From fx.coudert at chimieparistech.psl.eu Fri Nov 15 11:29:54 2024 From: fx.coudert at chimieparistech.psl.eu (Fx COUDERT) Date: Fri, 15 Nov 2024 09:29:54 +0000 Subject: [Cod-bugs] Filtering structures with/without disorder In-Reply-To: <999591ee-fb87-4ce3-9a88-a2c90ce72ff2@gmail.com> References: <956DDB2A-5D5A-4CD4-906C-DD3C79AD691A@chimieparistech.psl.eu> <3abf0a68-8d52-4d62-8d55-5211b77693b6@gmail.com> <629AF507-DACF-42A8-B26B-DF687431664E@chimieparistech.psl.eu> <999591ee-fb87-4ce3-9a88-a2c90ce72ff2@gmail.com> Message-ID: Hi Andrius, Thanks for your responses, and sorry for asking more. If there is a public forum or discussion board for COD, please let me know, I will ask there. I have looked at the https://github.com/cod-developers/cod-tools repository with COD-related tools. I see that there are some scripts that classify structures, but I have been unable to use them myself. I would like to sort structures between organic, inorganic, and hybrid. If you had any help / guidance on how to achieve this, I would be really appreciative. Best regards, -- 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 Fri Nov 15 11:37:31 2024 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Fri, 15 Nov 2024 11:37:31 +0200 Subject: [Cod-bugs] Filtering structures with/without disorder In-Reply-To: References: <956DDB2A-5D5A-4CD4-906C-DD3C79AD691A@chimieparistech.psl.eu> <3abf0a68-8d52-4d62-8d55-5211b77693b6@gmail.com> <629AF507-DACF-42A8-B26B-DF687431664E@chimieparistech.psl.eu> <999591ee-fb87-4ce3-9a88-a2c90ce72ff2@gmail.com> Message-ID: Hi, On 2024-11-15 11:29, Fx COUDERT wrote: > Thanks for your responses, and sorry for asking more. If there is a > public forum or discussion board for COD, please let me know, I will ask > there. We have a public issue tracker for the COD [1], it is mostly used for reporting bugs and feature requests. Nevertheless it is fine to converse in email form. > I have looked at thehttps://github.com/cod-developers/cod-tools > repository with COD-related tools. I see that there are some scripts > that classify structures, but I have been unable to use them myself. I > would like to sort structures between organic, inorganic, and hybrid. If > you had any help / guidance on how to achieve this, I would be really > appreciative. Right, there is a tool called cif_classify, which for every input CIF file outputs whether its structure has C-C and/or C-H bonds. We do not have any tools to classify into organic, inorganic and hybrid classes because such classification is difficult to describe both in human terms and computer heuristics. [1] https://projects.ibt.lt/repositories/projects/cod Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.