Iamkaant: Created page with "DataWarrior folks have implemented enumeration protocol in their soft. It is published in 10.1021/acs.jcim.1c01041 They store reactions in .rxn format, which is documented in..."

2022-06-06T21:14:39Z

Created page with "DataWarrior folks have implemented enumeration protocol in their soft. It is published in 10.1021/acs.jcim.1c01041 They store reactions in .rxn format, which is documented in..."

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DataWarrior folks have implemented enumeration protocol in their soft. It is published in 10.1021/acs.jcim.1c01041

They store reactions in .rxn format, which is documented in https://docs.chemaxon.com/display/docs/mdl-molfiles-rgfiles-sdfiles-rxnfiles-rdfiles-formats.md. The files can be found in "reactions" directory in https://github.com/joewah/Virtual-Fragment-Spaces

The .rxn files can be opened in ChemAxon MarvinSketch. Then just select the reaction, right click, Copy as -- Daylight SMARTS. And you get the correct SMARTS with all atom lists. For example, for amidation reaction I got

[#7,#8]-[#7H1:1](-[#6:2]=[#7,#8,#16])-[#6,#16]=[#7,#8,#16].[#6:3]-[#6:4](-[#8,#17;D1])=[O:5]>>[#6:2]-[#7:1]-[#6:4](-[#6:3])=[O:5]

Conversion of .rxn files to reaction SMARTS - Revision history

Iamkaant: Created page with "DataWarrior folks have implemented enumeration protocol in their soft. It is published in 10.1021/acs.jcim.1c01041 They store reactions in .rxn format, which is documented in..."