From grazulis at ibt.lt Mon Feb 12 10:18:18 2018 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Mon, 12 Feb 2018 10:18:18 +0200 Subject: [Cod-bugs] "crystal structure alarm" / feature suggestion In-Reply-To: <340292280.4944757.1517325961835@mail.yahoo.com> References: <340292280.4944757.1517325961835.ref@mail.yahoo.com> <340292280.4944757.1517325961835@mail.yahoo.com> Message-ID: Dear Behrnd, thank you for your e-mail and for the feature suggestion! Indeed, COD is updated frequently (in fact daily :), so you can use it to get the hottest info regarding solved crystal structures. The closest functionality of what you describe are the RSS feeds for the deposited COD structures, to which yo can subscribe using your favourite RSS client: http://www.crystallography.net/cod/structures.rss (I've noticed that we do not have a link to this feed on our front page; we'll fix that). As for a more detailed filtering, there are so many possibilities to select and filter the data that we can hardly come up with the "one size fits all" solution. What is interesting to me will be off-topic for you and possibly vice-versa. So the idea is that on top of the *open* database like COD anyone can (and some people do;) implement multiple filters, serving different parts of community. Also, please note that adding new features to COD need human work (design, coding, testing, integration, support), and that plainly costs money :). Since the COD web site does not generate any revenue directly, we have limited resources to implement new functionality, and therefore we are primarily focused on data quality and making all data available freely (as in "free speech", not as in "free beer") ;) Sincerely yours, Saulius On 2018-01-30 17:26, Behrnd Norwid wrote: > ??????? Dear developers and maintainers of COD, > > ??? the other day I set an alarm in Thomson-Reuter's / Clarivate's > literature data base /Web of Science/, i.e. periodically, the data base > will check if an article interesting for me was cited by an other > publication, and inform me -- even if the result shall be ``none'' (when > the data base is not aware about a recent additional citation of this work). > > ??? From this experience, on one side, and remembering that at least a > considerable fraction of the data deposited in the COD may be retrieved > by pattern comparison of Smiles which in turn may be automated, the > thought occured to me that something similar might be implemented in the > COD's portfolio.? There are two kind of alerts I am aware of: > > + The COD user wants to stay abreast about the discovery of new > polymorphs of organic molecules, with models already curated in the > COD.? This may be of interest for pharmacological relevant ingredients > since at least some of the exhibit different physicochemical / > pharmacocinetical properties and are patented / deplyed as "polymorph A" > rather than "polymorph B". > > + To the astonishment of a COD user, there is a gap -- a crystalline > compound was not yet characterized by diffraction analysis, or at least, > COD is not (yet) aware of such a data set.? Beside the option to perform > this characterization by himself / herself, s/he might be interested to > learn /when/ this characterization was done by someone else; and > subsequently access the original publication COD points to. > > ??? While I do not assume, that this list of reasons for such an alert > is exhaustive, the two perspectives are appealing enough to suggest such > an implementation in crystallographic data bases, too.? Provided COD is > updated much more frequently than CCDC's CSD file, /perhaps/ the > implementation shows of benefits earlier, than at CCDC to which I wrote, > too.? From which specialty within chemistry COD receives the most data > per unit of time?? This likely different ratio might contribute to > determine if such crawling across the newly curated data shall be > performed monthly, quarterly, once a year.? On the other hand, maybe the > task is facilitated because COD is backed by subversion; and the > repeatitive crawling "just" has to be told to go back in history to the > date of the last crawl per profile (in other words, commit #212121), > instead of digesting /all/ folder and data again. > > ??? With kind regards, > > Norwid Behrnd, PhD > > > Virenfrei. www.avg.com > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > -- 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 From grazulis at ibt.lt Mon Feb 12 14:47:45 2018 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Mon, 