Exemplo n.º 1
0
static TrajErr TRADESBenchmark(void)
{
	/* protein is 1CDZ, same as beta protein - mixed alpha/beta protein 96 AA */
	static Char sequence[]="ELPDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEKQKLLPHQLYGVVPQA";
	CharPtr pc;
	FILE *f;
	Char fnamseq[PATH_MAX];
	Char fnam[PATH_MAX];
	Char fnamtrj[PATH_MAX];
        Char fnuturndb[PATH_MAX];
	Int2 err,numAA,cnt;
	Int4 randseed,dbsize;
	pMakeTrjParamBlock mkdata;
	pFoldTrajParamBlock foldtrajprm; 
	CPUTimePtr pTime1,pTime2,pTime3,pTime4;
	BiostrucPtr bspBiostruc;
	PDNMS pdnmsModelstruc;
	PMSD pmsdHead;
	PDNML pdnmlModel;
	PMLD pmldThis;
	BiostrucIdPtr           pbi=NULL;
	BiostrucDescrPtr        pbd=NULL;


	printf("%d is the CODEBASE version here.\n6502:UNIX x86_32, 6503003:UNIX x86_64, 6500:Win32, 6401:UNIX PPC_32\n\n", S4VERSION);
        sprintf(fnuturndb,"UTURNDB"); /* to clean up errant U-Turn files CWVH 2010 */

	if (!OPENMMDBAPI(0,NULL)) {
	    ErrPostEx(SEV_ERROR,2,1,"Unable to open MMDBAPI");
	    return ERR_FAIL;
	}
	printf("One moment, opening rotamer library...\n");
	if (LoadRotLib()!=ERR_SUCCESS) {
		ErrPostEx(SEV_ERROR,1,8,"Cannot open rotamer library (%s%s) - if the file is missing, please re-install the software",CFG_local_datafilepath,NEWSCWRL_FNAM);
		return ERR_FAIL;
	}
	pc=DFPTmpNam(FALSE,FALSE);
	if ((f=FileOpen(pc,"w"))==NULL) {
		CLOSEMMDBAPI();
		FreeRotLib();
		ErrPostEx(SEV_ERROR,errno,1,"Failed to open %s file",pc);
		return ERR_FAIL;
	}
	fprintf(f,"%s\n",sequence);
	/* Make sure disk space was sufficient to write to file */
    if (fflush(f)==EOF) {
        FileClose(f);
		CLOSEMMDBAPI();
		FreeRotLib();
		ErrPostEx(SEV_ERROR,errno,1,"Failed to write to %s file",pc);
		return ERR_FAIL;
	}
	FileClose(f);
	StringCpy(fnamseq,pc);
	sprintf(fnam,"%s%s",CFG_local_datafilepath,BENCH_TRAJ);
	sprintf(fnamtrj,"%s%s%s",CFG_local_datafilepath,BENCH_TRAJ,ASN_EXT);

	mkdata = (pMakeTrjParamBlock)MemNew(sizeof(MakeTrjParamBlock));	
	mkdata->TrajMethod = 2; /* from sequence */
	mkdata->valfnamin = NULL;
	mkdata->pcChain = NULL;
	mkdata->modelnum = 1;
	mkdata->startres = 1;
	mkdata->endres = 0;
	mkdata->peakheight = 100;
	mkdata->noise = 0;
	mkdata->savechi = 0;
	mkdata->sigma_x = 0.0;
	mkdata->sigma_y = 0.0;
	mkdata->temperature = 0;
	mkdata->timestep = 0.0;
	mkdata->seqfnamin = fnamseq;
	mkdata->tgtype = 4;
	mkdata->sstrufname = NULL;
	mkdata->DoRPS = FALSE;
	mkdata->uturn = FALSE;
	mkdata->SStruinput = FALSE;
	mkdata->trjfnamout = fnam;
	mkdata->comprtype = USE_RLE;
	mkdata->constrfnamin = NULL;
	mkdata->units=UNITS_ARBITRARY;
	mkdata->templat=NULL;
	mkdata->zhangwindsize = 0;
	mkdata->alignfile=NULL;
	mkdata->ssmask=NULL;
	mkdata->dumpcsv=0;
	mkdata->benchmark=1;
	mkdata->all_coil = (Boolean)(FALSE);
	mkdata->all_beta = (Boolean)(FALSE);
	/* ensure config file is set right, even if user may have fudged it */
	if (SetConfigFileValues(WALK_PHIPSI,50.0/*errtol*/, 0.25/*abbb*/, 0.50/*absc*/, 0.0/*tunnelprob*/)!=ERR_SUCCESS) {
		CLOSEMMDBAPI();
		FreeRotLib();
		mkdata=MemFree(mkdata);
		FileRemove(pc);
#ifdef OS_UNIX
		ErrPostEx(SEV_ERROR,0,0,"Unable to write config file .foldtrajrc, cannot continue");
#else
		ErrPostEx(SEV_FATAL,0,0,"Unable to write config file foldtraj.ini, cannot continue");
#endif
		return ERR_FAIL;
	}
	printf("Predicting secondary structure and generating trajectory distribution...\n");
	pTime1=CPUTimeMeasure();
	MakeTrj((VoidPtr)mkdata);
        printf("MadeTrj complete, unpacking ASN.1 Trajectory Graph\n");
	pTime2=CPUTimeMeasure();
	mkdata=MemFree(mkdata);
	FileRemove(fnamseq);

