Re: [Rdkit-discuss] RDKit Windows binaries - exists ? Where ?

2017-05-05 Thread Jan Holst Jensen 

Hi Greg,

> Using conda makes the installation a lot simpler and saves me a fair 
amount of time while doing the builds.


Sounds like a good deal.

> Is using the anaconda python distribution a problem for you?

Actually not. I was concerned about its support for other packages, but 
it comes with pywin32 built-in so we can create COM services (think 
Excel...) and it does indeed make it much easier to install RDKit.


Thanks for the help.

Cheers
-- Jan

On 2017-05-05 04:48, Greg Landrum wrote:

Hi Jan,

I've stopped creating standalone windows binaries now that the conda 
packages are available.
Using conda makes the installation a lot simpler and saves me a fair 
amount of time while doing the builds.


Is using the anaconda python distribution a problem for you?

On Thu, May 4, 2017 at 5:41 PM, Jan Holst Jensen 
> wrote:


Hi,

I was trying to find Python Windows binaries for the latest RDKit
release. I could find them for the older 2016_03_1 release on
SourceForge but had no luck finding anything newer on SourceForge
or Github.

According to GitHub they should be there:
https://github.com/rdkit/rdkit/tree/Release_2017_03_1


Under "Installation":
"Windows binaries are available with each release." - but where :-) ?

Cheers
-- Jan



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[Rdkit-discuss] How to preserve stereochemistry in a SMARTS subgraph?

2017-05-05 Thread Thilo Bauer 
Dear Mailinglist-members,

in rdkit, when doing a MCS search for molecules bearing a chirality 
center, (how) is it possible to preserve the stereochemical information 
when exporting the subgraph to a SMARTS string?

Consider the following three molecules:

 >>> mol_ccw = Chem.MolFromSmiles('C1=C[C@H](Cl)CCC1')
 >>> mol_cw  = Chem.MolFromSmiles('C1=C[C@@H](Cl)CCC1')
 >>> mol_lin = Chem.MolFromSmiles('C=C[C@H](Cl)CCC')

Doing a chirality-sensitive subgraph search leads to the somewhat 
expected result:

 >>> rdFMCS.FindMCS([mol_ccw, mol_cw], matchChiralTag=True).smartsString
'[#6](=[#6])-[#6]-[#6]-[#6]-[#6]-[#17]'
 >>> rdFMCS.FindMCS([mol_ccw, mol_lin], matchChiralTag=True).smartsString
'[#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6]'
 >>> rdFMCS.FindMCS([mol_cw, mol_lin], matchChiralTag=True).smartsString
'[#6]-[#6]-[#6]-[#6]-[#6]'

The subgraph over mol_cw and mol_lin includes the stereocenter. But 
unfortunately, the chirality information is not stored in the SMARTS 
string, and using [#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6] for a 
chirality-sensitive substructure match leads to the expected result of 
the pattern made from that SMARTS string matching all three molecules:

 >>> patt = Chem.MolFromSmarts('[#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6]')
 >>> len({mol_cw, mol_ccw, mol_lin}.GetSubstructMatches(patt, 
useChirality=True))
1

Manually inserting a lazy @H or a &* at the stereocenter leads -of 
course- to the desired result:

 >>> patt = Chem.MolFromSmarts('[#6]=[#6]-[#6@H](-[#17])-[#6]-[#6]-[#6]')
 >>> len({mol_ccw, mol_lin}.GetSubstructMatches(patt, useChirality=True))
1
 >>> len(mol_cw.GetSubstructMatches(patt, useChirality=True))
0

Now, when matching mol_ccw and mol_lin, how do I get the 
stereochemistry-aware SMARTS string 
[#6]=[#6]-[#6&*](-[#17])-[#6]-[#6]-[#6] as the substructure in the 
first place?


