Query properties in molecule file formats

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

NameMDL MolfileSMARTS MarvinSketch
any atom yes (A)yes (*) queryAtoms=any
heteroatom yes (Q)yes (!C!H) queryAtoms=hetero
atom list yesyes queryAtoms=list
NOT list yesyes queryAtoms=notlist
valenceyesyes (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 yesyes (~) extraBonds=any
single or double yesnot in Marvin extraBonds=1or2
single or aromatic yesnot in Marvin extraBonds=aromany
double or aromatic yesnot in Marvin extraBonds=aromany
single up or down yesnot in Marvin extraBonds=either
double cis or trans yesyes extraBonds=either
double cis or unspecified yesyes extraBonds=ctu
double trans or unspecified yesyes extraBonds=ctu
"ring" bond yesno extraBonds=topology
"chain" bond yesno extraBonds=topology

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