Re: [Open Babel] Reading large coordinate files in C++ using Babel

Hi Sébastien, I have run into similar issues and eventually traced it back to the ring perception after using a profiler. Unfortunately, the ring perception can be triggered in unexpected places to avoid internal inconsistencies. (e.g. copying an OBMol in turn calculates OBAtom hybridization if n

Re: [Open Babel] Reading large coordinate files in C++ using Babel

Le 13/02/2018 à 22:28, Benjamin Bucior a écrit : Hi Sébastien, I have run into similar issues and eventually traced it back to the ring perception after using a profiler.  Unfortunately, the ring perception can be triggered in unexpected places to avoid internal inconsistencies. (e.g. copying

Re: [Open Babel] Reading large coordinate files in C++ using Babel

> as an example you use this file (silica glass SiO2 with 3000 atoms in PDB > format, written using Babel): ... > Is this the reason why it is so slow for this kind of coordinates is because > Babel looking for bonds ? My guess, based on your example, is ring / aromaticity perception. In PDB, w

Re: [Open Babel] Reading large coordinate files in C++ using Babel

Hi Sébastien, in principle you can disable the perception of connectivity, among other things, by using OBMol.BeginModify() (but somebody with more experience than me should confirm it). From the documentation[1]: "Call when making many modifications -- clears conformer/rotomer data. The meth