I went through a large dataset of PubChem 3D structures looking for
implicit H failures (removing, then adding Hs). 1/3 of the failures
are due to the following in atomtyp.txt:
INTHYB [$([#6]([#8D1])[#8D1])] 2 #sp2 carbon
This makes any C attached to two Os turn into sp2...even in gemina
> If it's commented out, then it works fine for these cases.
I'm willing to give it a try.
> days)? Perhaps it's to correct ligand structures from the PDB where
> all examples of this indicate COO-? If so, maybe the PDB cases are
> better handled in the code using the molecular geometry...?
I'm
On 11/10/2010 20:21, Noel O'Boyle wrote:
I went through a large dataset of PubChem 3D structures looking for
implicit H failures (removing, then adding Hs). 1/3 of the failures
are due to the following in atomtyp.txt:
INTHYB [$([#6]([#8D1])[#8D1])] 2 #sp2 carbon
This makes any C attach
On 11 October 2010 21:18, Chris Morley wrote:
> On 11/10/2010 20:21, Noel O'Boyle wrote:
>>
>> I went through a large dataset of PubChem 3D structures looking for
>> implicit H failures (removing, then adding Hs). 1/3 of the failures
>> are due to the following in atomtyp.txt:
>>
>> INTHYB [$([#6
On 11 October 2010 22:17, Noel O'Boyle wrote:
> On 11 October 2010 21:18, Chris Morley wrote:
>> On 11/10/2010 20:21, Noel O'Boyle wrote:
>>>
>>> I went through a large dataset of PubChem 3D structures looking for
>>> implicit H failures (removing, then adding Hs). 1/3 of the failures
>>> are due
On Oct 12, 2010, at 4:42 AM, Noel O'Boyle wrote:
>>> There may be other side effects I'm not aware of. Just before a release is
>>> not a good time to commit something like this (5 years ago would have been
>>> better), so I've just attached a patch (changes to 11 code lines), if you
>>> want to
On 12/10/2010 15:51, Geoffrey Hutchison wrote:
>
> On Oct 12, 2010, at 4:42 AM, Noel O'Boyle wrote:
>
There may be other side effects I'm not aware of. Just before a release is
not a good time to commit something like this (5 years ago would have been
better), so I've just attached a
On Oct 13, 2010, at 9:06 AM, Chris Morley wrote:
> I have corrected two molecules in formularesults.txt and added a rule
> so that formulatest passes. However, the source SMILES from the
> venerable attype.00.smi look suspicious:
>
> CCSC1=NCCN1.OP(=O)=O LABOTEST_LT-I_Mi_22 phosphonic_acid
> C
On 12 October 2010 15:51, Geoffrey Hutchison wrote:
>
> On Oct 12, 2010, at 4:42 AM, Noel O'Boyle wrote:
>
There may be other side effects I'm not aware of. Just before a release is
not a good time to commit something like this (5 years ago would have been
better), so I've just atta
On Oct 14, 2010, at 4:44 AM, Noel O'Boyle wrote:
> I'd prefer to make the implicit COO change, and file a bug on the
> PDB for addressing at some point in the future.
If this is causing incorrect formulas for SMILES, we should make this fix.
Since we don't know yet if there is an actual PDB iss
On Oct 11, 2010, at 4:18 PM, Chris Morley wrote:
> A simpler and more obvious model for this purpose has essentially a single
> IMPVAL for each charge state of the molecule. (Only if you are interested in
> radicals or hydrogen on the higher valency states of second row elements do
> you need
On 01/11/2011 02:27, Geoff Hutchison wrote:
>
> On Oct 11, 2010, at 4:18 PM, Chris Morley wrote:
>
>> A simpler and more obvious model for this purpose has essentially a single
>> IMPVAL for each charge state of the molecule. (Only if you are interested in
>> radicals or hydrogen on the higher va
On 2 November 2011 22:35, Chris Morley wrote:
> On 01/11/2011 02:27, Geoff Hutchison wrote:
>>
>> On Oct 11, 2010, at 4:18 PM, Chris Morley wrote:
>>
>>> A simpler and more obvious model for this purpose has essentially a single
>>> IMPVAL for each charge state of the molecule. (Only if you are i
On 29/11/2011 20:56, Noel O'Boyle wrote:
> On 2 November 2011 22:35, Chris Morley wrote:
>> On 01/11/2011 02:27, Geoff Hutchison wrote:
>>>
>>> On Oct 11, 2010, at 4:18 PM, Chris Morley wrote:
>>>
A simpler and more obvious model for this purpose has essentially a single
IMPVAL for each
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