Bugs item #3107218, was opened at 2010-11-11 11:49 Message generated for change (Tracker Item Submitted) made by martinguetlein You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3107218&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Library Functions Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Martin Gütlein (martinguetlein) Assigned to: Nobody/Anonymous (nobody) Summary: OBBuilder terminates while building 3d Initial Comment: Hi All, the builder fails on building 3d (example code below) for smiles: N12[C@@H]([C@@H](NC([C@@H](c3ccsc3)C(=O)O)=O)C2=O)SC(C)(C)[C@@-]1C(=O)O Message is: terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check Aborted Best regards, Martin P.S.: * I am using ob 2.3.0. * It works if the rotation info (@@) is removed. * The smiles is from a well known bbb dataset: http://www.cheminformatics.org/datasets/#perm, first in list. #include <iostream> #include <openbabel/mol.h> #include <openbabel/obconversion.h> #include <openbabel/builder.h> using namespace std; using namespace OpenBabel; int main(int argc,char **argv) { OBMol * mol = new OBMol(); OBConversion obconversion; obconversion.SetInFormat("smiles"); //obconversion.ReadString(mol, "C1(N=C(NC(C)C)N=C(N=1)OC)NC(C)C"); obconversion.ReadString(mol, "N12[C@@H]([C@@H](NC([C@@H](c3ccsc3)C(=O)O)=O)C2=O)SC(C)(C)[C@@-]1C(=O)O"); cout << "formula "<< mol->GetFormula() << "\n"; cout << "Has3D: " << mol->Has3D() << "\n"; OBBuilder builder; builder.Build(*mol); cout << "Has3D: " << mol->Has3D() << "\n"; delete(mol); return 0; } ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3107218&group_id=40728 ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
