I haven't had a chance to test this but it looks like you're deleting pointers that you shouldn't be. Only call "delete" if there is a corresponding "new". The general rule is that you shouldn't delete pointers returned by Open Babel API calls, unless the documentation explicitly states that the caller is responsible for freeing the memory. In 99% of cases, the pointer is to a data structure that is managed by something else. In short, trying commenting out "delete[] xyz".
On Mon, 2 Mar 2020 at 11:58, Alessandro S. Nascimento < asnascime...@ifsc.usp.br> wrote: > Hi Noel, > > thanks for your reply. > > A complete code is pasted below. > > The code is compiled with no problems and when executed, I get the > following (and expected) output: > > > $ McConf 169517407.mol2.gz > > **************************************************************************************************** > > **************************************************************************************************** > * McConf - Conformer Generation for McLiBELa > * > > * University of Sao Paulo > > * More Info: > > * http://www.biotechmol.ifsc.usp.br/ > > * > > > **************************************************************************************************** > > **************************************************************************************************** > Original energy for molecule 169517407.mol2.gz: 43.9004 > ..tot conformations = 5184 > ..tot confs tested = 1000 > ..below energy threshold = 95 > Energy/RMSD for conformer [ 0]: 44.3411 kcal/mol / 0.0000 Ang > Energy/RMSD for conformer [ 1]: 35.4359 kcal/mol / 1.7079 Ang > Energy/RMSD for conformer [ 2]: 35.5114 kcal/mol / 1.7735 Ang > Energy/RMSD for conformer [ 3]: 35.9091 kcal/mol / 1.5028 Ang > Energy/RMSD for conformer [ 4]: 36.0429 kcal/mol / 1.5053 Ang > Energy/RMSD for conformer [ 5]: 36.0517 kcal/mol / 1.8496 Ang > Energy/RMSD for conformer [ 6]: 36.0932 kcal/mol / 1.3544 Ang > Energy/RMSD for conformer [ 7]: 36.2786 kcal/mol / 1.1911 Ang > Energy/RMSD for conformer [ 8]: 36.8942 kcal/mol / 1.9949 Ang > Energy/RMSD for conformer [ 9]: 36.9710 kcal/mol / 1.5969 Ang > Number of conformers: 39 > > However, when I add a "delete mol" in the line just before the "return > (file_read);", the code remains compiled with no errors, but the output of > the execution gives me: > > $McConf 169517407.mol2.gz > > **************************************************************************************************** > > **************************************************************************************************** > * McConf - Conformer Generation for McLiBELa > > * > > * University of Sao Paulo > > * More Info: > > * http://www.biotechmol.ifsc.usp.br/ > > * > > > **************************************************************************************************** > > **************************************************************************************************** > Original energy for molecule 169517407.mol2.gz: 43.9004 > ..tot conformations = 5184 > ..tot confs tested = 1000 > ..below energy threshold = 95 > Energy/RMSD for conformer [ 0]: 43.9004 kcal/mol / 0.0000 Ang > Energy/RMSD for conformer [ 1]: 34.9952 kcal/mol / 1.7079 Ang > Energy/RMSD for conformer [ 2]: 35.0707 kcal/mol / 1.7735 Ang > Energy/RMSD for conformer [ 3]: 35.4684 kcal/mol / 1.5028 Ang > Energy/RMSD for conformer [ 4]: 35.6022 kcal/mol / 1.5053 Ang > Energy/RMSD for conformer [ 5]: 35.6110 kcal/mol / 1.8496 