Chris,
Thank you for your example - I was able to modify my code so that the
OBReaction is allocated on stack as you showed. I'm still a bit
concerned though if I should be doing anything different about
deallocating shared_ptr:
string convert_page_to_reaction(const vector
&page_of_structures, co
P , 2012-05-14 16:09 -0400, Igor Filippov [Contr] rakstīja:
> Has any of this been a problem for OpenBabel?
If it makes life harder for developers, if it offputs new contributors,
then yes it is a problem for OpenBabel. And from my perspective it has
been.
Reinis
--
Well, subjectively, I should say the reverse has been true for me with
the exception of pull requests on github and saving your HD space:)
Has any of this been a problem for OpenBabel?
Igor
On Mon, 2012-05-14 at 16:00 -0400, My Th wrote:
> P , 2012-05-14 15:48 -0400, Igor Filippov [Contr] rakst
On Mon, May 14, 2012 at 3:48 PM, Igor Filippov [Contr] <
filipp...@mail.nih.gov> wrote:
> I vote for keeping svn.
> What problem is going to be solved by moving to git?
Distributed repositories, offline development, easier branching, and
perhaps most noticeably, speed. I have an svn checkout and
P , 2012-05-14 15:48 -0400, Igor Filippov [Contr] rakstīja:
> I vote for keeping svn.
> What problem is going to be solved by moving to git?
To name few:
- Easier managing of branches and patches
- Better history record
- Pull requests (e.g. on GitHub)
- Easier distributed development
- Less space
I vote for keeping svn.
What problem is going to be solved by moving to git?
Igor
On Mon, 2012-05-14 at 15:40 -0400, David Lonie wrote:
> On Mon, May 14, 2012 at 3:34 PM, My Th wrote:
> > > By the way, is a general migration to git still off the
> table?
> >
> > I
On Mon, May 14, 2012 at 3:34 PM, My Th wrote:
> > > By the way, is a general migration to git still off the table?
> >
> > I'm OK with this, but I think we'd need a more comprehensive vote.
>
> That is two, how about others? :)
>
Make that three ;-)
A better question may be, who wants to keep s
P , 2012-05-14 15:02 -0400, Geoffrey Hutchison rakstīja:
> > My guess is that all API breaking changes are still not allowed in trunk
> > (ABI breaks would be allowed for 2.4, but API breaks only for 3.0).
>
> Right.
>
> As for the "experimental" branch, it's essentially dead. I'd probably
> keep
> This is discussed in the OB paper. 3D structure generation fails stereo in
> many cases of bridged rings, as we use ring templates of a particular stereo.
The only good solution to this is distance geometry like RDKit.
-Geoff
> My guess is that all API breaking changes are still not allowed in trunk
> (ABI breaks would be allowed for 2.4, but API breaks only for 3.0).
Right.
As for the "experimental" branch, it's essentially dead. I'd probably keep a
new branch with a more descriptive name for any experiments.
> I'v
Hi!
I've seen that people started to break ABI in trunk so it is probably
going for the 2.4 release. In connection to that I have a question about
the v3.0 project [1] and experimental branch [2].
Experimental branch has not seen any activity in a very long time, so is
it still pursued? Or should
On Mon, May 14, 2012 at 8:57 AM, Noel O'Boyle wrote:
> Hello all,
>
> The current SMILES writer does not output cis/trans bond symbols for double
> bonds in rings of size 12 or less. In the course of other work, I've come
> across example of cis/trans bonds in rings of size 9 for example:
> https:
Chris,
Here is my code. The function takes a vector of molecules in text form -
e.g. MDL MOL format, and returns a string of reaction-specific format,
e.g. rsmi.
The execution segfaults if I uncomment "delete react", or if I allocate
OBReaction on the stack. So I'm rather confused what's going on.
Hello all,
The current SMILES writer does not output cis/trans bond symbols for double
bonds in rings of size 12 or less. In the course of other work, I've come
across example of cis/trans bonds in rings of size 9 for example:
https://www.ebi.ac.uk/chembldb/compound/inspect/CHEMBL520004 versus
htt
Igor
My post yesterday did not properly address the problem you were having
with OBReaction. The molecules in the reaction need to be handled in a
particular way.
OBReaction uses shared_ptr member variables for the reactant and product
molecules. A molecule to be used in a reaction should be m
I usually run 3D generation as follows:
obabel -:OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H
]2CCC2=CC(=O)CC[C@]12C)F --gen3d -osdf
==
*** Open Babel Warning in OpenBabel::OBBuilder::CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
See also this thread:
http://www.mail-archive.com/blueobelisk-discuss@lists.sourceforge.net/msg00665.html
where Greg Landrum dissuades me from including stereo in 0D Mol file.
- Noel
On 14 May 2012 11:32, Noel O'Boyle wrote:
> The issue is only regarding cis/trans stereo so I'll confine my
The issue is only regarding cis/trans stereo so I'll confine my comments to
that. (We do store tet stereo twice, as well as provide an option to read
the chirality flag if desired.)
You assume that there is a convention for storing cis/trans stereo in the
bond block, but that OB is not following i
Patches item #3526485, was opened at 2012-05-14 00:45
Message generated for change (Tracker Item Submitted) made by th9
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=428742&aid=3526485&group_id=40728
Please note that this message will contain a full copy of the co
19 matches
Mail list logo