Thank you & kind regards,
Thilo


-- 
Dr. Thilo Bauer

Computer-Chemie-Centrum
Friedrich-Alexander-Universität
Nägelsbachstr. 25
91052 Erlangen

+49 170 9738141

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Re: [Rdkit-discuss] How to preserve stereochemistry in a SMARTS subgraph?

2017-05-05 Thread Greg Landrum 
Hi Thilo,

This is a bug in the generation of the SMARTS from the MCS code. It's not a
new one and I was pretty sure that it had already been filed in github, but
I can't seem to find it. I'll file the bug report and will hopefully be
able to get it fixed in the not-too-distant future.

-greg



On Fri, May 5, 2017 at 11:37 AM, Thilo Bauer  wrote:

> Dear Mailinglist-members,
>
> in rdkit, when doing a MCS search for molecules bearing a chirality
> center, (how) is it possible to preserve the stereochemical information
> when exporting the subgraph to a SMARTS string?
>
> Consider the following three molecules:
>
>  >>> mol_ccw = Chem.MolFromSmiles('C1=C[C@H](Cl)CCC1')
>  >>> mol_cw  = Chem.MolFromSmiles('C1=C[C@@H](Cl)CCC1')
>  >>> mol_lin = Chem.MolFromSmiles('C=C[C@H](Cl)CCC')
>
> Doing a chirality-sensitive subgraph search leads to the somewhat
> expected result:
>
>  >>> rdFMCS.FindMCS([mol_ccw, mol_cw], matchChiralTag=True).smartsString
> '[#6](=[#6])-[#6]-[#6]-[#6]-[#6]-[#17]'
>  >>> rdFMCS.FindMCS([mol_ccw, mol_lin], matchChiralTag=True).smartsString
> '[#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6]'
>  >>> rdFMCS.FindMCS([mol_cw, mol_lin], matchChiralTag=True).smartsString
> '[#6]-[#6]-[#6]-[#6]-[#6]'
>
> The subgraph over mol_cw and mol_lin includes the stereocenter. But
> unfortunately, the chirality information is not stored in the SMARTS
> string, and using [#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6] for a
> chirality-sensitive substructure match leads to the expected result of
> the pattern made from that SMARTS string matching all three molecules:
>
>  >>> patt = Chem.MolFromSmarts('[#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6]')
>  >>> len({mol_cw, mol_ccw, mol_lin}.GetSubstructMatches(patt,
> useChirality=True))
> 1
>
> Manually inserting a lazy @H or a &* at the stereocenter leads -of
> course- to the desired result:
>
>  >>> patt = Chem.MolFromSmarts('[#6]=[#6]-[#6@H](-[#17])-[#6]-[#6]-[#6]')
>  >>> len({mol_ccw, mol_lin}.GetSubstructMatches(patt, useChirality=True))
> 1
>  >>> len(mol_cw.GetSubstructMatches(patt, useChirality=True))
> 0
>
> Now, when matching mol_ccw and mol_lin, how do I get the
> stereochemistry-aware SMARTS string
> [#6]=[#6]-[#6&*](-[#17])-[#6]-[#6]-[#6] as the substructure in the
> first place?
>
>
> Thank you & kind regards,
> Thilo
>
>
> --
> Dr. Thilo Bauer
>
> Computer-Chemie-Centrum
> Friedrich-Alexander-Universität
> Nägelsbachstr. 25
> 91052 Erlangen
>
> +49 170 9738141
>
> 
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Re: [Rdkit-discuss] nitro-compounds from smarts

2017-05-05 Thread Rafal Roszak 
Curt & Greg,

Thx for clarification.
 
> But it's not clear to me why you would need to query in this way.

in my code I use(d) smarts as a smiles with extra features ("regex",
atom numbering). As far as I remember I had some problem with smiles
and therefore decided to switch to smarts. Now I back to
smiles-version and realized the problem is in different place and smarts
only mask true problem.

Thanks again for comments and explanations.

Best,

Rafał

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