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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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CHEBI:51730 MDL molfile is a query, not a structure #280

Closed muthuvenkat closed 8 years ago

muthuvenkat commented 14 years ago

Mark Rijnbeek filed a bug report about the CDK MDLV2000Reader not parsing bond types 4-8 as found in the ChEBI entry:

http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51730

The MDL molfile specification (version "November 2007") reserves bond orders 4-8 as query bond types, to be used in search queries.

I guess it is reasonable that a functional group in ChEBI is represented as query, but I was wondering how I should see from the MDL SD file if the entry is an actual chemical structure or another entity like a functional group query specification? Or do I need to browse the ChEBI ontology for that and see that it ultimately is marked as like organic group?

Reported by: egonw

muthuvenkat commented 13 years ago

Very late response to this, sorry.

A group is normally represented by an asterisk in the atom block as per IUPAC specification. It also has the name bla-bla group and yes its linked within the ontology. P

Original comment by: pauladematos

muthuvenkat commented 8 years ago

Original comment by: muthuvenkat