Ang > Energy/RMSD for conformer [ 6]: 35.6525 kcal/mol / 1.3544 Ang > Energy/RMSD for conformer [ 7]: 35.8379 kcal/mol / 1.1911 Ang > Energy/RMSD for conformer [ 8]: 36.4535 kcal/mol / 1.9949 Ang > Energy/RMSD for conformer [ 9]: 36.5303 kcal/mol / 1.5969 Ang > Number of conformers: 39 > McConf(52198,0x7fffabacf3c0) malloc: *** error for object 0x7fd53071fd90: > pointer being freed was not allocated > *** set a breakpoint in malloc_error_break to debug > Abort trap: 6 > > That's what I still can't understand.... I believe it should be possible > to deallocate the memory from the OBMol object before ending the code. I > could not figure out where am I messing up here..... > > *** > > #include <iostream> > > #include <cstdlib> > > #include <vector> > > #include "../LiBELa/Mol2.cpp" > > #include "../LiBELa/Conformer.cpp" > > #include "../LiBELa/PARSER.cpp" > > #include "../LiBELa/WRITER.cpp" > > #include "../LiBELa/COORD_MC.cpp" > > #include <openbabel/mol.h> > > #include <openbabel/obconversion.h> > > #include <openbabel/forcefield.h> > > #include <openbabel/math/vector3.h> > > > > using namespace std; > > > int main(int argc, char* argv[]) { > > > > printf("****************************************************************************************************\n"); > > > printf("****************************************************************************************************\n"); > > printf("* McConf - Conformer Generation for > McLiBELa *\n"); > > printf("* > *\n"); > > printf("* University of Sao Paulo > *\n"); > > printf("* More Info: > *\n"); > > printf("* http://www.biotechmol.ifsc.usp.br/ > *\n"); > > printf("* > *\n"); > > > printf("****************************************************************************************************\n"); > > > printf("****************************************************************************************************\n"); > > > > if (argc < 2){ > > printf("Usage: %s file.mol2 [input_file]\n", argv[0]); > > exit(1); > > } > > > PARSER* Input = new PARSER; > > Mol2* Mol = new Mol2(Input, string(argv[1])); > > WRITER* Writer = new WRITER("McConf", Input); > > > if (argc > 2){ > > Input->set_parameters(argv[2]); > > } > > > Input->write_mol2 = true; > > Input->dock_mode = true; > > > > bool file_read; > > OBMol* mol = new OBMol ; > > OBConversion* conv = new OBConversion; > > OBFormat *format = conv->FormatFromExt(argv[1]); > > if (!format || !conv->SetInFormat(format)) { > > printf("Could not find input format for file\n"); > > exit(1); > > } > > > ifstream ifs(argv[1]); > > if (!ifs) { > > printf("Could not open %s for reading\n", argv[1]); > > exit(1); > > } > > > if (!conv->Read(mol, &ifs)) { > > printf("Could not read molecule from file\n"); > > exit(1); > > } > > > OBMol* ref_mol = new OBMol; > > ifstream ifs2(argv[1]); > > conv->Read(ref_mol, &ifs2); > > > delete conv; > > format->~OBFormat(); > > > OBForceField* OBff = OBForceField::FindForceField("GAFF"); > > > if (!OBff){ > > printf("Could not find OpenBabel FF parameters!