Dear Geoff, We're in the process of adding our existing tests to the Open Babel source. This will contain a number of 'authentic' files that have not been generated by Open Babel.
Concerning your questions on QEq: we have implemented our own version, following the original paper by Rappé and Goddard [J. Phys. Chem 95 (1991) 3358] as closely as possible. That was around 2010-2011. We did take a look at the Open Babel implementation (which was then new) but we decided to make our own implementation. We had noticed that Open Babel makes a number of simplifications for QEq (hydrogen parameters not charge-dependent and using Gaussians instead of Slater-type orbitals for the Coulomb integrals). Perhaps more importantly, the charges did not seem to match very well with the ones from the Rappé and Goddard paper. Looking at it again now, it seems that the charges from Open Babel's QEq often have the wrong sign or are simply unreasonably large. I have no idea what causes that, as I only had a cursory look at the code. But it looks as if there's more going on than just the additional simplifications to QEq: even the QTPIE charges do not seem to reproduce those from the QTPIE paper by Chen and Martinez (e.g. the charges on phenol as reported in the preprint on arXiv, https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've used the charge model options in the wrong way, but they seemed quite straightforward. I can send the molecule geometries that we used in validating our QEq against the Rappé and Goddard article, if that would be of help, or run our QEq implementation on a set of molecules of your choice and send back the results. Our coverage of elements is limited to that in the original paper, which covers H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs. Kind regards, Paul Becherer Development Scientist Culgi B.V. Galileiweg 8 2333 BD Leiden The Netherlands +31-71-332-2056 -----Original Message----- From: Geoffrey Hutchison <geoff.hutchi...@gmail.com> Sent: Friday, February 22, 2019 03:38 To: Paul Becherer <paul.beche...@culgi.com> Cc: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] Contributed code for new file format > We could not really find hard guidelines for coding standards, or what kinds > of tests are desired, so I'd appreciate any feedback on that. The code in the > patch is based on the exampleformat.cpp template and was further developed by > two colleagues and myself at Culgi. We presently test conversion to and from > the MOL and MOL2 formats in our own test suite. We would definitely appreciate some "authentic" files for testing. I should get the broader round-trip test suite going again, but having "original" files (i.e., not created by Open Babel) is definitely a help when testing. One side question - your website mentions QEq charges. Are you using the OB code for that? There has been some question as to the OB implementation of QEq charges, but there obviously isn't an open test set. If you have an independent implementation, I'd be curious to compare point charges across a range of molecules. Thanks, -Geoff _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
