Query Properties in Molecule File Formats

Query properties are supported in Molfiles and SMILES/SMARTS files. The following table shows the details.

Name

MDL Molfile

SMARTS

MarvinSketch
parameter

any atom

yes (A)

yes (*)

queryAtoms=any

heteroatom

yes (Q)

yes (!C!H)

queryAtoms=hetero

atom list

yes

yes

queryAtoms=list

NOT list

yes

yes

queryAtoms=notlist

valence

yes

yes (v)

queryAtoms=val

hydrogens

no (extension)

yes (H)

queryAtoms=H

connections

no (extension)

yes (X)

queryAtoms=conn

rings

no (extension)

yes (R)

queryAtoms=rings

smallest ring size

no (extension)

yes (r)

queryAtoms=srs

aromatic atom

no (extension)

yes (a)

queryAtoms=arom

aliphatic atom

no (extension)

yes (A)

queryAtoms=arom

any bond

yes

yes (~)

extraBonds=any

single or double

yes

yes (-,=)

extraBonds=1or2

single or aromatic

yes

yes (-,:)

extraBonds=aromany

double or aromatic

yes

yes (=,:)

extraBonds=aromany

single up or down

yes

not in Marvin

extraBonds=either

double cis or trans

yes

yes

extraBonds=either

double cis or unspecified

yes

yes

extraBonds=ctu

double trans or unspecified

yes

yes

extraBonds=ctu

"ring" bond

yes

yes (@)

extraBonds=topology

"chain" bond

yes

yes([email protected])

extraBonds=topology

Extensions: Marvin generated Molfiles and Compressed Molfiles to support extra SMARTS properties also.