On Sep 22, 2010, at 2:21 PM, Craig A. James wrote:
> Is there any harm in printing SP (and the other point groups) by default?
> Are we worried that it will break other SMILES parsers?
My viewpoint is that the SMILES spec describes those and implementors
should feel free to ignore those fields i
On 9/22/10 1:33 PM, Geoffrey Hutchison wrote:
>> Is there any harm in printing SP (and the other point groups) by default?
>> Are
>> we worried that it will break other SMILES parsers?
>
> That would be my worry. That we'd print SP or TB or whatever, and users would
> come back and complain it'
> Is there any harm in printing SP (and the other point groups) by default?
> Are we worried that it will break other SMILES parsers?
That would be my worry. That we'd print SP or TB or whatever, and users would
come back and complain it's not valid SMILES using Open Eye or ChemDraw or
somesuc
On 9/22/10 8:27 AM, Geoffrey Hutchison wrote:
> IMHO, since very little software handles SP stereo information, it should
> be enabled as an option to output with SMILES or canonical SMILES.
Is there any harm in printing SP (and the other point groups) by default? Are
we worried that it will br
Hi Noel,
> (http://my.cdash.org/viewBuildError.php?type=1&buildid=99451) is full
> of warnings in the Inchi code. This is 3rd party code for which we are
Actually, there's one problem with the Clang build. It's not really Clang --
it's compiling with the Clang analyzer, because the C++ support i
Hi Marcus,
The Clang build
(http://my.cdash.org/viewBuildError.php?type=1&buildid=99451) is full
of warnings in the Inchi code. This is 3rd party code for which we are
not responsible. Is it possible to filter out warnings about the InChI
code at the Dashbord submission stage somehow? Or should we
> atom should be tetrahedral or square planar. I currently have a short
> list of atoms that are sp AFAIK: Rh, Ir, Pd, Pt, Au. There are also
> metals like Ni that can be both it seems. Can anyone give some advise
I think the main question should be "when do we output SP stereo?" Certainly,
if we
Hi Chris,
Just last week I needed to be able to access the fragments generated
by the FP2 fingerprint. To do so, I just uncommented a debug statement
in finger2.cpp:
//PrintFpt(*itr,hash);
However, I wasn't able to figure out how to enable this through an
option to the fingerprint format. For ex
Hi,
FindStereogenicUnits doesn't detect square planar centers yet. It
would not be hard to add this but I'm not sure how to decide when an
atom should be tetrahedral or square planar. I currently have a short
list of atoms that are sp AFAIK: Rh, Ir, Pd, Pt, Au. There are also
metals like Ni that c
On Wed, Sep 22, 2010 at 10:00 AM, Noel O'Boyle wrote:
> Looks very good now. Nice work.
Yes, I enabled the python bindings again here. I still have swig 1.3 though...
I reimplemented rule 1 for the rule based stereogenic units and the
results are now the same as for the automorphisms based versi
On 22 September 2010 12:20, Konstantin Tokarev wrote:
>
>
> 22.09.2010, 11:54, "Noel O'Boyle" :
>> Hi all,
>>
>> Just a note to say that we now have an automated build hosted by
>> Christoph Steinbeck's group at the EBI (European Bioinformatics
>> Centre) outside Cambridge. I was over there for a
22.09.2010, 11:54, "Noel O'Boyle" :
> Hi all,
>
> Just a note to say that we now have an automated build hosted by
> Christoph Steinbeck's group at the EBI (European Bioinformatics
> Centre) outside Cambridge. I was over there for a week working with
> his student Pablo Moreno, and I thought it'd
Looks very good now. Nice work.
On 21 September 2010 11:38, Noel O'Boyle wrote:
> I'm afraid I'm seeing problems with roundtripping from SMILES through
> 0D, 2D or 3D MDL.
>
> If you run pytest_sym (e.g. "ctest -R pytest_sym -VV"), you should see
> several errors (http://my.cdash.org/testDetails.
Hi all,
Just a note to say that we now have an automated build hosted by
Christoph Steinbeck's group at the EBI (European Bioinformatics
Centre) outside Cambridge. I was over there for a week working with
his student Pablo Moreno, and I thought it'd be nice to set this up.
It's a CentOS Linux 64-b
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