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(!@) extraBonds=topology

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