I was going to comment on the process, but I got sidetracked.
I've just remembered because I've just seen a question in the user mailing list about the
stereoisomery and the enumeration of stereo-configurations.
Is there any work planned for that?
A while back I looked at the code trying to fix a few problems (chirality of protonated
nitrogens, to name one), but I couldn't understand the code well enough to do anything useful.
Also, in my lab we've done some work on the hydrogen bond typing, following Noel's advice
on using SMARTS instead of convoluted functions for different chemical group. I have to
double-check the status of that code, but if you think it's worth looking at, I'll be
happy to contribute.
S
On 01/12/2018 08:45 AM, Geoffrey Hutchison wrote:
I’m mostly just grumpy because these changes broke my build. Have you
considered
going through a deprecated phase?
While I appreciate the grumpiness, you don't have to break a build - the "master" branch
is naturally going to have changes. I'd like to think Noel (and I) were pretty clear with
discussion on-list and on GitHub going back into the summer and fall. The specific change
that you mention seems to relate to:
https://github.com/openbabel/openbabel/pull/1601
This was discussed in June-July and merged in August.
Regarding IsSingle(), the situation is more clear cut. This is a function
which
appears to be (and is documented to be) synonymous with GetBondOrder() ==
1. Aha,
but it is not, and only by looking at the source code would you have
realised the
difference. It was a surprise to me, and I think it is used synonymous with
GetBondOrder==1 throughout the codebase...but there's no way to tell what
the
caller intended. All we can do is prevent nasty surprises for users in the
future.
This change was made in combination with an overhaul of the treatment of
kekulization and aromaticity last year.
In general, Noel has been undertaking a significant effort to clean up API calls to match
"least surprise."
Thus, the version number has been bumped. This release makes a clear effort to indicate
"Hey, something big is different - it's version 3!"
As to a generic OBAtom::IsElement(OBElement::Hydrogen) call, I look forward to a pull
request. I'm not sure I'll have time to do it myself today, but:
- We haven't released v3 yet, so we appreciate concern and comments
- I bumped the version number to indicate backwards-incompatibility
- Yes, migration notes would be helpful, but aren't done yet
If you don't like the changes, I suggest using a release branch:
https://github.com/openbabel/openbabel/tree/openbabel-2-4-x
-Geoff
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Dept. of Integrative Structural
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