Пример #1
0
  // ------------------------------------------------------------------
  //
  //  Reads a template and library of sidechains from input files.
  //   the template file should be a mol file and the sidechain files
  //   SD files
  //
  // ------------------------------------------------------------------
  RWMOL_SPTR_VECT enumFromFiles(const char *templateName,
			    std::vector<const char *> &sidechainNames){
    PRECONDITION(templateName,"bad template file name passed in");

    // build and mark the template molecule
    RWMol *templ = MolFileToMol(templateName,false);
    if(!templ) throw EnumException("could not construct template molecule"); 
    markAttachmentPoints(templ,'X');

    // now build and mark each set of sidechains:
    RWMOL_SPTR_VECT sidechains;
    VECT_RWMOL_SPTR_VECT allSidechains;
    for(std::vector<const char*>::const_iterator i=sidechainNames.begin();
	i!=sidechainNames.end();i++){
      sidechains = SDFileToMols(*i,false);
      if(!sidechains.size()){
	std::string err="no sidechains read from file: ";
	err += *i;
	throw EnumException(err.c_str());
      }
      prepareSidechains(&sidechains,'X');
      allSidechains.push_back(sidechains);
    }

    // enumerate the library:
    RWMOL_SPTR_VECT library=enumerateLibrary(templ,allSidechains);


    //--------------------------
    //
    // Clean up the molecules and sidechains we constructed along the
    // way. 
    //
    //--------------------------
    delete templ;
#if 0
    VECT_RWMOL_SPTR_VECT::iterator vmpvI;
    for(vmpvI=allSidechains.begin();vmpvI!=allSidechains.end();vmpvI++){
      RWMOL_SPTR_VECT::iterator mpvI;
      for(mpvI=vmpvI->begin();mpvI!=vmpvI->end();mpvI++){
	delete *mpvI;
      }
      vmpvI->clear();
    }
#endif
    allSidechains.clear();

    return library;
  }  
Пример #2
0
void test1() {
  // single attachment point, small list
  std::cout << " ----------> Test1 " << std::endl;
  RWMOL_SPTR_VECT library;
  std::vector<const char *> fileNames;
  fileNames.push_back("esters.2.sdf");
  fileNames.push_back("esters.2.sdf");
  library = enumFromFiles("template.1.mol", fileNames);

  CHECK_INVARIANT(library.size() == 2, "");
  CHECK_INVARIANT(library[0]->getNumAtoms() == 10, "");
  CHECK_INVARIANT(library[1]->getNumAtoms() == 11, "");

  library.clear();
  std::cout << " <---------- Done " << std::endl;
}
Пример #3
0
void test5() {
  // test working from SMILES
  std::cout << " ----------> Test5 " << std::endl;
  RWMol *m1 = SmilesToMol("[Xa]CC([Xb])CC", 0, 0);
  CHECK_INVARIANT(m1, "");
  markAttachmentPoints(m1, 'X');

  RWMOL_SPTR_VECT sidechains;
  sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)", 0, 0)));
  sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)C", 0, 0)));
  sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)CCC", 0, 0)));
  prepareSidechains(&sidechains, 'X');

  VECT_RWMOL_SPTR_VECT allSideChains;
  allSideChains.push_back(sidechains);
  allSideChains.push_back(sidechains);

  RWMOL_SPTR_VECT library;
  library = enumerateLibrary(m1, allSideChains, false);

  CHECK_INVARIANT(library.size() == 9, "");
  CHECK_INVARIANT(library[0]->getNumAtoms() == 10, "");
  CHECK_INVARIANT(library[1]->getNumAtoms() == 11, "");
  CHECK_INVARIANT(library[2]->getNumAtoms() == 13, "");
  CHECK_INVARIANT(library[3]->getNumAtoms() == 11, "");
  CHECK_INVARIANT(library[4]->getNumAtoms() == 12, "");
  CHECK_INVARIANT(library[5]->getNumAtoms() == 14, "");
  CHECK_INVARIANT(library[6]->getNumAtoms() == 13, "");
  CHECK_INVARIANT(library[7]->getNumAtoms() == 14, "");
  CHECK_INVARIANT(library[8]->getNumAtoms() == 16, "");

  library.clear();
  std::cout << " <---------- Done " << std::endl;
}
Пример #4
0
void test4() {
  // test templates that have repeated attachment points
  std::cout << " ----------> Test4 " << std::endl;
  RWMOL_SPTR_VECT library;
  std::vector<const char *> fileNames;
  fileNames.push_back("esters.2.sdf");
  fileNames.push_back("esters.2.sdf");
  library = enumFromFiles("template.2.mol", fileNames);