12 Feb 2018 14:47:45 +0200 Subject: [Cod-bugs] COD - setting up mysql database for a local COD copy In-Reply-To: References: Message-ID: <91265908-9806-27d3-3b1d-64828ea2d79e@ibt.lt> Dear Pavol, thank you for you e-mail. On 2018-01-27 00:59, Pavol Juhas wrote: > I hope all is well, we met a while ago at a software demo > session at the IUCr meeting in Montreal. > > I am trying to setup a copy of the COD database on my > iMac desktop with a local mysql server. I have downloaded > the CIF files from the cod-cifs-mysql.tgz tarball and then updated > them with the rsync command as described at > http://wiki.crystallography.net/howtoobtaincod. Great! Another way would be SVN checkout, it could make updates even easier :) > The files seem to include a database dump in > mysql/data.txt file, but I am a bit at loss how to > use it to run a mysql server instance. I was > not able to find instructions at the COD wiki or > within the COD file tree. Well, I'm afraid we do not have instructions how to set up the SQL database itself ? given that there are some 5-6 popular platforms and similar amount of mainstream SQL implementations, we have no chance to cover all combinations. Most SQL engines are properly documented, so I would refer you to the corresponding OS+SQL documentation. I personally run Debian-based GNU/Linux systems (Ubuntu, Mint or Debian proper) and MySQL or SQLite engines (https://dev.mysql.com/doc/, .https://sqlite.org/docs.html). On these combinations, and from the command line, getting COD into a database is easy: For MySQL: sh$ sudo apt-get install mysql-client mysql-server # Go to the directory where you have unpacked cod-cifs-mysql.tgz: sh$ cd mysql sh$ mysql -u root -p mysql> create database cod default character set utf8; mysql> use cod; mysql> SOURCE ./data.sql; mysql> ALTER TABLE data DISABLE KEYS; mysql> LOAD DATA LOCAL INFILE 'data.txt' INTO TABLE data CHARACTER SET utf8 FIELDS TERMINATED BY '\t'; mysql> ALTER TABLE data ENABLE KEYS; mysql> quit # Be patient, 'ENABLE KEYS' may take a while :) # Instead of loading the MySQL database "by hand", you can use a # pre-packed script from the mysql/ directory; instead of running # commands in mysql> shell please run the following: sh$ mysql -u root -p cod -e 'create database cod default character set utf8' sh$ ./cod-load-mysql-dump.sh # You can now query the COD: sh$ mysql -u root -p cod -e 'select count(*) from data' and so on. You may want to create use cod_reader at localhost without a password with just SELECT privilege (https://dev.mysql.com/doc/refman/5.7/en/privileges-provided.html) for querying the database without a password, and possibly a password-protected account for yourself for COD administration and updates. Other COD tables can be loaded in a similar way. For SQLite: sh$ sudo apt-get install sqlite3 libsql-translator-perl # Go to the directory where you have unpacked cod-cifs-mysql.tgz: sqlt -f MySQL -t SQLite data.sql | sqlite3 cod.db perl -pe 's/"/\\"/g; s/\\\n$/\\n/' data.txt > data.txt.sqlite sqlite3 -separator "$(echo -e "\t")" cod.db '.import data.txt.sqlite data' # The database which is created is in the file 'cod.db'. # You can now query it: sqlite3 cod.db 'select count(*) from data' Please note that MySQL and SQLite3 have slightly different escaping conventions, so the actual content of text fields in the 'cod.db' might somewhat differ from their MySQL counterparts. SQLite2 database "lives" in a file, can be copied and backed up using regular filesystem tools, and is easier to set up safely (file access permissions also regulate the database). MySQL, on the other hand, could be faster and is accessible simultaneously from multiple computers. See which tool suits better your needs. I have put this text to our COD Wiki at http://wiki.crystallography.net/creatingSQLdatabase/ Hope this helps. Regards, 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 From mjauregui at cicenergigune.com Tue Feb 13 13:56:41 2018 From: mjauregui at cicenergigune.com (=?iso-8859-1?Q?Mar=EDa_J=E1uregui?=) Date: Tue, 13 Feb 2018 11:56:41 +0000 Subject: [Cod-bugs] FW: COD database for Bruker Message-ID: Dear Advisory Board, My name is Maria Jauregui, and actually I'm the responsible of the diffraction service in the CIC Energigune. I have been checking in your website if there is any new version of COD database for Bruker, and there isn't. Could you kindly tell me which is the last version for this kind of equipment? I look forward to hearing from you. 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