// ------------------------------------------------------------------
//
// 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;
}
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;
}
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;
}
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;
}
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;
}