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00017 #include <iostream>
00018 #include <stdio.h>
00019 #include <stdlib.h>
00020 #include <string.h>
00021 #include <ctype.h>
00022
00023
00024 #ifndef __MSD_USER_H__
00025 #include "msd_user.h"
00026 #endif
00027
00028
00029
00030
00031 int main(int argc, char* argv[]) {
00032 MSDManager* msdm;
00033 char select_stm[3072];
00034
00035 int nDepId = 13156;
00036 int nMaxCells = 2;
00037 int nDepDepId = nDepId;
00038 char szExpType[255] = {0};
00039 short nExpTypeInd = 0;
00040 short nInd;
00041 int nContactType;
00042 int nContactType1;
00043 int nContactType2;
00044 int nValueType;
00045 double dblValue, dblAngle, dblDist1, dblDist2;
00046 int nActiveSiteType1, nActiveSiteType2;
00047 int nAtomId1, nAtomId2;
00048 char szAtomName1[12], szAtomName2[12];
00049 int nAtomSiteId1, nAtomSiteId2;
00050 int nComponentId1, nComponentId2;
00051 int nChainId1, nChainId2;
00052 int nActiveSiteId1, nActiveSiteId2, nActiveSiteId3;
00053 int nAssemblyId, nAssemblySerial;
00054 int nModelId;
00055 char szCode3letter1[4];
00056 char szCode3letter2[4];
00057 char szChainID1[4];
00058 char szChainID2[4];
00059 int nPdbSeq1, nPdbSeq2;
00060 int nCarbonIndex = getElementNo(" C");
00061 int nNeighbourTypeId;
00062 int nNeighbourTypeId1;
00063 int nNeighbourTypeId2;
00064 int nOrdering;
00065 char chLigandAcceptorDonor[2];
00066 char chNeighbourAcceptorDonor[2];
00067 char szSymbol1[3];
00068 char szSymbol2[3];
00069
00070
00071 char S1[100];
00072 char S2[100];
00073 double dblMinDist;
00074 int nSeqDist;
00075 PSContact vContact = NULL;
00076 int nContacts = 0;
00077 msdbConnect db;
00078 msdbConnect::msdbInit();
00079 try
00080 {
00081 db.rlogon("search/search55@msdsrchd");
00082 printf("\nLogin Seccessfull.");
00083 }
00084 catch(msdbException& p){
00085 cerr<<p.msg<<endl;
00086 cerr<<p.stm_text<<endl;
00087 cerr<<p.var_info<<endl;
00088
00089 }
00090
00091 InitMatType();
00092 msdm=new MSDManager();
00093
00094 SetMakersCAtom ( (void*)newCDBAtom,(void*)streamNewCDBAtom );
00095
00096
00097 connectivity_d* connect_d = new connectivity_d[1000];
00098 connectivity_a* connect_a = new connectivity_a[1000];
00099 int nDCount = 0, nACount = 0;
00100
00101
00102 if (msdm->LoadWarehouse(db,38175) != S_OK)
00103 { printf("\nData MSDManger not loaded.");
00104 exit(1);
00105 }
00106 printf("\nData MSDManger loaded successfully.");
00107 printf("\nNumber of Atoms for this entry: = %d atoms.\n", msdm->GetNumberOfAtoms());
00108 printf("\nPDB Code for this entry: = %s (PDB Code)\n", msdm->GetEntryID());
00109
00110 sprintf(select_stm,"%s","select /*+ INDEX(ENTRY)*/ entry.SHORT_EXPERIMENT_TYPE "
00111 " from entry where entry.entry_id = :nDepDepId <int> ");
00112
00113 try{
00114 msdbStream imsd (50, select_stm, db);
00115 imsd << nDepDepId;
00116
00117 while (!imsd.eof()){
00118 imsd >> szExpType;
00119 nExpTypeInd = imsd.is_null();
00120 if (!nExpTypeInd)
00121 trimRight(szExpType);
00122 else
00123 szExpType[0] = 0;
00124
00125 ExpType::EExpType nType = ExpType::nUNKNOWN;
00126 if (!strcmp("XRAY", szExpType))
00127 nType = ExpType::nXRAY;
00128 else if (!strcmp("NMR", szExpType))
00129 nType = ExpType::nNMR;
00130 else if (!strcmp("SSNMR", szExpType))
00131 nType = ExpType::nNMR;
00132 int nCells = nType == ExpType::nXRAY? nMaxCells : -1;
00133 if (nCells >= 0 && msdm->IsTheoretical() == S_OK)
00134 nCells = -1;
00135
00136 dblMinDist = 0.1;
00137 nSeqDist = 1;
00138
00139 if (nCells >= 0)
00140 {
00141 if (!msdm->isCrystInfo())
