From fx.coudert at chimieparistech.psl.eu Mon Nov 4 16:52:21 2024 From: fx.coudert at chimieparistech.psl.eu (Fx COUDERT) Date: Mon, 4 Nov 2024 14:52:21 +0000 Subject: [Cod-bugs] Filtering structures with/without disorder In-Reply-To: <3abf0a68-8d52-4d62-8d55-5211b77693b6@gmail.com> References: <956DDB2A-5D5A-4CD4-906C-DD3C79AD691A@chimieparistech.psl.eu> <3abf0a68-8d52-4d62-8d55-5211b77693b6@gmail.com> Message-ID: <629AF507-DACF-42A8-B26B-DF687431664E@chimieparistech.psl.eu> Hi, > Yes, disorder flag is stored in the COD's SQL database. It is probably easiest to access it via queries to COD's SQL database [1][2]. Disordered entries are marked with string "has disorder" in 'flags' column of 'data' SQL table. REST API [3] and COD's OPTIMADE implementation does not expose this flag yet. Thanks. Is there a simple, complete example on how to query the COD server through SQL? The page you linked to says "The more sophisticated queries however may need direct access to the COD SQL server?. I can see how to create a local copy of your SQL database at https://wiki.crystallography.net/creatingSQLdatabase/ but I do not see how to connect directly to your server? Best, -- Dr. Fran?ois-Xavier Coudert Senior Researcher / Directeur de Recherche CNRS at Chimie ParisTech Professeur attach? ENS / PSL University Webpage: https://www.coudert.name/ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Mon Nov 4 16:57:18 2024 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Mon, 4 Nov 2024 16:57:18 +0200 Subject: [Cod-bugs] Filtering structures with/without disorder In-Reply-To: <629AF507-DACF-42A8-B26B-DF687431664E@chimieparistech.psl.eu> References: <956DDB2A-5D5A-4CD4-906C-DD3C79AD691A@chimieparistech.psl.eu> <3abf0a68-8d52-4d62-8d55-5211b77693b6@gmail.com> <629AF507-DACF-42A8-B26B-DF687431664E@chimieparistech.psl.eu> Message-ID: <999591ee-fb87-4ce3-9a88-a2c90ce72ff2@gmail.com> Hi, On 11/4/24 16:52, Fx COUDERT wrote: > Thanks. Is there a simple, complete example on how to query the COD server through SQL? The page you linked to says "The more sophisticated queries however may need direct access to the COD SQL server?. I can see how to create a local copy of your SQL database athttps://wiki.crystallography.net/creatingSQLdatabase/ but I do not see how to connect directly to your server? The following Bash command should give all COD IDs of entries without explicitly marked disorder: mysql -u cod_reader -h sql.crystallography.net cod -e 'select file from data where flags NOT LIKE "%has disorder%"' -N | wc -l Please notice the 'wc -l' at the end, which I use in order not to overflow my terminal with the IDs. It is better to redirect the output to a file. Hope this helps, Andrius -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From guilhem.dezanneau at centralesupelec.fr Tue Nov 5 12:10:19 2024 From: guilhem.dezanneau at centralesupelec.fr (Guilhem Dezanneau) Date: Tue, 05 Nov 2024 11:10:19 +0100 Subject: [Cod-bugs] COD + API Message-ID: <4653c-6729ef00-5b-268bc440@47490967> Hello ? I am Guilhem Dezannneau from CNRS france. ? I try to download some cif files from a list of elements, using the API BUT I do not manage. I did it for phase identification and it seems to work but, for some reason i don't understand, i cannot manage to do the same with a list of elements. ? Could you tell me how should look like the script get a response, for instance to have all structures? with only those two elements Zr and O. ? ? ? Many thanks in advance. Warm regard from Paris G. Dezanneau -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: