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.