00142 {cerr << "Missing cell parameters (a,b,c,alpha,beta,gamma)" << endl;
00143 return (1);
00144 }
00145 else if (!msdm->isSpaceGroup())
00146 {cerr << "Missing space group of symmetry"<< endl;
00147 return (2);
00148 }
00149 else if (!msdm->isTransfMatrix())
00150 {cerr << "Orthogonalization/fractionalization is impossible"<< endl;
00151 return (3);
00152 }
00153 }
00154 }
00155 }
00156 catch(msdbException& p){
00157 cerr<<"get experiment type error"<<endl;
00158 cerr<<p.msg<<endl;
00159 cerr<<p.stm_text<<endl;
00160 cerr<<p.var_info<<endl;
00161 }
00162
00163 db.logoff();
00164
00165 CDBAssembly** vpAssembly = NULL;
00166 msdm->GetAssemblyArray(&vpAssembly);
00167 int nAssemblyCount = 0;
00168 msdm->GetAssemblyCount(&nAssemblyCount);
00169 CDBAtom** vpMacroMolAtom = new CDBAtom*[msdm->GetAtomArrayLength()];
00170 CDBAtom** vpLigandAtom = new CDBAtom*[msdm->GetAtomArrayLength()];
00171 CDBAtom** vpWaterAtom = new CDBAtom*[msdm->GetAtomArrayLength()];
00172 CAtom** vpMaxOccAtom = new CAtom*[msdm->GetAtomArrayLength()];
00173 CAtom** vpFirstReserveAtom = new CAtom*[msdm->GetAtomArrayLength()];
00174 CAtom** vpSecondReserveAtom = new CAtom*[msdm->GetAtomArrayLength()];
00175 int* vnActiveSiteId = new int[msdm->GetAtomArrayLength() + 1];
00176 for (int l = 0; l < nAssemblyCount; l++)
00177 {
00178 CDBAssembly* pAssembly = vpAssembly[l];
00179 pAssembly->GetId(&nAssemblyId);
00180 pAssembly->GetSerial(&nAssemblySerial);
00181 int nModelAssemblyCount = 0;
00182 pAssembly->GetModelAssemblyCount(&nModelAssemblyCount);
00183 for (int im = 0; im < nModelAssemblyCount; im++)
00184 {
00185 memset(vnActiveSiteId, 0, sizeof(int) * (msdm->GetAtomArrayLength() + 1));
00186 CDBModelAssembly* pModelAssembly = NULL;
00187 pAssembly->GetModelAssembly(&pModelAssembly, im);
00188 CDBModel* pModel = NULL;
00189 pModelAssembly->GetModel(&pModel);
00190 pModel->GetId(&nModelId);
00191 int nMacroMolAtoms = 0;
00192 int nLigandAtoms = 0;
00193 int nWaterAtoms = 0;
00194 int nMaxOccAtoms = 0;
00195 for (int nc = 0; nc < pModel->GetNumberOfChains(); nc++)
00196 {
00197 CDBChain* pChain = (CDBChain*)pModel->GetChain(nc);
00198 char szType[20];
00199 pChain->GetType(szType);
00200 bool bIsWater = (szType[0] != 0 && szType[1] == 'W') || szType[0] == 'W';
00201 bool bIsLigand = (szType[0] != 0 && szType[1] == 'B') || szType[0] == 'B';
00202 bool bIsMacromol = (szType[0] != 0 && szType[1] == 'C') || szType[0] == 'C';
00203 bool bIsModRes = false;
00204 if (bIsLigand || bIsMacromol || bIsWater) for (int nr = 0; nr < pChain->GetNumberOfResidues(); nr++)
00205 {
00206 CDBResidue* pResidue = (CDBResidue*)pChain->GetResidue(nr);
00207 if (bIsMacromol && pChain->IsProtein() == S_OK)
00208 bIsModRes = !isStdAminoAcid(pResidue->name);
00209 int nResAssemblyId = 0;
00210 if (pResidue->GetAssemblyId(&nResAssemblyId) != S_OK ||
00211 nAssemblyId != nResAssemblyId)
00212 continue;
00213 rvector occupancy = NULL;
00214 int nAltLocs,alflag;
00215 AltLoc aLoc;
00216 PAltLoc aL = NULL;
00217 pResidue->GetAltLocations ( nAltLocs, aL, occupancy, alflag );
00218 PCAtom pPrevAtom = NULL;
00219 double dx = -2.0;
00220 aLoc[0] = char(0);
00221 if (nAltLocs > 1)
00222 {
00223 for (int i=0;i<nAltLocs;i++)
00224 if ((aL[i][0]) && (occupancy[i]>dx)) {
00225 dx = occupancy[i];
00226 strcpy ( aLoc,aL[i] );
00227 }
00228 }
00229 else
00230 {
00231 if (strcmp(aLoc,aL[0]))
00232 strcpy ( aLoc,aL[0] );
00233 }
00234 for (int na = 0; na < pResidue->nAtoms; na++)
00235 {
00236 CDBAtom* pAtom = (CDBAtom*)pResidue->atom[na];
00237 if (!pAtom || pAtom->Ter)