	if (UnPackAsnTrajGraph(fnam,&numAA,sequence,NULL,&pbi,&pbd,NULL)==NULL) {
		CLOSEMMDBAPI();
		FreeRotLib();
		FileRemove(fnamtrj);
		ErrPostEx(SEV_ERROR,2,3,"Unable to read trajectory distribution %s, please create a new one",fnam);
		return ERR_FAIL;
	}
	randseed=54374;
	RandomSeed(randseed);
	StringCpy(tmpskelfname,DFPTmpNam(FALSE,FALSE));
	/* make the ASN.1 file for this protein's chemical graph */
	BuildSkelASN(sequence,tmpskelfname);
	InitBSPLog(randseed,sequence,totalstruc);
	TGInit(tmpdbasename,DB_READ,&dbsize);
	printf("Folding protein...\n");
	pTime3=CPUTimeMeasure();
	for (cnt=0;cnt<100;cnt++) {
		bspBiostruc=NULL;
		bspBiostruc=MIMEBiostrucAsnGet(tmpskelfname,"r",NULL);
		if (bspBiostruc==NULL) {
			CLOSEMMDBAPI();
			FreeRotLib();
			FileRemove(fnamtrj);
			BSFree(bspTempLog);
			FileRemove(tmpskelfname);
			TGClose();
			CleanUpDB(tmpdbasename);
                        CleanUpDB(fnuturndb);        
			ErrPostEx(SEV_ERROR,3,1,"Unable to fetch Biostruc");
			return ERR_FAIL;
		}
		if (pbi!=NULL) {
			if (bspBiostruc->id!=NULL)
				AsnGenericChoiceSeqOfFree(bspBiostruc->id,(AsnOptFreeFunc)BiostrucIdFree);
			bspBiostruc->id=pbi;
			pbi=NULL;
		}
		if (pbd!=NULL) {
			if (bspBiostruc->descr!=NULL)
				AsnGenericChoiceSeqOfFree(bspBiostruc->descr,(AsnOptFreeFunc)BiostrucDescrFree);
			bspBiostruc->descr=pbd;
			pbd=NULL;
		}
		/* now the chemical graph is correctly in memory as a modelstruc, with
			co-ordinates (and hence PALDs) assigned only to a-carbons */
		pdnmsModelstruc=MakeAModelstruc(bspBiostruc);
		if (pdnmsModelstruc==NULL) {
			CLOSEMMDBAPI();
			FreeRotLib();
			FileRemove(fnamtrj);
			BSFree(bspTempLog);
			FileRemove(tmpskelfname);
			TGClose();
			CleanUpDB(tmpdbasename);
                        CleanUpDB(fnuturndb);        
			ErrPostEx(SEV_ERROR,4,1,"Unable to convert Biostruc to Modelstruc. Please ensure your protein only contains the 20 standard amino acids.");
			return ERR_FAIL;
		}
		pmsdHead=(PMSD)(pdnmsModelstruc->data.ptrvalue);

