On Tue, Jun 22, 2010 at 6:28 PM, Craig A. James wrote:
> On 6/21/10 2:49 PM, Tim Vandermeersch wrote:
>
>>> The LSSR algorithm is simple:
>>>
>>> for S in (3, 4, 5, 6, ...)
>>> find all rings of size S, add to LSSR
>>> if all cyclic atoms and bonds are included in at
>>> least one ring
On 6/21/10 2:49 PM, Tim Vandermeersch wrote:
>> The LSSR algorithm is simple:
>>
>> for S in (3, 4, 5, 6, ...)
>> find all rings of size S, add to LSSR
>> if all cyclic atoms and bonds are included in at
>> least one ring in the LSSR, quit
>
> This would give 10 rings for cubane wi
On Tue, Jun 22, 2010 at 4:31 AM, Craig A. James wrote:
> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
>> wrote:
The changes are in svn trunk. The current test set (aromatics.smi,
attype.00.smi& nci.smi) is not good though.
>>>
>>>
On Tue, Jun 22, 2010 at 12:05 PM, Noel O'Boyle wrote:
> On 22 June 2010 09:06, Noel O'Boyle wrote:
>> On 22 June 2010 03:31, Craig A. James wrote:
>>> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
wrote:
>> The changes are in svn
On Tue, Jun 22, 2010 at 10:06 AM, Noel O'Boyle wrote:
> On 22 June 2010 03:31, Craig A. James wrote:
>> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
>>> wrote:
> The changes are in svn trunk. The current test set (aromatics.smi,
>
On 22 June 2010 09:06, Noel O'Boyle wrote:
> On 22 June 2010 03:31, Craig A. James wrote:
>> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
>>> wrote:
> The changes are in svn trunk. The current test set (aromatics.smi,
> attype.00.s
On 22 June 2010 03:31, Craig A. James wrote:
> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
>> wrote:
The changes are in svn trunk. The current test set (aromatics.smi,
attype.00.smi& nci.smi) is not good though.
>>>
>>> By that,
On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
> wrote:
>>> The changes are in svn trunk. The current test set (aromatics.smi,
>>> attype.00.smi& nci.smi) is not good though.
>>
>> By that, I assume you mean that the current test set is not suf
On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
wrote:
>> The changes are in svn trunk. The current test set (aromatics.smi,
>> attype.00.smi & nci.smi) is not good though.
>
> By that, I assume you mean that the current test set is not sufficient for
> SSSR vs. LSSR? I can probably generate
> The changes are in svn trunk. The current test set (aromatics.smi,
> attype.00.smi & nci.smi) is not good though.
By that, I assume you mean that the current test set is not sufficient for SSSR
vs. LSSR? I can probably generate a *MUCH* larger test set if that's what you
need.
-Geoff
On Mon, Jun 21, 2010 at 11:14 PM, Craig A. James wrote:
> On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
>
>>> For most "ordinary" molecules, the LSSR is the same as the SSSR. The
>>> LSSR and
>>> SSSR only differ with "cage" structures, where the rings themselves form
>>> rings,
>>> i.e. when the
> No, there's nothing that I know of that exercises all of the cases that
> should be tested.
There's a start in the aromatic unit test. It includes a list of molecules for
which all non-hydrogens should be aromatic. Additional smiles can be added to
test/files/aromatics.smi.
It's a small set
BTW, I sent Geoff some new kekulize.cpp code this morning. If anyone's
interested, here are the comments that describe how it works. Comments
welcome... Note that "SSSR" could/should be replaced by "LSSR" since LSSR is
easier to compute for these very large molecules. We've been using the ne
On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
> Craig: Do you have test cases for aromaticity?
No, there's nothing that I know of that exercises all of the cases that should
be tested.
Craig
--
ThinkGeek and WIRED's Gee
On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
>> For most "ordinary" molecules, the LSSR is the same as the SSSR. The LSSR
>> and
>> SSSR only differ with "cage" structures, where the rings themselves form
>> rings,
>> i.e. when there exists a set of R rings that "covers" all atoms, but R is
>
On Mon, Jun 21, 2010 at 7:24 PM, Tim Vandermeersch
wrote:
> On Mon, Jun 21, 2010 at 6:43 PM, Craig A. James wrote:
>> The recent discussion of SSSR bugs prompted me to dig back through my emails
>> to one I wrote on 20 November 2007 to the BlueObelisk mailing list. Here it
>> is in its entiret
On Mon, Jun 21, 2010 at 6:43 PM, Craig A. James wrote:
> The recent discussion of SSSR bugs prompted me to dig back through my emails
> to one I wrote on 20 November 2007 to the BlueObelisk mailing list. Here it
> is in its entirety.
>
> Craig
>
>
>
>
> Andrew s
Craig,
Thanks for bringing up your previous message, it's definitely relevant. Was
that really in 2007?!
> I propose, for argument's sake, that we should be using a LSSR, "Largest Set
> of Smallest Rings." It would go like this: A breadth-first search for rings,
> which terminates when all ri
The recent discussion of SSSR bugs prompted me to dig back through my emails to
one I wrote on 20 November 2007 to the BlueObelisk mailing list. Here it is in
its entirety.
Craig
Andrew suggested an algorithmic description of aromaticity. I think this is a
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