Required Parameters

-query <filename>

File containing molecules or a single grid to use a shape query.

For molecule queries, available formats (and file extensions) include:

File type Extension
OEBinary .oeb .oeb.gz
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz

For grid queries, available formats (and file extensions) include:

Grid File type Extension
OpenEye .grd
Grasp .phi
CCP4 .map .ccp4
XPLOR .xplor .xplmap
ASCII Grid .agd

For shape queries, only available format and file extension is:

Shape Query type Extension
OpenEye .sq
-dbase <filename>

File containing one or more 3D molecules to overlay against query from above. This flag supports all the same molecule file formats (not grids or shape queries) as -query plus the ROCS DB format .rocsdb and the list file (.lst or .list) as described in the The Database File section.