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 ********************************************************
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