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 to support extra SMARTS properties also.