Oxygen and nitrogen counts.

Hello,

I would like to count the number of aromatic and aliphatic nitrogens and oxygens in a set of smiles.

Could you suggest the syntax to do this with evaluate please?

Thanks,

Tim Ritchie.

Hi,

Count

- aliphatic nitrogens:

$ evaluate -e "matchCount('N')" "NCc1c[nH]cn1"
1

- aromatic nitrogens:

$ evaluate -e "matchCount('n')" "NCc1c[nH]cn1"
2

- all nitrogens:

$ evaluate -e "matchCount('[#7]')" "NCc1c[nH]cn1"
3

Count oxigens: similarly, use 'O', 'o', and '[#8]'.

Zsolt

Hello,

I tried 

evaluate -e "matchCount('N')" "NCc1c[nH]cn1"

 but I just get syntax errors ("implicit multiplication not enabled").

Any thoughts?

Regards,

Tim Ritchie.

To use matchCount() Chemical Terms function JChem has to be installed (MarvinBeans package does not contain MolSearch). Do you have JChem installed?

Zsolt

 

No, I don't think I have JChem, only Marvin Beans.

I managed to get the desired result by using the count function, filtering on the atomic number, and whether the atoms were aromatic or aliphatic.

Regards,

Tim.