\n"); > > exit(1); > > } > > > // Original conformation energy > > OBff->Setup(*mol); > > mol->SetTotalCharge(mol->GetTotalCharge()); > > double energy = OBff->Energy(); > > if (OBff->GetUnit() == "kJ/mol"){ // Converting to kcal/mol, if > needed. > > energy = energy/4.18; > > } > > > printf("Original energy for molecule %s: %10.4f\n", argv[1], energy); > > > // Conformer Search > > OBff->DiverseConfGen(0.5, 1000, 50.0, false); > > OBff->GetConformers(*mol); > > > double rmsd; > > int conformers = Input->lig_conformers; > > if (mol->NumConformers() > 0){ > > int i=0; > > if (mol->NumConformers() < conformers) { > > conformers = mol->NumConformers(); > > } > > while (i < conformers){ > > double *xyz = new double [mol->NumAtoms()*3]; > > vector<double> v3; > > vector<vector<double> > xyz_tmp; > > mol->SetConformer(i); > > OBff->Setup(*mol); > > OBff->GetCoordinates(*mol); > > energy = OBff->Energy(); > > if (OBff->GetUnit() == "kJ/mol"){ // Converting to > kcal/mol, if needed. > > energy = energy/4.18; > > } > > > OBAlign* align = new OBAlign; > > align->SetRefMol(*ref_mol); > > align->SetTargetMol(*mol); > > align->Align(); > > rmsd = align->GetRMSD(); > > align->UpdateCoords(mol); > > > printf("Energy/RMSD for conformer [%3d]: %10.4f kcal/mol / %10.4f > Ang\n", i, energy, rmsd); > > > delete align; > > > xyz = mol->GetCoordinates(); > > for (unsigned j=0; j<mol->NumAtoms(); j++){ > > v3.push_back(xyz[3*j]); > > v3.push_back(xyz[(3*j)+1]); > > v3.push_back(xyz[(3*j)+2]); > > xyz_tmp.push_back(v3); > > v3.clear(); > > } > > > Writer->writeMol2(Mol,xyz_tmp, energy, rmsd, "McConf"); > > xyz_tmp.clear(); > > delete[] xyz; > > i++; > > } > > file_read = true; > > } > > else { > > file_read = false; > > } > > > printf("Number of conformers: %4d\n", mol->NumConformers()); > > > delete ref_mol; > > > delete Writer; > > delete Mol; > > delete Input; > > > return (file_read); > > } > > > > > Em dom., 1 de mar. de 2020 às 06:37, Noel O'Boyle <baoille...@gmail.com> > escreveu: > >> It would help us if you could provide the shortest possible (but >> complete) example code that exhibits the problem. As it is, you say the >> problem is when you delete the molecule, but there is no line that deletes >> the molecule. >> >> On Thu, 27 Feb 2020 at 16:19, Alessandro S. Nascimento < >> asnascime...@ifsc.usp.br> wrote: >> >>> Dear OpenBabel users, >>> >>> I am trying to write a piece of C++ code to generate conformers using >>> the OpenBabel API. My current code is mostly based on OB tutorials... not >>> really a big deal. >>> >>> Almost everything seems to be working. The problem is with memory >>> allocation. When my function gets out of scope, it gives me a mem leak: >>> malloc: *** error for object 0x103300350: pointer being freed was not >>> allocated >>> *** set a breakpoint in malloc_error_break to debug. >>> which seems to be related to the object mol (OBMol mol). >>> >>> I tried the dynamic allocation with new/delete and got exactly the same >>> thing when trying to delete the object mol in the second function below. No >>> problems when deleting the ref_mol object. >>> >>> My initial guess was that I had to clear the conformers generated before >>> deleting the object. I then tried to use DeleteConformer function with no >>> success. >>> >>> Any clues/ideas? They are all very welcome! >>> >>> My OB version is 3.0.0 and my current OS is MacOS Sierra 10.12.6: >>> $g++ -v >>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr >>> --with-gxx-include-dir=/usr/include/c++/4.2.1 >>> Apple LLVM version 9.0.0 (clang-900.0.39.2) >>> Target: x86_64-apple-darwin16.7.0 >>> Thread model: posix >>> InstalledDir: >>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>> >>> Thanks in advance, >>> >>> -Alessandro >>> >>> OBMol Conformer::GetMol(const std::string &molfile){ >>> >>> OBMol mol; >>> >>> OBConversion conv; >>> >>> OBFormat *format = conv.FormatFromExt(molfile.c_str()); >>> >>> if (!format || !conv.SetInFormat(format)) { >>> >>> printf("Could not find input format for file\n"); >>> >>> return mol; >>> >>> } >>> >>> ifstream ifs(molfile.c_str()); >>> >>> if (!ifs) { >>> >>> printf("Could not open %s for reading\n", molfile.c_str()); >>> >>> return mol; >>> >>> } >>> >>> if (!conv.Read(&mol, &ifs)) { >>> >>> printf("Could not read molecule from file\n"); >>> >>> return mol; >>> >>> } >>> >>> return mol; >>> >>> } >>> >>> >>> ****************************************************************** >>> >>> bool file_read; >>> >>> OBMol mol = this->GetMol(molfile); >>> >>> OBMol ref_mol = this->GetMol(molfile); >>> >>> >>> OBForceField* OBff; >>> >>> if (Input->ligand_energy_model == "GAFF" or Input->ligand_energy_model >>> == "gaff"){ >>> >>> OBff = OBForceField::FindForceField("GAFF"); >>> >>> } >>> >>> else { >>> >>> OBff = OBForceField::FindForceField("MMFF94"); >>> >>> } >>> >>> >>> if (!OBff){ >>> >>> printf("Could not find OpenBabel FF parameters!\n"); >>> >>> exit(1); >>> >>> } >>> >>> >>> OBff->Setup(mol); >>> >>> mol.SetTotalCharge(mol.GetTotalCharge()); // necessary? >>> >>> double energy = OBff->Energy(); >>> >>> if (OBff->GetUnit() == "kJ/mol"){ // Converting to kcal/mol, if >>> needed. >>> >>> energy = energy/4.18; >>> >>> } >>> >>> Lig->conformer_energies.push_back(energy); >>> >>> Lig->mcoords.push_back(Lig->xyz); >>> >>> >>> // Conformer >>> >>> OBff->DiverseConfGen(0.5, 1000, 50.0, false); >>> >>> OBff->GetConformers(mol); >>> >>> >>> if (mol.NumConformers() > 0){ >>> >>> for (int i=0; i<mol.NumConformers(); i++){ >>> >>> double* xyz = new double[mol.NumAtoms()*3]; >>> >>> vector<double> v3; >>> >>> vector<vector<double> > xyz_tmp; >>> >>> mol.SetConformer(i); >>> >>> OBff->Setup(mol); >>> >>> OBff->GetCoordinates(mol); >>> >>> energy = OBff->Energy(); >>> >>> if (OBff->GetUnit() == "kJ/mol"){ // Converting to >>> kcal/mol, if needed. >>> >>> energy = energy/4.18; >>> >>> } >>> >>> Lig->conformer_energies.push_back(energy); >>> >>> >>> OBAlign* align = new OBAlign; >>> >>> align->SetRefMol(ref_mol); >>> >>> align->SetTargetMol(mol); >>> >>> align->Align(); >>> >>> align->UpdateCoords(&mol); >>> >>> delete align; >>> >>> >>> xyz = mol.GetCoordinates(); >>> >>> for (unsigned j=0; j<mol.NumAtoms(); j++){ >>> >>> v3.push_back(xyz[3*j]); >>> >>> v3.push_back(xyz[(3*j)+1]); >>> >>> v3.push_back(xyz[(3*j)+2]); >>> >>> xyz_tmp.push_back(v3); >>> >>> v3.clear(); >>> >>> } >>> >>> Lig->mcoords.push_back(xyz_tmp); >>> >>> xyz_tmp.clear(); >>> >>> >>> delete[] xyz; >>> >>> } >>> >>> file_read = true; >>> >>> } >>> >>> else { >>> >>> file_read = false; >>> >>> } >>> >>> >>> ref_mol.Clear(); >>> >>> mol.Clear(); >>> >>> >>> return file_read; >>> >>> >>> -- >>> ******************************************************** >>> Alessandro S. Nascimento >>> Professor >>> São Carlos Institute of Physics (IFSC) >>> University of São Paulo (USP) >>> E-mail: asnascime...@ifsc.usp.br >>> Phone: +55-16-3373-8709 >>> ******************************************************** >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >> > > -- > ******************************************************** > Alessandro S. Nascimento > Professor > São Carlos Institute of Physics (IFSC) > University of São Paulo (USP) > E-mail: asnascime...@ifsc.usp.br > Phone: +55-16-3373-8709 > ******************************************************** >
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
