From nbehrnd at yahoo.com Mon Jun 8 15:03:11 2020 From: nbehrnd at yahoo.com (Norwid Behrnd) Date: Mon, 8 Jun 2020 12:03:11 +0000 Subject: [Cod-bugs] {Filename?} feature suggestion COD's display array of results References: <20200608120311.371e198c.ref@carnot2> Message-ID: <20200608120311.371e198c@carnot2> Warning: This message has had one or more attachments removed Warning: (1513289.cif.sdf.png, 1505735.cif.sdf.png, 1512247.cif.sdf.png, 1512220.cif.sdf.png). Warning: Please read the "IBT-Attachment-Warning.txt" attachment(s) for more information. Dear Ladies and Gentlemen, today I searched in the COD for entries sharing a motif expressed by the SMILES string of c1scc2OCCOc12. As anticipated, the database successfully indicated multiple entries. Based on this and earlier queries in the COD, I would like to suggest a modification of the GUI of your database, namely a rearrangement of the initial array of results displayed shown prior to accessing the individual structure cards. To document observations and suggestions, a there are twelve attachements to this e-mail, too. I would like to suggest to move the very left-hand column with links to the homepage of COD and different documentations would be pivoted into an horizontal arrangement, preferably just below the ?title line? of ?COD Crystallographic Open Database?, however before the search-dependent array ?Search results? starts (motif_rearrange.png). The currently four topics of ?COD Home?, ?Accessing COD Data?, ?Add Your Data?, and ?Documentation? could, yet need not to be organized in pull-down menus. This move may then offer additional overall width for the array about the results to follow. Inspired by the line-drawings CCDC's interface conquest offers to document a search in a .pdf file, I subsequently suggest the addition of similar illustrations intended as a preview of the structure models. As shown in motif_a.png and motiv_b.png, this possibly could be either just below the COD ID number, or in a separate column currently the layout not contains. Publications in Acta Cryst E typically include the chemical name of the molecule or complex studied; yet sometimes, these names may be long. COD's data sources sources thankfully include publications ?not typically? crystallographic one where the title offers less information about the model deposit; e.g. if it is about a catalyst, or a synthetic intermediate. Equally, a publication may cover multiple models, too. Thus, a preview -- at low dimension -- may accelerate the identification of an interesting entry in the COD for a query departing from a motif in common. This suggestion partially overlaps with a suggestion sent to one of you, Antanas Vaitkus on June 3rd, which should have been deposited here instead. With openbabel (version 3.1.0) and cod-tools (version 2.10) accessible to Linux Debian 10 / bullseye (branch testing), I searched for a programmatic generation of ?conquest-like? structure formulae as already used within the Python API of the CSD. As observed, however, this first approach lacks speed of execution. Larger, possibly conformational flexible ring systems (like entry 1505735.cif / 1505735.cif.rdf.png) actually yield representations which are not quite helpful. Perhaps there are options in openbabel or other program libraries more suitable to generate these illustrations both reliably and rapidly, too. With best regards, Norwid Behrnd ---- 8>< ---- md5sum ---- ---- file attached ---- b173f254b7e49d9732d64c926198f403 1505735.cif 8156c5804818eade5976502b5173def8 1505735.cif.sdf.png ccf225ac9cf9be328c271d26a543e1f1 1512220.cif a5c1148d077a67a904cd72e2571b365a 1512220.cif.sdf.png 6baa2a3b0021bb4ca2c34b1c0459f6a9 1512247.cif b0cc52edca7d7d0bb730413341ec5da1 1512247.cif.sdf.png 9ed542c6424f28512152c9a2d9135622 1513289.cif 3cbf4af5e13344a716f1f85b42dc2a9a 1513289.cif.sdf.png b1c761142b2b142ac197243007113c1a motif_a.png 739fdee133e5979639fdef3d5f517292 motif_b.png 5d3967f597d2047a43c4e6e9fdc2266b motif_rearrange.png 182323e992968304136708fcd25fe62f test_convert.sh ---- -------------- next part -------------- A non-text attachment was scrubbed... Name: 1512220.cif Type: application/octet-stream Size: 42431 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1505735.cif Type: application/octet-stream Size: 20764 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1513289.cif Type: application/octet-stream Size: 10107 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1512247.cif Type: application/octet-stream Size: 18315 bytes Desc: not available URL: -------------- next part -------------- This is a message from the MailScanner E-Mail Virus Protection Service ---------------------------------------------------------------------- The original e-mail attachment "1505735.cif.sdf.png" is on the list of unacceptable attachments for this site and has been replaced by this warning message. If you wish to receive a copy of the original attachment, please e-mail helpdesk and include the whole of this message in your request. Alternatively, you can call them, with the contents of this message to hand when you call. 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Name: motif_rearrange.png Type: image/png Size: 193539 bytes Desc: not available URL: From nbehrnd at yahoo.com Mon Jun 8 16:00:28 2020 From: nbehrnd at yahoo.com (Norwid Behrnd) Date: Mon, 8 Jun 2020 13:00:28 +0000 Subject: [Cod-bugs] Fw: feature suggestion COD's display array of results References: <20200608130028.4d7d486c.ref@carnot2> Message-ID: <20200608130028.4d7d486c@carnot2> Dear Ladies and Gentlemen, the message below indicated me some of the illustrations sent to you were not accepted by your mail system. Thus, removing in each's name the string of '.cif.sdf', I try again to send them to you. With best regards, Norwid Behrnd ---- 8>< ---- md5sum ---- ---- attached file 8156c5804818eade5976502b5173def8 1505735.png a5c1148d077a67a904cd72e2571b365a 1512220.png b0cc52edca7d7d0bb730413341ec5da1 1512247.png 3cbf4af5e13344a716f1f85b42dc2a9a 1513289.png ---- Begin forwarded message: Date: Mon, 8 Jun 2020 15:07:54 +0300 (EEST) From: "MailScanner" To: nbehrnd at yahoo.com Subject: Warning: E-mail viruses detected Our e-mail content detector has just been triggered by a message you sent: To: cod-bugs at ibt.lt Subject: feature suggestion COD's display array of results Date: Mon Jun 8 15:07:53 2020 One or more of the attachments (1513289.cif.sdf.png, 1505735.cif.sdf.png, 1512247.cif.sdf.png, 1512220.cif.sdf.png) are on the list of unacceptable attachments for this site and will not have been delivered. Consider renaming the files to avoid this constraint. 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