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 |
|
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.