[Open Babel] Heuristic to convert .xyz to SMILES

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 fin

Re: [Open Babel] Strange behaviour with pdbqt format

Have you tried the latest code? If the problem persists with the latest development code, could you please file a bug. Thanks, Noel On Wed, 18 Sep 2019 at 11:38, HORACIO EMILIO PEREZ SANCHEZ wrote: > Hi, >we are using Open Babel 2.4.1 and we have found a very strange > behaviour when con

Re: [Open Babel] Heuristic to convert .xyz to SMILES

Thank you for the extremely detailed answer, that is exactly what I was looking for! Best, Ignacio On Thu, Oct 3, 2019 at 2:33 PM Andrew Dalke wrote: > 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,

Re: [Open Babel] Heuristic to convert .xyz to SMILES

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.ConnectT

Re: [Open Babel] Heuristic to convert .xyz to SMILES

> Thank you for the extremely detailed answer, that is exactly what I was > looking for! Beyond Andrew's great answer - PerceiveBondOrders code is based on Roger Sayle's "Cruft to Content" talk: https://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html