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;
}
/*****************************************************************************
*
* PrintTemplateSetPtr PrintTemplateSetLoad()
* loads PrintTemplates
* If path== NULL, looks for "prt.prt" in the "data" directory
*
*****************************************************************************/
static Boolean PrintTemplateSetLoadInt ( CharPtr path, Boolean verbose )
{
AsnIoPtr aip;
FILE *f;
Boolean retval;
Char filename [80];
Char fullpath [PATH_MAX];
CharPtr ptr;
ErrSev lastLevel;
aip = NULL;
if (path != NULL && *path != '\0' && StringRChr (path, DIRDELIMCHR) != NULL) {
StringNCpy (fullpath, path, sizeof (fullpath) - 1);
if ((aip = AsnIoOpen (fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
} else {
if (path != NULL && *path != '\0') {
StringNCpy (filename, path, sizeof (filename) - 1);
} else {
StringCpy (filename, "prt.prt");
}
ProgramPath (fullpath, sizeof (fullpath) - 1);
ptr = StringRChr (fullpath, DIRDELIMCHR);
if (ptr != NULL) {
*ptr = '\0';
}
FileBuildPath (fullpath, NULL, filename);
/* silence SEV_INFO errors from FileOpen() */
if ((lastLevel = ErrGetMessageLevel()) < SEV_WARNING)
ErrSetMessageLevel (SEV_WARNING);
if ((f = FileOpen (fullpath, "r")) == NULL) {
ErrSetMessageLevel (lastLevel);
if (FindPath ("NCBI", "NCBI", "DATA", fullpath, sizeof (fullpath) - 1)) {
FileBuildPath (fullpath, NULL, filename);
if ((aip = AsnIoOpen (fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
} else {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "FindPath failed in PrintTemplateSetLoad - ncbi configuration file missing or incorrect");
}
return FALSE;
}
} else {
ErrSetMessageLevel (lastLevel);
FileClose (f);
if ((aip = AsnIoOpen(fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
}
}
retval = PrintTemplateSetAsnRead(aip);
AsnIoClose(aip);
return retval;
}
