[OpenBabel-Devel] Bug in OBCisTransStereo?

2012-05-15 Thread Craig James
This looks like a bug but I wanted to post it here before adding it to the bug database. It's using some memory after freeing it. This is output from valgrind. The first stack trace reports the invalid free, and the second stack trace shows the code that freed the memory earlier. Craig ==23964

Re: [OpenBabel-Devel] reactions and polymers in openbabel

2012-05-15 Thread Igor Filippov
Chris, Thank you for the examples and the explanation! Igor On Tue, 2012-05-15 at 21:55 +0100, Chris Morley wrote: > Igor > > I'm not an expert but in your code it looks like the shared_ptr > objects will be destroyed just before the return statement. This will > automatically delete the OBM

Re: [OpenBabel-Devel] reactions and polymers in openbabel

2012-05-15 Thread Chris Morley
Igor I'm not an expert but in your code it looks like the shared_ptr objects will be destroyed just before the return statement. This will automatically delete the OBMol objects, so the Clear() statements are unnecessary. There are actually two copies of each shared_ptr, and its OBMol is delet

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread My Th
O , 2012-05-15 14:20 -0400, David Lonie rakstīja: > On Tue, May 15, 2012 at 2:02 PM, Igor Filippov [Contr] < > filipp...@mail.nih.gov> wrote: > > > > (master) $ git checkout -b myNewBranch > > > (myNewBranch) $ emacs someSourceCode.cpp #edit > > > (myNewBranch) $ git commit > > > (myNewBranch) $ g

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread David Lonie
On Tue, May 15, 2012 at 2:02 PM, Igor Filippov [Contr] < filipp...@mail.nih.gov> wrote: > > (master) $ git checkout -b myNewBranch > > (myNewBranch) $ emacs someSourceCode.cpp #edit > > (myNewBranch) $ git commit > > (myNewBranch) $ git checkout master > > (master) $ git merge myNewBranch > > One

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread My Th
O , 2012-05-15 14:02 -0400, Igor Filippov [Contr] rakstīja: > > > > > > (master) $ git checkout -b myNewBranch > > (myNewBranch) $ emacs someSourceCode.cpp #edit > > (myNewBranch) $ git commit > > (myNewBranch) $ git checkout master > > (master) $ git merge myNewBranch > > > > One important det

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread Rajarshi Guha
Agree with the YMMV, but I've always felt that was the *key* feature - do whatever I want with the code on my own laptop and only when I feel it's worth making public do I push it out. But in the meanwhile I can always keep in sync with other public updates to master (or any public branch for that

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread Igor Filippov [Contr]
> > > (master) $ git checkout -b myNewBranch > (myNewBranch) $ emacs someSourceCode.cpp #edit > (myNewBranch) $ git commit > (myNewBranch) $ git checkout master > (master) $ git merge myNewBranch > One important detail is the commit doesn't actually commit anything - everything is still on you

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread David Lonie
On Tue, May 15, 2012 at 12:43 PM, Craig James wrote: > On Mon, May 14, 2012 at 1:00 PM, David Lonie > wrote: > > I think the most practical reason to switch is the cheap > > branching. Being able to work on several new features/bug fixes from the > > same checkout is a very handy feature, and o

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread Craig James
On Mon, May 14, 2012 at 1:00 PM, David Lonie wrote: > I think the most practical reason to switch is the cheap > branching. Being able to work on several new features/bug fixes from the > same checkout is a very handy feature, and one that I sorely miss when I > have to work on an svn-hosted proj

Re: [OpenBabel-Devel] Git migration?

2012-05-15 Thread Craig James
On Mon, May 14, 2012 at 12:40 PM, 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'm OK with this, but I think we'd need a more comprehensive vote. >> >> That is two, how about others? :) > > >

[OpenBabel-Devel] [ openbabel-Bugs-3526933 ] Stereo lost at tet N due to N=O marked as sp2

2012-05-15 Thread SourceForge . net
Bugs item #3526933, was opened at 2012-05-15 07:24 Message generated for change (Tracker Item Submitted) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3526933&group_id=40728 Please note that this message will contain a full copy of th

[OpenBabel-Devel] [ openbabel-Bugs-3526902 ] Reading some InChI radicals fails

2012-05-15 Thread SourceForge . net
Bugs item #3526902, was opened at 2012-05-15 04:45 Message generated for change (Tracker Item Submitted) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3526902&group_id=40728 Please note that this message will contain a full copy of th

[OpenBabel-Devel] [ openbabel-Bugs-3526900 ] Chiral centers not always identified

2012-05-15 Thread SourceForge . net
Bugs item #3526900, was opened at 2012-05-15 04:26 Message generated for change (Tracker Item Submitted) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3526900&group_id=40728 Please note that this message will contain a full copy of th

[OpenBabel-Devel] [ openbabel-Bugs-3526866 ] Incorrect reading number of bonds from V2000 MOL/SDF

2012-05-15 Thread SourceForge . net
Bugs item #3526866, was opened at 2012-05-15 01:18 Message generated for change (Tracker Item Submitted) made by jvoorhees You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3526866&group_id=40728 Please note that this message will contain a full copy of the