From annvolkova96 at gmail.com  Mon Jun 10 10:24:32 2019
From: annvolkova96 at gmail.com (Anna Volkova)
Date: Mon, 10 Jun 2019 10:24:32 +0300
Subject: [Cod-bugs] The bug in the COD site's link
Message-ID: <CA+v+51rB9jwoPbzVDTmkO-ZPmC50Pn69Wg8YPjAo-uv1rSTmvg@mail.gmail.com>

  Hello, dear COD group

You created a great project, thank you a lot!

I find a problem with a link, which offers to download all cif files with
element which  I am interested in.
I did search by element "Eu" and COD finds 2792 results. I wonder to
download all Eu cif files for further analysis by link " archive of CIF
files (ZIP
<http://crystallography.net/cod/result.php?format=zip&CODSESSION=2ued87s02upgh13d3s83prfcfbqfo0pk>)",
but unfortunatly it takes time for trying to download and at the result
site shows me information "Crystallography.net cannot process this request
yet." Error HTTP ERROR 500

Could you  please solve this problem? I am really intrested in this data,
but I am not a good proger for writing code for automatic download.

Thank you in advance,

*Anna Volkova*
*Master student*

*Lomonosov MSU*

*Chemistry department*

*Radiochemistry division*
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From antanas.vaitkus90 at gmail.com  Mon Jun 10 13:50:16 2019
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Mon, 10 Jun 2019 13:50:16 +0300
Subject: [Cod-bugs] The bug in the COD site's link
In-Reply-To: <CA+v+51rB9jwoPbzVDTmkO-ZPmC50Pn69Wg8YPjAo-uv1rSTmvg@mail.gmail.com>
References: <CA+v+51rB9jwoPbzVDTmkO-ZPmC50Pn69Wg8YPjAo-uv1rSTmvg@mail.gmail.com>
Message-ID: <CALHYoX5=Ff2h7rphTArVHAPBYcwycxm8QHN3M4t17tH34W4N5g@mail.gmail.com>

Dear Anna Volkova,

thank You for using the COD. We have identified the problem, but it might
take some time to correct it.
We will inform You when it is completed.

For the time of being we have compiled the files You requested into a
separate zip file that can be downloaded
from
https://www.crystallography.net/U8ti7N77pHVu9TvnBNfL-Anna-Volkova-2019-06-10/COD-Eu-r215790.zip
.

The file will be removed after a week. Will this suffice for now?

Sincerely,
Antanas Vaitkus

On Mon, 10 Jun 2019 at 13:08, Anna Volkova <annvolkova96 at gmail.com> wrote:

>   Hello, dear COD group
>
> You created a great project, thank you a lot!
>
> I find a problem with a link, which offers to download all cif files with
> element which  I am interested in.
> I did search by element "Eu" and COD finds 2792 results. I wonder to
> download all Eu cif files for further analysis by link " archive of CIF
> files (ZIP
> <http://crystallography.net/cod/result.php?format=zip&CODSESSION=2ued87s02upgh13d3s83prfcfbqfo0pk>)",
> but unfortunatly it takes time for trying to download and at the result
> site shows me information "Crystallography.net cannot process this request
> yet." Error HTTP ERROR 500
>
> Could you  please solve this problem? I am really intrested in this data,
> but I am not a good proger for writing code for automatic download.
>
> Thank you in advance,
>
> *Anna Volkova*
> *Master student*
>
> *Lomonosov MSU*
>
> *Chemistry department*
>
> *Radiochemistry division*
>
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>


-- 
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania
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From annvolkova96 at gmail.com  Mon Jun 10 13:25:35 2019
From: annvolkova96 at gmail.com (Anna Volkova)
Date: Mon, 10 Jun 2019 13:25:35 +0300
Subject: [Cod-bugs] The bug in the COD site's link
In-Reply-To: <CALHYoX5=Ff2h7rphTArVHAPBYcwycxm8QHN3M4t17tH34W4N5g@mail.gmail.com>
References: <CA+v+51rB9jwoPbzVDTmkO-ZPmC50Pn69Wg8YPjAo-uv1rSTmvg@mail.gmail.com>
 <CALHYoX5=Ff2h7rphTArVHAPBYcwycxm8QHN3M4t17tH34W4N5g@mail.gmail.com>
Message-ID: <CA+v+51pHzDedxb547mnWUm2sDdXM0iBAkxVa1aLg2BKo_RxvzQ@mail.gmail.com>

Dear Antanas Vaitkus,

Yes, this is great,
thank you for the zip with cif files.

