Calculate fraction of sp3 atoms

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Andrew Orry

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Sep 22, 2020, 11:46:51 AM9/22/20
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Q. How to calculate the fraction of the saturated (sp3) parts of a chemical (as opposed to aromatic)?
A.

You can calculate fraction of sp3 atoms in command line for a table 't'

add column t Rarray(Nof(t.mol,"[!H;^3]")) / Nof( t.mol, "[!H]" ) name="sp3_fract"

In GUI you can do this in few steps:

  • Add column with number of sp3 atoms (right click -> Insert Column Dialog -> Chemistry -> Nof_Atoms ->paste [!H;^3] into atom smarts)
  • Add column with total number of heavy atoms in similar way
  • Add ratio using 'Insert Column Dialog -> Arithmetic -> / )

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