS pdnmsThis); not necessary */
/* This can be done individually - but all Modelstrucs */
/* remaining are freed in CloseMMDBAPI() */
/* Shut Down MMDBAPI */
CloseMMDBAPI();
return TRUE;
}
Boolean LIBCALL VastToMage(WWWInfoPtr www_info)
{
FILE *pFile = NULL;
FILE *pIn = NULL;
Char pcBuf[100], pcLine[256], giBuf[20], URL[200];
CharPtr pcTest, pcL1 = NULL, www_arg;
CharPtr JobID = NULL, pcPass;
Int4 GetGi, Fid, Fsid, iFileExists = 0, indx, complexity;
BiostrucAnnotSetPtr pbsa = NULL;
BiostrucAnnotSetPtr pbsaShort = NULL;
PDNMS pdnmsMaster = NULL, pdnmsSlave = NULL;
Int2 iTest = 0, iPDB = 0, iColor, ret;
AsnIoPtr aip = NULL;
Byte bRender;
Char *IPAddress = getenv("REMOTE_HOST");
Boolean Chain;
if ((indx = WWWFindName(www_info, "uid")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>No accession (PDB ID) was input - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
GetGi = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Non-numeric MMDB-id input - no results.</h3>\n");
return 0;
}
/* vsid and pass are to look at alignments from VAST Search */
if ((indx = WWWFindName(www_info, "vsid")) >= 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
JobID = StringSave(www_arg);
if ((indx = WWWFindName(www_info, "pass")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Password required.</h3>\n");
return 0;
}
else {
www_arg = WWWGetValueByIndex(www_info, indx);
pcPass = StringSave(www_arg);
if ((ret = Check_VastSearch_Password(pcPass, JobID)) != 1) {
if (ret == 2) return 0;
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Incorrect password.</h3>\n");
return 0;
}
}
}
if ((indx = WWWFindName(www_info, "hit")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<br>\n<h2>No alignment was selected!</h2>\n");
printf("<h3>Please click on a box in the leftmost column of the table.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fid = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Non-numeric slave alignment code - no results.</h3>\n");
return 0;
}
if ((indx = WWWFindName(www_info, "chaindom")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>No feature set ID (master alignment code) - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fsid = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Non-numeric master alignment code - no results.</h3>\n");
return 0;
}
if ((indx = WWWFindName(www_info, "chn_complexity")) < 0)
Chain = TRUE;
else
{
www_arg = WWWGetValueByIndex(www_info, indx);
complexity =(Int2)atoi(www_arg);
if (complexity) Chain = TRUE;
else Chain = FALSE;
}
/* action == 0 indicates MIME; action == 1 is text; action == 2 is save */
if ((indx = WWWFindName(www_info, "action")) < 0)
iPDB = 0;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
iPDB = (Int4) atoi(www_arg);
else
iPDB = 0;
}
if (VASTInit() != TRUE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Can't find VAST data on server.\n");
printf("Contact [email protected]</h3>\n");
return 0;
}
OpenMMDBAPI((POWER_VIEW /* ^ FETCH_ENTREZ */), NULL);
if (JobID == NULL)
pbsa = VASTBsAnnotSetGet(Fsid);
else
pbsa = LocalGetFeatureSet(GetGi, Fsid, JobID);
if (pbsa == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>No master alignment record exists for %ld.</h3>\n", (long) GetGi);
return 0;
}
pbsaShort = BiostrucAnnotSetGetByFid(pbsa, Fid, Fsid);
if (pbsaShort == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Can't find alignment record.</h3>\n");
return 0;
}
if (MMDBInit() == FALSE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>MMDBInit failed.</h3>\n");
return 0;
}
/* A note to myself for when I get back from Xmas break. This is the situation:
* The call to VastToMage is failing on the check where pdnmsSlave == NULL. For
* some reason the slave structure is not getting loaded into the global data
* structure. It appears that the next function call to InstBSAnnotSet() loads
* the master structure. However, I do not see where the slave structure gets
* loaded. Absurdly enough, though, the locally compiled vastsrv works fine, and
* the slave is indeed getting properly loaded there.
*
* I think I see it. There are massive differences between the local mmdbapi1.c
* and the checked-in one. In particular, BiostrucAddFeature is grossly different
* between the two. It looks like the slaves are loaded in the latter routine.
* InstBSAnnotSet calls BiostrucAddFeature.
*/
InstBSAnnotSet(pbsaShort, JobID, Chain, VSPATH); /* now uses mmdbapi1 version */
pdnmsMaster = GetMasterModelstruc();
/***** This is causing a problem at line 126, where pmsdThis->pbsBS does not exist!
pdnmsMaster = GetSelectedModelstruc();
*****/
if (pdnmsMaster == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Unable to load master structure.</h3>\n");
return 0;
}
pdnmsSlave = GetSlaveModelstruc();
if (pdnmsSlave == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToMage)</h2>\n");
printf("<h3>Unable to load slave structure.</h3>\n");
return 0;
}
/* Kinemage file generation */
if (iPDB == 2)
{
fprintf(stdout, "Content-type: application/octet-stream\n\n");
}
else if (iPDB == 1)
{
fprintf(stdout, "Content-type: text/html\n\n");
fprintf(stdout, "<HTML><body><pre>\n");
}
else
fprintf(stdout, "Content-type: chemical/x-kinemage\n\n"); /* MIME */
bRender = (Byte) (KIN_VIRTUAL | KIN_HET);
iColor = KIN_COLOR_NUMBER;
iTest = WriteKinPairAlign(pdnmsMaster, pdnmsSlave, stdout, iColor, bRender);
if (!iTest)
{
printf("Content-type: text/html\n\n");
printf("<h2>Error</h2>\n");
printf("Kinemage File write failed on Server.<p>\n");
RemoveTempFiles();
CloseMMDBAPI();
MMDBFini();
VASTFini();
exit(1);
}
fflush(stdout);
CloseMMDBAPI();
MMDBFini();
VASTFini();
RemoveTempFiles();
return 0;
} /* end of VastToMage */
