From baoilleach at gmail.com  Thu Jul 23 18:16:22 2020
From: baoilleach at gmail.com (Noel O'Boyle)
Date: Thu, 23 Jul 2020 16:16:22 +0100
Subject: [Cod-bugs] Download using subversion or rsync not working
In-Reply-To: <311be650-a4fe-bdce-5beb-68476060f1dc@ibt.lt>
References: <CAOC-GK0J-=SAOzKR42bhhv71ob+nF2jepQiBo6U12XHq5960rA@mail.gmail.com>
 <e39b13b7-f018-78bb-6d2b-a66b421e46cc@ibt.lt>
 <CAOC-GK14v0Toh-rEVgsj0mnian=m-cTX=u8z17msTkAfs2aUiQ@mail.gmail.com>
 <311be650-a4fe-bdce-5beb-68476060f1dc@ibt.lt>
Message-ID: <CAOC-GK3rTLXU6j6yDnhO1qJWWxRTAEp7TuKPiDeJ_02xNBr4Nw@mail.gmail.com>

To follow up, it was indeed a port problem locally which is now resolved.

Could I ask an additional question - the sync is in progress, but I'm
wondering whether it will include SMILES for the molecules? This is really
what I'm interested in, so I'm wondering do I have to do that conversion
myself. If so, what conversion procedure do you recommend?

Regards,
- Noel

On Thu, 9 Jul 2020 at 16:14, Saulius Gra?ulis <grazulis at ibt.lt> wrote:

> On 2020-07-09 17:37, Noel O'Boyle wrote:
> > Apologies. As you suggested, I tried from another location and rsync
> > seems to be working fine. I've turned the firewall off on my machine so
> > it looks like it is being blocked higher up.
>
> Good news! I'm glad it works for you now. Best with using the COD, feel
> free to e-mail if there are any problems.
>
> Sincerely,
> Saulius
>
> --
> Dr. Saulius Gra?ulis
> Vilnius University Institute of Biotechnology, Saul?tekio al. 7
> LT-10257 Vilnius, Lietuva (Lithuania)
> fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
> mobile: (+370-684)-49802, (+370-614)-36366
>
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From andrius.merkys at gmail.com  Fri Jul 24 13:58:00 2020
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Fri, 24 Jul 2020 13:58:00 +0300
Subject: [Cod-bugs] Download using subversion or rsync not working
In-Reply-To: <CAOC-GK3rTLXU6j6yDnhO1qJWWxRTAEp7TuKPiDeJ_02xNBr4Nw@mail.gmail.com>
References: <CAOC-GK0J-=SAOzKR42bhhv71ob+nF2jepQiBo6U12XHq5960rA@mail.gmail.com>
 <e39b13b7-f018-78bb-6d2b-a66b421e46cc@ibt.lt>
 <CAOC-GK14v0Toh-rEVgsj0mnian=m-cTX=u8z17msTkAfs2aUiQ@mail.gmail.com>
 <311be650-a4fe-bdce-5beb-68476060f1dc@ibt.lt>
 <CAOC-GK3rTLXU6j6yDnhO1qJWWxRTAEp7TuKPiDeJ_02xNBr4Nw@mail.gmail.com>
Message-ID: <ba8e6ab2-05b9-e029-78d6-3250aebc4363@gmail.com>

Hi Noel,

On 2020-07-23 18:16, Noel O'Boyle wrote:
> Could I ask an additional question - the sync is in progress, but I'm
> wondering whether it will include SMILES for the molecules? This is
> really what I'm interested in, so I'm wondering do I have to do that
> conversion myself. If so, what conversion procedure do you recommend?

rsync for rsync://www.crystallography.net/cif/ will download only CIF
files. You can download the whole COD SMILES collection as a single file
from here:

https://www.crystallography.net/cod/smi/allcod.smi

These are manually curated SMILES descriptors, derived
semi-automatically as a result of an ongoing project led by Miguel
Quir?s Oloz?bal. The process of their derivation is described in detail
in Quir?s et al. 2018, doi:10.1186/s13321-018-0279-6.

Hope this helps,
Andrius


From baoilleach at gmail.com  Sat Jul 25 17:05:35 2020
From: baoilleach at gmail.com (Noel O'Boyle)
Date: Sat, 25 Jul 2020 15:05:35 +0100
Subject: [Cod-bugs] Download using subversion or rsync not working
In-Reply-To: <ba8e6ab2-05b9-e029-78d6-3250aebc4363@gmail.com>
References: <CAOC-GK0J-=SAOzKR42bhhv71ob+nF2jepQiBo6U12XHq5960rA@mail.gmail.com>
 <e39b13b7-f018-78bb-6d2b-a66b421e46cc@ibt.lt>
 <CAOC-GK14v0Toh-rEVgsj0mnian=m-cTX=u8z17msTkAfs2aUiQ@mail.gmail.com>
 <311be650-a4fe-bdce-5beb-68476060f1dc@ibt.lt>
 <CAOC-GK3rTLXU6j6yDnhO1qJWWxRTAEp7TuKPiDeJ_02xNBr4Nw@mail.gmail.com>
 <ba8e6ab2-05b9-e029-78d6-3250aebc4363@gmail.com>
Message-ID: <CAOC-GK11CBd2tN2+f03_UsCgHS09fyZoiAR9xEazachFZXkO0A@mail.gmail.com>

Thanks Andrius, I should have asked about the SMILES first. That's great.

Regards,
    Noel

On Fri, 24 Jul 2020 at 11:58, Andrius Merkys <andrius.merkys at gmail.com>
wrote:

> Hi Noel,
>
> On 2020-07-23 18:16, Noel O'Boyle wrote:
> > Could I ask an additional question - the sync is in progress, but I'm
> > wondering whether it will include SMILES for the molecules? This is
> > really what I'm interested in, so I'm wondering do I have to do that
> > conversion myself. If so, what conversion procedure do you recommend?
>
> rsync for rsync://www.crystallography.net/cif/ will download only CIF
> files. You can download the whole COD SMILES collection as a single file
> from here:
>
> https://www.crystallography.net/cod/smi/allcod.smi
>
> These are manually curated SMILES descriptors, derived
> semi-automatically as a result of an ongoing project led by Miguel
> Quir?s Oloz?bal. The process of their derivation is described in detail
> in Quir?s et al. 2018, doi:10.1186/s13321-018-0279-6.
>
> Hope this helps,
> Andrius
>
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