Re: [Rdkit-discuss] delete a substructure

[Peter S. Shenkin]

Sounds like Daylight's "depictmatch", unfortunately no longer available on
line

-P.

On Fri, Mar 10, 2017 at 1:28 PM, David Cosgrove 
wrote:

> Hi,
> In the RDKit source, under the 2d drawing code in the c++ part there's the
> full source code for a QT program that will run one or more SMARTS patterns
> against a set of molecules, split any matches and non-matches into 2
> displays side by side and colour the atoms that the SMARTS match. It needs
> a bit of persistence to compile and has only been tried on Linux but is
> very helpful for writing new SMARTS. If there's interest, when I have a bit
> of spare time over the next few weeks I can make sure it's easier to
> compile. If you poke about in my website (cozchemix.co.uk) you'll find a
> link to my GitHub repo with an earlier version which has been compiled
> under Linux recently and has instructions. Sorry not to put links in, I
> don't have access to a computer st the moment, just phone.
>
> Cheers,
> Dave
>
> On Thu, 9 Mar 2017 at 18:41, Chenyang Shi  wrote:
>
>> Thank you Chris. I found that one too; it is quite convenient to
>> visualize both SMARTS and SMILES strings.
>>
>> On Thu, Mar 9, 2017 at 11:28 AM, Chris Swain  wrote:
>>
>> I use SMARTSviewer at Univ of Hamburg
>>
>> http://www.zbh.uni-hamburg.de/en/bioinformatics-server.html
>>
>> Chris
>>
>> On 9 Mar 2017, at 17:21, rdkit-discuss-requ...@lists.sourceforge.net
>> wrote:
>>
>> One last question I have is do you guys have convenient online or local
>> documents to look up desired SMARTS.
>> Greg mentioned $RDBASE/Data/Functional_Group_Hierarchy.txt, which comes
>> with the installation of RDKIT.
>> Brian suggested daylight website,
>> http://www.daylight.com/dayhtml_tutorials/languages/
>> smarts/smarts_examples.html, which is a good place as well.
>>
>> Best,
>> Chenyang
>>
>>
>>
>> 
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> http://cozchemix.co.uk
>
>
> 
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Re: [Rdkit-discuss] Van der Waals radius

[Guillaume GODIN]

Dear Colin,


Those values are not calculated, they come from a dictionary (the 
PeriodicalTable file).


Best regards,?

Dr. Guillaume GODIN
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De : Bournez Colin 
Envoyé : vendredi 10 mars 2017 16:51
À : rdkit-discuss@lists.sourceforge.net
Objet : [Rdkit-discuss] Van der Waals radius

Dear all,

Is it possible to know how the vdw radii are calculated with the function 
Chem.GetPeriodicTable().GetRvdw ?

Colin Bournez
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