Hi Paolo,
Thanks very much for the patch. Unfortunately, the OBForceField functions
that you patched are never called at all during the SDF-to-SMILES
conversion process, so the patch doesn't resolve my issue. OBForceField
only seems to be called if I use the --gen3D option.
Best regards,
Craig
On Thu, May 17, 2012 at 3:03 AM, Paolo Tosco <paolo.to...@unito.it> wrote:
> Dear Craig,
>
> I have faced the identical problem with MMFF94, and I have previously
> submitted a similar patch which has already been applied to SVN OpenBabel.
> However, now I realize that my fix had only solved my own problem, but not
> a more general problem connected with formal charges.
> So I have attached a much better patch, which reverts my previous one, and
> instead applies it on the OBMol copy constructor, so that it becomes of
> general use.
>
> To make a long story short, if you patch the current OpenBabel SVN version
> with the attached patch your issue will be solved.
>
> From the OpenBabel root folder:
>
> patch -p0 < patch_17-05-2012.patch
>
> Dear Geoff, would you please apply it also to the SVN trunk so that also
> other OpenBabel users may benefit from that? It also includes a small patch
> on "A T O M T Y P E S" logging that I had left behind previously.
>
> Best regards,
> Paolo
>
>
> On 05/17/2012 01:44 AM, Craig James wrote:
>
> Here's another problem in 2.3.x that's not in 2.2.x. I realize these are
> bogus molecules, but it illustrates a serious problem.
>
> $ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o can
> [Fe-2][Fe+2].[Fe-2].[Fe+2]
>
> Everything looks good -- charges are maintained. Now go through the SDF
> format:
>
> $ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o sdf | babel -i sdf
> -o can
> [Fe+2][Fe].[Fe].[Fe]
>
> Not so good -- charges are dropped. Where is the problem? It turns out
> the SDF is correct:
>
> $ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o sdf
>
> OpenBabel05161216052D
>
> 4 1 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 Fe 0 2 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 Fe 0 6 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 Fe 0 2 0 0 0 15 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 Fe 0 6 0 0 0 15 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> M CHG 4 1 2 2 -2 3 2 4 -2
> M END
> $$$$
>
> The charges are all properly marked in the atom block and in the M CHG
> line. And the "15" in atoms 3 and 4 means "zero valence" which is right.
> Yet the SMILES is wrong.
>
> It turns out this same thing happens if you use atom->SetFormalCharge().
> It sometimes works and sometimes doesn't.
>
> Note that it works correctly in OpenBabel 2.2.x:
>
> $ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o sdf | babel -i sdf
> -o can
> [Fe-2].[Fe-2][Fe+2].[Fe+2]
>
> Anyone have any idea what changed, either in the OpenBabel internals or
> the SMILES generator, that would affect the way charges are interpreted?
>
> Craig
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> OpenBabel-discuss mailing
> listOpenBabel-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
>
> --
> ==========================================================
> Paolo Tosco, Ph.D. Phone: +39 011 6707680
> Department of Drug Science Fax: +39 011 6707687
> and Technology Mob: +39 348 5537206
> Via Pietro Giuria, 9
> 10125 Torino, Italy
> http://open3dalign.org
> E-mail: paolo.to...@unito.it http://open3dqsar.org
> ==========================================================
>
>
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
