Hi Ignacio, The xyz parser is in openbabel/src/formats/xyzformat.cpp .
The code you are looking for is called on lines 276 and 278, see https://github.com/openbabel/openbabel/blob/master/src/formats/xyzformat.cpp#L276 if (!pConv->IsOption("b",OBConversion::INOPTIONS)) mol.ConnectTheDots(); if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS)) mol.PerceiveBondOrders(); ConnectTheDots() is in src/mol.cpp starting at line 2937. https://github.com/openbabel/openbabel/blob/master/src/mol.cpp#L2937 This method adds single bonds between all atoms closer than their combined atomic covalent radii, then "cleans up" making sure bonded atoms are not closer than 0.4A and the atom does not exceed its valence. It implements blue-obelisk:rebondFrom3DCoordinates. PerceiveBondOrders() starts on line 3139 of the same file https://github.com/openbabel/openbabel/blob/master/src/mol.cpp#L3139 This method uses bond angles and geometries from current connectivity to guess atom types and then filling empty valences with multiple bonds. It currently has a pass to detect some frequent functional groups. It still needs a pass to detect aromatic rings to "clean up." AssignSpinMultiplicity(true) is called at the end of the function. The true states that there are no implict hydrogens in the molecule. Cheers, Andrew da...@dalkescientific.com > On Oct 3, 2019, at 18:43, Ignacio Pickering <ign.picker...@gmail.com> wrote: > > I found that OpenBabel can convert .xyz files to SMILES strings, which means > that it must be using some sort of heuristic to determine the connectivity of > a molecule based on distances and nuclear charges. > > I've been trying to find references to the specific algorithm implemented but > I couldn't find anything, and I haven't been able to find the code that does > this conversion in github (probably because I'm not too familiar with the > repo, It should be there somewhere right?). > > I was wondering if someone could point me in the right direction regarding > this, since its a very useful feature I would like to use, and I would like > to be more familiar with its inner workings to check how reliable/robust it > is, and what approximations its making. > > Best, > > Ignacio > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
