Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.
Hi Riccardo, thanks, I found the problem. As suspected it was related to conda and had nothing to do with RDKit (https://github.com/conda/conda/issues/2212#issuecomment-228277548). Many thanks for your help. Kind regards, Axel On 27.06.2016 22:44, Riccardo Vianello wrote: Hi Axel, thanks a lot for your help, using the development branch and the Release_2016_03_2 git tag in rdkit/meta.yaml worked. I now get a strange error in anaconda when actually trying to install the package (Error: Invalid version spec: ==), but that seems to be unrelated to RDKit (there is already an issue on anaconda github). My understanding was that the preferred way to install the RDKit was via anaconda (RDKit was the reason I started using anaconda), is that still correct? I'm not exactly sure about the commands you used, but I'm afraid I wasn't able to reproduce the described problem using conda 4.1.4 and conda-build 1.21.2 on my fedora box. In case the error persisted, could you please provide some additional context? Best regards, Riccardo -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial
Hi Dmitri,
The results that come back from the MCS in that examples really describe
queries, not necessarily stable molecules or things that can be accurately
translated into SMILES.
I'll describe below what's going on to cause the error, but the more
important question is: what are you trying to do?
In this case there are two problems. One has to do with the aromatic bonds
in the SMILES coming from C atoms that are written as capital letters.
Here's a simplified version of your example:
In [11]: Chem.MolFromSmiles('O=C1:[NH]:C:N:N2:C:*:C:C:1:2')
[06:43:37] Explicit valence for atom # 1 C, 5, is greater than permitted
If I rewrite the SMILES to have the atoms with aromatic bonds written with
lower case letters everything is fine:
In [12]: Chem.MolFromSmiles('O=c1:[nH]:c:n:n2:c:*:c:c:1:2')
Out[12]:
This shouldn't make a difference in SMILES, so I'm inclined to think that
it's a bug.
The second problem was the missing hydrogen specification on the aromatic
nitrogen that has an H (I fixed this in the SMILES above). Since the RDKit
does not attempt to guess at chemistry, the general rule is that aromatic
heteroatoms should have Hs specified if they have any. There have been a
number of mailing list threads on this topic.
Best,
-greg
On Mon, Jun 27, 2016 at 8:26 PM, DmitriR wrote:
> Dear RDKitters,
>
> I would appreciate any comments on the following:
>
> I am looking at the 'SureChEMBL iPython Notebook Tutorial'
>
> http://nbviewer.jupyter.org/github/rdkit/UGM_2014/blob/master/Notebooks/Vardenafil.ipynb
>
> following along with rdkit '2016.03.1' on OSX
>
> In Cell 142, there is this SMILES:
>
> MCS SMILES: O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2
> This is a representation of a generalized structure, not any
> particular molecule.
>
> It was generated with Chem.MolToSmiles(mcsM,isomericSmiles=True)
>
> But when I try
> Chem.MolFromSmiles('O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2')
>
> I get "RDKit ERROR: [14:11:32] Explicit valence for atom # 1 C, 5, is
> greater than permitted"
>
> So there is no "round-trip" possible here.
>
> Which behavior is "correct", given the aromaticity and structure as
> specified?
> Should this be rendering/creating molecule, or failing?
>
> Thanks!
>
> (MarvinSketch does display the SMILES without complaints.;
> image is attached)
>
> Dmitri
>
>
>
>
> --
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
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>
>
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.
Hi Axel, thanks a lot for your help, using the development branch and the > Release_2016_03_2 git tag in rdkit/meta.yaml worked. > I now get a strange error in anaconda when actually trying to install the > package (Error: Invalid version spec: ==), but that seems to be unrelated > to RDKit (there is already an issue on anaconda github). > My understanding was that the preferred way to install the RDKit was via > anaconda (RDKit was the reason I started using anaconda), is that still > correct? > I'm not exactly sure about the commands you used, but I'm afraid I wasn't able to reproduce the described problem using conda 4.1.4 and conda-build 1.21.2 on my fedora box. In case the error persisted, could you please provide some additional context? Best regards, Riccardo -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial
Dear RDKitters,
I would appreciate any comments on the following:
I am looking at the 'SureChEMBL iPython Notebook Tutorial'
http://nbviewer.jupyter.org/github/rdkit/UGM_2014/blob/master/Notebooks/Vardenafil.ipynb
following along with rdkit '2016.03.1' on OSX
In Cell 142, there is this SMILES:
MCS SMILES: O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2
This is a representation of a generalized structure, not any particular
molecule.
It was generated with Chem.MolToSmiles(mcsM,isomericSmiles=True)
But when I try
Chem.MolFromSmiles('O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2')
I get "RDKit ERROR: [14:11:32] Explicit valence for atom # 1 C, 5, is greater
than permitted"
So there is no "round-trip" possible here.
Which behavior is "correct", given the aromaticity and structure as specified?
Should this be rendering/creating molecule, or failing?
Thanks!
(MarvinSketch does display the SMILES without complaints.;
image is attached)
Dmitri
--
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
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