  CHECK_INVARIANT(library.size() == 2, "");
  library[0]->debugMol(std::cout);
  std::cout << "smi0: " << MolToSmiles(*library[0], 0) << std::endl;
  std::cout << "smi1: " << MolToSmiles(*library[1], 0) << std::endl;
  CHECK_INVARIANT(library[0]->getNumAtoms() == 14, "");
  CHECK_INVARIANT(library[1]->getNumAtoms() == 16, "");

  library.clear();
  std::cout << " <---------- Done " << std::endl;
}
Пример #5
0
void test7() {
  // test transforms
  std::cout << " ----------> Test7 " << std::endl;
  RWMOL_SPTR_VECT library;
  RWMOL_SPTR mol;
  Atom *at1, *at2;
  int i;
  std::vector<const char *> fileNames;
  fileNames.push_back("Ts.1.sdf");
  library = enumFromFiles("box.1.mol", fileNames);
  CHECK_INVARIANT(library.size() == 1, "");
  CHECK_INVARIANT(library[0]->getNumAtoms() == 8, "");
  mol = library[0];
  at1 = mol->getAtomWithIdx(0);
  at2 = mol->getAtomWithIdx(4);
  CHECK_INVARIANT(feq(mol->getConformer().getAtomPos(at1->getIdx()).x,
                      mol->getConformer().getAtomPos(at2->getIdx()).x),
                  "");
  CHECK_INVARIANT(mol->getConformer().getAtomPos(at1->getIdx()).y -
                          mol->getConformer().getAtomPos(at2->getIdx()).y ==
                      -1.0,
                  "");
  library.clear();

  // try another orientation of the sidechain molecule:
  fileNames.clear();
  fileNames.push_back("Ts.4.sdf");
  library = enumFromFiles("box.1.mol", fileNames);
  CHECK_INVARIANT(library.size() == 1, "");
  CHECK_INVARIANT(library[0]->getNumAtoms() == 8, "");
  mol = library[0];
  std::cout << MolToMolBlock(*mol);
  std::cout << std::endl;

  at1 = mol->getAtomWithIdx(0);
  at2 = mol->getAtomWithIdx(7);
  TEST_ASSERT(
      feq(mol->getConformer().getAtomPos(7), RDGeom::Point3D(-.5, 2.5, 0.0)));
  library.clear();

  // now use an SD file that has the same molecule in different
  // orientations as sidechains:
  fileNames.clear();
  fileNames.push_back("Ts.sdf");
  library = enumFromFiles("box.1.mol", fileNames);
  CHECK_INVARIANT(library.size() == 4, "");

  CHECK_INVARIANT(library[0]->getNumAtoms() == 8, "");
  CHECK_INVARIANT(library[1]->getNumAtoms() == 8, "");
  CHECK_INVARIANT(library[2]->getNumAtoms() == 8, "");
  CHECK_INVARIANT(library[3]->getNumAtoms() == 8, "");

  for (i = 0; i < library.size(); i++) {
    std::cout << "------ Mol: " << i << "------" << std::endl;
    mol = library[i];
    std::cout << MolToMolBlock(*mol);
    std::cout << std::endl;
  }
  for (i = 0; i < library[0]->getNumAtoms(); i++) {
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[1]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[1]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[1]->getConformer().getAtomPos(i).z),
                    "");

    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[2]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[2]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[2]->getConformer().getAtomPos(i).z),
                    "");

    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i),
                        library[3]->getConformer().getAtomPos(i)),
                    "");
  }
  library.clear();

  // move the attachment point on the template.  This should
  // make no difference.
  library = enumFromFiles("box.1a.mol", fileNames);
  CHECK_INVARIANT(library.size() == 4, "");

  CHECK_INVARIANT(library[0]->getNumAtoms() == 8, "");
  CHECK_INVARIANT(library[1]->getNumAtoms() == 8, "");
  CHECK_INVARIANT(library[2]->getNumAtoms() == 8, "");
  CHECK_INVARIANT(library[3]->getNumAtoms() == 8, "");

  for (i = 0; i < library[0]->getNumAtoms(); i++) {
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[1]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[1]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[1]->getConformer().getAtomPos(i).z),
                    "");

    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[2]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[2]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[2]->getConformer().getAtomPos(i).z),
                    "");

    // std::cout << i << "\t" << library[0]->getConformer().getAtomPos(i) <<
    // std::endl;
    // std::cout << "\t" << library[3]->getConformer().getAtomPos(i) <<
    // std::endl;
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[3]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[3]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[3]->getConformer().getAtomPos(i).z),
                    "");
  }
  library.clear();

  // move the attachment point on the template.  This should
  // make no difference.
  library = enumFromFiles("box.mol", fileNames);
  CHECK_INVARIANT(library.size() == 4, "");

  CHECK_INVARIANT(library[0]->getNumAtoms() == 20, "");
  CHECK_INVARIANT(library[1]->getNumAtoms() == 20, "");
  CHECK_INVARIANT(library[2]->getNumAtoms() == 20, "");
  CHECK_INVARIANT(library[3]->getNumAtoms() == 20, "");

  for (i = 0; i < library[0]->getNumAtoms(); i++) {
    at1 = library[0]->getAtomWithIdx(i);

    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[1]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[1]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[1]->getConformer().getAtomPos(i).z),
                    "");

    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[2]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[2]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[2]->getConformer().getAtomPos(i).z),
                    "");

    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).x,
                        library[3]->getConformer().getAtomPos(i).x),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).y,
                        library[3]->getConformer().getAtomPos(i).y),
                    "");
    CHECK_INVARIANT(feq(library[0]->getConformer().getAtomPos(i).z,
                        library[3]->getConformer().getAtomPos(i).z),
                    "");
  }
  library.clear();

  std::cout << " <---------- Done " << std::endl;
}