Tim,
You are absolutely right. As soon as I removed openbabel rpm which came
with my Fedora 12 installation I could compile and link things properly
with the svn snapshot libopenbabel.
Thank you,
Igor
P.S. Chris the fix for atomic aliases works like a charm, thanks once
again!
On Mon, 2010-08-
On Mon, Aug 9, 2010 at 5:50 PM, Igor Filippov [Contr]
wrote:
> Chris,
>
> Thank you. I'm trying to test it with the latest trunk (r3955) but even
> though OB itself compiled fine I'm getting the following error when
> trying to link libopenbabel to my program:
>
> undefined reference to `OpenBabel
Chris,
Thank you. I'm trying to test it with the latest trunk (r3955) but even
though OB itself compiled fine I'm getting the following error when
trying to link libopenbabel to my program:
undefined reference to `OpenBabel::AliasData::GetAlias(bool) const'
collect2: ld returned 1 exit status
Wa
Thanks. Corrected in r3897.
Chris
On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
> I've run into a problem with an SD file generated by OB with atomic
> aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
> displayed correctly by ChemAxxon MarvinSketch.
> CamridgeSoft suppor
On 12/07/2010 17:45, Tim Vandermeersch wrote:
> On Mon, Jul 12, 2010 at 6:30 PM, Igor Filippov
> wrote:
>> Is there any way to set atomic labels in openbabel to non-existent
>> elements - i.e. X, Y, R1, R2, R3... ?
>>
>> So far I see only SetAtomicNum to specify atom type, but nothing to set
>> t
On 12/07/2010 18:38, Igor Filippov wrote:
> Tim, Geoff - thank you! Got it working for SDF, is there any way to have
> it in SMILES?
There is an SMILES extension described in
http://www.opensmiles.org/spec/open-smiles-6-extensions.html#6.1
but it looks as if the name of the group has to be specifi
Tim, Geoff - thank you! Got it working for SDF, is there any way to have
it in SMILES?
Igor
On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>
> >> So far I see only SetAtomicNum to specify atom type, but nothing to set
> >> t
On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>> So far I see only SetAtomicNum to specify atom type, but nothing to set
>> the atomic label to something like "R1".
>
> You can use AliasData for this.
See src/formats/mdlformat.cpp for an exact example.
Hope that helps,
-Geoff
---
On Mon, Jul 12, 2010 at 6:30 PM, Igor Filippov
wrote:
> Is there any way to set atomic labels in openbabel to non-existent
> elements - i.e. X, Y, R1, R2, R3... ?
>
> So far I see only SetAtomicNum to specify atom type, but nothing to set
> the atomic label to something like "R1".
You can use Ali
