LigPrep Use of ligfilter

ligfilter is a versatile utility for filtering molecules based on property values and descriptor counts. LigPrep uses ligfilter to filter molecules, usually to eliminate those matching certain conditions (e.g., molecular weight > 650 amu), although other types of filtering are possible. This section briefly documents ligfilter as it is used within LigPrep. See Filtering Structures by Property: ligfilter for details of this utility.

LigPrep does not perform filtering unless the -f option is used, which accepts the name of a file containing criteria to use for filtering. For example, to remove molecules with a molecular weight greater than 650, molecules that have too many hydrogen bond acceptors and donors, and too few atoms, you could create a file with the following content:

# Remove molecules that have a molecular weight of greater than 650
Molecular_weight                         > 650
# Remove molecules with too many H-bond acceptor and donor atoms
Acceptor_groups                          > 3
Donor_groups                             > 3
# Remove molecules with fewer than 10 atoms
Num_atoms                                < 10

The spaces between the descriptors and the conditions are not significant.

The following command filters the input structures using the above file, saved as ligfilter.lff:

ligprep -f ligfilter.lff -isd input.sd -omae output.mae