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Descriptors
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Jelica

Joined: 11 Jun 2013
Posts: 2

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Link to postPosted: Tue Aug 20, 2013 8:40 pmPost subject: Descriptors Reply with quote

Can someone tell me how to calculate following molecular descriptors:

 

number of acyclic monovalent nodes, acyclic  (cyclic) divalent nodes, acyclic (cyclic) trivalent nodes,  acyclic (cyclic) tetravalent nodes, atoms shared by fused rings, bonds shared by fused rings, acyclic (cyclic) nitrogen, acyclic (cyclic) oxigen.

Thanks

 

László
ChemAxon personnel
Joined: 14 Jan 2011
Posts: 78

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Link to postPosted: Wed Aug 21, 2013 9:29 pmPost subject: Reply with quote

Dear Jelica,

You can use the following Chemical Terms functions.

//number of acyclic monovalent nodes
evaluate -e "count(filter('valence() == 1'))" test.smiles

//number of acyclic divalent nodes
evaluate -e "count(filter('valence() == 2 && chainAtom()'))" test.smiles

//number of cyclic divalent nodes
evaluate -e "count(filter('valence() == 2 && ringAtom()'))" test.smiles

//number of atoms shared by fused rings
evaluate -e "count(filter('ringCountOfAtom() > 1'))" test.smiles

//number of bonds shared by fused rings
evaluate -e "sum(ringCountOfAtom(filter('ringAtom()'))) - ringBondCount()" test.smiles

//number of acyclic nitrogen
evaluate -e "filter('atno() == 7 && chainAtom()')" test.smiles

//number of cyclic nitrogen
evaluate -e "filter('atno() == 7 && ringAtom()')" test.smiles

See more details:
http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html



Best regards,
Laszlo

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