Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread Noel O'Boyle
An SDF file describes the number of hydrogens on each atom. Open Babel is neither adding nor removing them. AddHydrogens() is just making them explicit. Regards, - Noel On Tue, 26 Nov 2019 at 06:50, David van der Spoel wrote: > Hi, > > I was trying to use obprop on an SDF file, but found out th

Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread David van der Spoel
Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle: An SDF file describes the number of hydrogens on each atom. Open Babel is neither adding nor removing them. AddHydrogens() is just making them explicit. Unfortunately, no. The structure below has 7 hydrogens and one charge but obprop adds one H and

Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread Noel O'Boyle
Hi David, Can you provide the input file? Regards, - Noel On Tue, 26 Nov 2019 at 09:50, David van der Spoel wrote: > Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle: > > An SDF file describes the number of hydrogens on each atom. Open Babel > > is neither adding nor removing them. AddHydrogens()

Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread David van der Spoel
Den 2019-11-26 kl. 13:06, skrev Noel O'Boyle: Hi David, Can you provide the input file? Attached, thanks for looking into this. Regards, - Noel On Tue, 26 Nov 2019 at 09:50, David van der Spoel > wrote: Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle: > A

Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread Noel O'Boyle
The "M CHG" line looks dubious. It states that there is a single charge, a +5 charge on atom 1. What is the source of this SDF file? Regards, - Noe On Tue, 26 Nov 2019 at 12:12, David van der Spoel wrote: > Den 2019-11-26 kl. 13:06, skrev Noel O'Boyle: > > Hi David, > > > > Can you provide th

Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread David van der Spoel
Den 2019-11-26 kl. 13:58, skrev Noel O'Boyle: The "M  CHG" line looks dubious. It states that there is a single charge, a +5 charge on atom 1. What is the source of this SDF file? Emacs :( Regards, - Noe On Tue, 26 Nov 2019 at 12:12, David van der Spoel > wrote:

Re: [OpenBabel-Devel] Hydrogen management bug

2019-11-26 Thread Noel O'Boyle
Should have used vim. :-) On Tue, 26 Nov 2019 at 13:12, David van der Spoel wrote: > Den 2019-11-26 kl. 13:58, skrev Noel O'Boyle: > > The "M CHG" line looks dubious. It states that there is a single > > charge, a +5 charge on atom 1. What is the source of this SDF file? > > Emacs :( > > > > >