[ghemical-devel] ghemical on Ubuntu 5.10

[Tommi Hassinen]

On Thu, 3 Nov 2005, Michael Banck wrote:

> On Thu, Nov 03, 2005 at 02:13:37PM -0800, Jordan Mantha wrote:
>> I am running on a 32-bit system. I am currently working with Michael
>> Banck on this. He has confirmed it on Debian. I am sure he will let us
>> know if he finds something.
>
> Well, it tries to add a bond instead of an atom, for some reason I have
> not figured out yet:
>
> 444             if (p1.atmr[0]->mdl != p1.atmr[1]->mdl ||
> p1.atmr[0]->mdl == NULL)
> (gdb) n
>
> Program received signal SIGSEGV, Segmentation fault.
> 0xb7620287 in model::AddBond (this=0x8244290, p1=@0xbfff9db8) at
> model.cpp:444
> 444             if (p1.atmr[0]->mdl != p1.atmr[1]->mdl || p1.atmr[0]->mdl == NULL)
> (gdb) bt
> #0  0xb7620287 in model::AddBond (this=0x8244290, p1=@0xbfff9db8)
>    at model.cpp:444

Hello.

When I look at the above stuff, I see that it is at the libghemical side. 
The operations for adding/removing atoms/bonds at libghemical has not 
changed for a looong time (years?) now, so it's very stabilized.

I don't think the problem is there.

The stuff below is from the ghemical (application) side. This code has 
been changed recently, to fix the problems in 64-bit systems.

Now, looking at the line numbers, and comparing them to the line numbers 
in current CVS version, I find differences:
 	- in my working copy, project::AddBond is at line 724
 	- in my working copy, project::DrawEvent is at line 3453

I wonder what has changed... If the code is older than this:

http://bioinformatics.org/pipermail/ghemical-devel/2005-October/000354.html

it will not work properly.  :(

> #1  0x0806c3a4 in project::AddBond (this=0x8244290, p1=@0xbfff9db8)
>    at ./project.cpp:656
> #2  0x0806ceb6 in project::DrawEvent (this=0x8244290, gv=0x8289764,
>    names=@0xbfff9ec8) at ./project.cpp:3426

> project::AddAtom is not being called, at least a breakpoint there is not
> triggered, as opposed to project:AddBond.
>
> Any idea why this would be?  I'd update to current CVS, but this seems
> to involve doing libghemical and libmopac updates as well, and I'd
> rather wait for released versions if possible.

I will release the v1.91 of ghemical/libghemical next week.

Regards,

 	Tommi