00238 continue;
00239 if (bIsLigand || bIsModRes)
00240 vpLigandAtom[nLigandAtoms++] = pAtom;
00241 else if (bIsMacromol && !bIsModRes)
00242 vpMacroMolAtom[nMacroMolAtoms++] = pAtom;
00243 else if (bIsWater)
00244 vpWaterAtom[nWaterAtoms++] = pAtom;
00245 if (pAtom->element[0] == 0)
00246 continue;
00247 if (nAltLocs > 1)
00248 {
00249 bool B = !strcmp(aLoc, pAtom->altLoc);
00250 if ((!B) && (!pAtom->altLoc[0])) {
00251
00252
00253 for (int ja=na+1;(ja<pResidue->nAtoms) && (!B);ja++)
00254 if (pResidue->atom[ja]) {
00255 if ((!pResidue->atom[ja]->Ter) &&
00256 (!strcmp(pResidue->atom[ja]->name, pAtom->name)))
00257 B = !strcmp(aLoc,pResidue->atom[ja]->altLoc);
00258 }
00259
00260
00261 B = !B;
00262 }
00263 if (B)
00264 vpMaxOccAtom[nMaxOccAtoms++] = pAtom;
00265 }
00266 else
00267 vpMaxOccAtom[nMaxOccAtoms++] = pAtom;
00268 }
00269 }
00270 }
00271
00272 if (!nMacroMolAtoms || !nLigandAtoms)
00273 continue;
00274
00275 donor_out* d_out = new donor_out[nMaxOccAtoms];
00276 next_d* nextd = new next_d[nMaxOccAtoms];
00277 int nDonorCount = 0;
00278 acceptor_out* a_out = new acceptor_out[nMaxOccAtoms];
00279 next_a* nexta = new next_a[nMaxOccAtoms];
00280 int nAcceptorCount = 0;
00281 std::map<CAtomKey*, int, ltatom> mapDonor;
00282 initDonorOut(vpMaxOccAtom, nMaxOccAtoms,
00283 connect_d, nDCount, mapDonor,
00284 d_out, nextd, &nDonorCount);
00285 std::map<CAtomKey*, int, ltatom> mapAcceptor;
00286 initAcceptorOut(vpMaxOccAtom, nMaxOccAtoms,
00287 connect_a, nACount, mapAcceptor,
00288 a_out, nexta, &nAcceptorCount);
00289 vContact = NULL;
00290 nContacts = 0;
00291
00292 msdm->CMMDBManager::SeekContacts((PPCAtom)vpLigandAtom, nLigandAtoms,
00293 (PPCAtom)vpMacroMolAtom, nMacroMolAtoms,
00294 0, 5, 2,
00295 vContact, nContacts, 0, NULL, 1);
00296
00298 printContacts(0, 0, vContact, nContacts,
00299 (CAtom**)vpLigandAtom, nLigandAtoms, (CAtom**)vpMacroMolAtom, nMacroMolAtoms,
00300 NULL);
00302
00303 if (nContacts>0) {
00304 printf ( " Found %i contacts:\n",nContacts );
00305 for (int i=0;i<nContacts;i++)
00306 printf ( " %s <-> %s %10.4f A\n",
00307 vpLigandAtom[vContact[i].id1]->GetAtomID(S1),
00308 vpMacroMolAtom[vContact[i].id2]->GetAtomID(S2),
00309 vContact[i].dist );
00310 } else
00311 printf ( " No contact found.\n" );
00312 vContact = NULL;
00313 nContacts = 0;
00314 msdm->CMMDBManager::SeekContacts((PPCAtom)vpLigandAtom, nLigandAtoms,
00315 (PPCAtom)vpLigandAtom, nLigandAtoms,
00316 0, 5, 2,
00317 vContact, nContacts, 0, NULL, 2);
00318
00319 if (nContacts>0) {
00320 printf ( " Found %i contacts:\n",nContacts );
00321 for (int i=0;i<nContacts;i++)
00322 printf ( " %s <-> %s %10.4f A\n",
00323 vpLigandAtom[vContact[i].id1]->GetAtomID(S1),
00324 vpLigandAtom[vContact[i].id2]->GetAtomID(S2),
00325 vContact[i].dist );
00326 } else
00327 printf ( " No contact found.\n" );
00328 vContact = NULL;
00329 nContacts = 0;
00330 msdm->CMMDBManager::SeekContacts((PPCAtom)vpLigandAtom, nLigandAtoms,
00331 (PPCAtom)vpWaterAtom, nWaterAtoms,
00332 0, 5, 2,
00333 vContact, nContacts, 0, NULL, 3);
00334
00335 if (nContacts>0) {
00336 printf ( " Found %i contacts:\n",nContacts );
00337 for (int i=0;i<nContacts;i++)
00338 printf ( " %s <-> %s %10.4f A\n",
00339 vpLigandAtom[vContact[i].id1]->GetAtomID(S1),
00340 vpWaterAtom[vContact[i].id2]->GetAtomID(S2),
00341 vContact[i].dist );
00342 } else
00343 printf ( " No contact found.\n" );
00344
00345 }
00346 }
00347
00348
00349 if (vContact)
00350 delete [] vContact;
00351 if (msdm)
00352 delete msdm;
00353
00354 return (0);
00355 }
00356