Best regards,
Anna
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From jz449 at cam.ac.uk  Tue Jun 11 20:49:37 2019
From: jz449 at cam.ac.uk (J. Zhao)
Date: Tue, 11 Jun 2019 18:49:37 +0100
Subject: [Cod-bugs] Question about search by SMILES
Message-ID: <a384c74ea212ca76977211ffec69ca77@cam.ac.uk>

 

Hi, 

I was trying to search for chemical structures by SMILES. But whatever I
entered in the 'Enter SMILES' at
http://www.crystallography.net/cod/search.html [1], it just returned all
the structures in the database. 

Could you please let me know how to properly search by SMILES? And is
there a way to use RESTful API to search by SMILES? 

Many thanks! 

Regards, 

Jiuyang 
 

Links:
------
[1] http://www.crystallography.net/cod/search.html
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From andrius.merkys at gmail.com  Wed Jun 12 12:29:47 2019
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Wed, 12 Jun 2019 11:29:47 +0200
Subject: [Cod-bugs] Question about search by SMILES
In-Reply-To: <a384c74ea212ca76977211ffec69ca77@cam.ac.uk>
References: <a384c74ea212ca76977211ffec69ca77@cam.ac.uk>
Message-ID: <CAEZpsw2OjE2Nk4yMa2v9JOqrKOLmdsZHx1+RccAx3s_qYufJmw@mail.gmail.com>

Hi Jiuyang,

Could you please provide a single example of a query which you performed? I
will look into the issue then.

Best wishes,
Andrius

On Wed, 12 Jun 2019, 09:16 J. Zhao, <jz449 at cam.ac.uk> wrote:

> Hi,
>
> I was trying to search for chemical structures by SMILES. But whatever I
> entered in the 'Enter SMILES' at
> http://www.crystallography.net/cod/search.html, it just returned all the
> structures in the database.
>
> Could you please let me know how to properly search by SMILES? And is
> there a way to use RESTful API to search by SMILES?
>
> Many thanks!
>
> Regards,
>
> Jiuyang
>
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>
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From andrius.merkys at gmail.com  Wed Jun 12 20:49:38 2019
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Wed, 12 Jun 2019 19:49:38 +0200
Subject: [Cod-bugs] Question about search by SMILES
In-Reply-To: <7e26db5bd8de13f4425f4321ddb16c94@cam.ac.uk>
References: <a384c74ea212ca76977211ffec69ca77@cam.ac.uk>
 <CAEZpsw2OjE2Nk4yMa2v9JOqrKOLmdsZHx1+RccAx3s_qYufJmw@mail.gmail.com>
 <7e26db5bd8de13f4425f4321ddb16c94@cam.ac.uk>
Message-ID: <CAEZpsw00-FBfn5tYRQKQkOXhaXRBLyAvZ=zgBZXauncaX_4CRw@mail.gmail.com>

Dear Jiuyang,

Thanks a lot for the detailed description of the problem. Indeed, the
search is not working as it should be. We will try to investigate and fix
the problem as soon as possible. For the time being you may use
applet-based substructure search (
http://www.crystallography.net/cod/jsme_search.html).

Best regards,
Andrius

On Wed, 12 Jun 2019, 13:20 J. Zhao, <jz449 at cam.ac.uk> wrote:

> Hi Andrius,
>
> Thanks for your reply.
>
> So if you go to this url http://www.crystallography.net/cod/search.html,
> at the second search box "Enter SMILES", enter "c1ccccc1" which is the
> SMILES for benzene.
>
> Then click 'Search', then the new page will tell you "Results: there are
> 402769 entries in the selection". And whatever I entered in that search
> box, it always return 402769 entires as result - which is the total number
> of entries of COD.
>
> So does it mean the SMILES search not working properly? And is there a way
> to use RESTful API to perform SMILES search?
>
> The normal RESTful API page is here
> http://wiki.crystallography.net/RESTful_API/#index1h1, and it doesn't say
> anything about search by SMILES.
>
> Thanks again!
>
> Regards,
>
> Jiuyang
>
> On 2019-06-12 10:29, Andrius Merkys wrote:
>
> Hi Jiuyang,
>
> Could you please provide a single example of a query which you performed?
> I will look into the issue then.
>
> Best wishes,
> Andrius
>
> On Wed, 12 Jun 2019, 09:16 J. Zhao, <jz449 at cam.ac.uk> wrote:
>
>> Hi,
>>
>> I was trying to search for chemical structures by SMILES. But whatever I
>> entered in the 'Enter SMILES' at
>> http://www.crystallography.net/cod/search.html, it just returned all the
>> structures in the database.
>>
>> Could you please let me know how to properly search by SMILES? And is
>> there a way to use RESTful API to search by SMILES?
>>
>> Many thanks!
>>
>> Regards,
>>
>> Jiuyang
>>
>> _______________________________________________
>> Cod-bugs mailing list
>> Cod-bugs at lists.crystallography.net
>> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>
>
>
>
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