		/* remove ppAsnOrder for all models so it will be rebuilt
			in WriteAsnAllModel */
		pdnmlModel=pmsdHead->pdnmlModels;
		while (pdnmlModel) {
			pmldThis=(PMLD)(pdnmlModel->data.ptrvalue);
			if (pmldThis->ppAsnOrder) {
				PTRVectorFree(pmldThis->ppAsnOrder,0);
				pmldThis->ppAsnOrder=NULL;
			}
			pdnmlModel=pdnmlModel->next;
		}
		if (dbsize!=((PMMD)((pmsdHead->pdnmmHead)->data.ptrvalue))->iResCount) {
			CLOSEMMDBAPI();
			FreeRotLib();
			FreeAModelstruc(pdnmsModelstruc);
			BSFree(bspTempLog);
			FileRemove(fnamtrj);
			FileRemove(tmpskelfname);
			TGClose();
			CleanUpDB(tmpdbasename);
                       	CleanUpDB(fnuturndb);        
			ErrPostEx(SEV_ERROR,1,1,"protein length inconsistency error, expect: %d actual: %d, possibly due to corrupt trajectory file; aborting",((PMMD)((pmsdHead->pdnmmHead)->data.ptrvalue))->iResCount,dbsize);
			return ERR_FAIL;
		}
		foldtrajprm=(pFoldTrajParamBlock)MemNew(sizeof(FoldTrajParamBlock));
		foldtrajprm->pmsdRoot=pmsdHead;
		foldtrajprm->Model=1;
		foldtrajprm->err=0;
		foldtrajprm->gen=0;
		foldtrajprm->errorfile=NULL;
		/* do the folding here */
		TRADEProtein((VoidPtr)foldtrajprm,1);
		err=foldtrajprm->err;
		foldtrajprm=MemFree(foldtrajprm);
		FreeAModelstruc(pdnmsModelstruc);
        if (err!=ERR_SUCCESS && err!=ERR_INCOMPLETE) {
			FileRemove(fnamtrj);
			FileRemove(tmpskelfname);
			BSFree(bspTempLog);
			TGClose();
			CleanUpDB(tmpdbasename);
  	                CleanUpDB(fnuturndb);        
			CLOSEMMDBAPI();
			FreeRotLib();
			ErrPostEx(SEV_ERROR,1,1,"Benchtraj returned a folding error %d",err);
			return ERR_FAIL;
		}
	}
	pTime4=CPUTimeMeasure();
	FileRemove(fnamtrj);
	FileRemove(tmpskelfname);
	BSFree(bspTempLog);
	TGClose();
	CleanUpDB(tmpdbasename);        
        CleanUpDB(fnuturndb);
	CLOSEMMDBAPI();
	FreeRotLib();
	printf("Benchmark complete.\n\nSummary\n-------\n          Usr time  Sys time\n          --------  --------\n");
	printf("Maketrj  %9.3f %9.3f\nFoldtraj %9.3f %9.3f\n\n",CPUTimeGetUser(pTime2)-CPUTimeGetUser(pTime1),CPUTimeGetSys(pTime2)-CPUTimeGetSys(pTime1),CPUTimeGetUser(pTime4)-CPUTimeGetUser(pTime3),CPUTimeGetSys(pTime4)-CPUTimeGetSys(pTime3));
        printf("Benchtraj successful\n");
	return ERR_SUCCESS;
}
Exemplo n.º 2
0
PCSAN CSANStructMask(Int4 iMMDBid, Int4 iGiStruc)
{

    Int4 iNumSeq = 0;
    BiostrucPtr pbsThis = NULL;
    Int4 iStrucLen = 0;
    PDNMS pdnmsStructure = NULL;
    PMSD  pmsdThis = NULL;
    PMMD  pmmdMol = NULL;
    PCSAN pcsanStruc = NULL;
    PCSAN pcsanMask = NULL;
    Char pcName[31];


    if (iGiStruc == 0)
      return NULL;

     /* get a pdnms to the structure MMDBid, then a pdnmm to the embedded Gi */

     if((pbsThis = SHoundGet3D(iMMDBid))!= NULL)
        pdnmsStructure = MakeAModelstruc(pbsThis);

     if (!pdnmsStructure)
       {
         ErrPostEx(SEV_ERROR, 0, 0,"Fatal Error during MMDB structure retrieval %ld\n", (long) iMMDBid);
         return NULL;
       }

    pmmdMol = MMDBGetMoleculeByGI(pdnmsStructure, iGiStruc);
    pmsdThis = (PMSD) pdnmsStructure->data.ptrvalue;


    pcsanMask = NewCSAN();
    pcsanMask->iGi = iGiStruc;
    pcsanMask->next = NewCSAN();
    pcsanStruc= pcsanMask->next;
    pcsanMask->iLen = pmmdMol->iResCount;
    pcsanStruc->iGi = iGiStruc;
    pcsanStruc->iLen = pmmdMol->iResCount;

    /* name of stru = "%s" */
    /* name of SS = "!SS_%s" */

    pcName[0] = '\0';
    sprintf(pcName,"!SS_gi|%ld|pdb|%4s|%1s",(long) iGiStruc, pmsdThis->pcPDBName, pmmdMol->pcMolName);
    pcsanMask->pcSeqName = StringSave(pcName);
    if (StringLen(pcName) > 23) pcsanMask->pcSeqName[23] = '\0';
    sprintf(pcName,"gi|%ld|pdb|%4s|%1s",(long) iGiStruc, IsNullStr(pmsdThis->pcPDBName), IsNullStr(pmmdMol->pcMolName));
    pcsanStruc->pcSeqName = StringSave(pcName);
    if (StringLen(pcName) > 23) pcsanMask->pcSeqName[23] = '\0';

    /* fill the sec-structure mask with the structure, pad the remainder */
    FillCSANWithMask(pcsanMask, pmmdMol, pmmdMol->iResCount);

    /* fill the CSAN node with the structure, pad the remainder if shorter */
    FillCSANWithStru(pcsanStruc, pmmdMol, pmmdMol->iResCount);

    ClearStructures();

    return pcsanMask;

}
Exemplo n.º 3
0
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;
}
Exemplo n.º 4
0
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;
}