A description of the command line interface can be obtained by executing FILTER with the --help option.
prompt> filter --help
will generate the following output:
Help functions: filter --help simple : Get a list of simple parameters filter --help all : Get a complete list of parameters filter --help <parameter> : Get detailed help on a parameter filter --help html : Create an html help file for this program
This section has a series of example FILTER command-line executions. Each example is followed by a brief description of its behavior.
prompt> filter drugs.smi drugs.oeb.gz prompt> filter -in drugs.smi -out drugs.oeb.gz
These two commands will yield identical results. These execute FILTER with the default parameters. The file drugs.smi is opened in SMILES format for input, and the output is written to the file drugs.oeb.gz in gzipped OEBinary version 2 format.
prompt> filter -in drugs.smi -out drugs.sdf -filter myfilter
This command is the same as the one above except for the -filter flag. It executes FILTER with the parameters found in the myfilter file. The file drugs.smi is opened in SMILES format for input, and the output is written to the file drugs.oeb.gz in gzipped OEBinary version 2 format.
prompt> filter -param myparameters drugs.smi drugs.oeb.gz prompt> filter drugs.smi drugs.oeb.gz -param myparameters
The first of these two commands will yield exactly the same results as the example above. The file drugs.smi will be mapped to the -in flag and drugs.oeb.gz will be mapped to the -out flag being the second to last and last command-line arguments respectively. Unfortunately, the second of these two commands, will fail to parse because the implicit input and output arguments are not the final two arguments in the list.
prompt> filter -in drugs.smi -out drugs.oeb.gz -table drugs.table
This executes FILTER on the file drugs.smi and writes molecules that pass the filter to the file drugs.oeb.gz. It also writes the all of the filter data to the tab-separated value file drugs.table.
prompt> cat maybridge.05-1.sdf |filter -in .sdf -out .ism|omega .ism m.oeb.gz
This command presumes that you have an SD format file called maybridge.05-1.sdf. That file is piped to the FILTER program. The -in .sdf flag indicates that FILTER should read .sdf format from std::in. Since no -filter flag is specified, the default filter will be used. The -out .ism flag indicates FILTER will write isomeric smiles format to std::out. The output would then be piped into OMEGA.
prompt> filter -in drugs.smi -out drugs.oeb.gz -select "[N;$(*-a)]"
This command will filter the compounds in drugs.smi with the default filter and write the output to drugs.oeb.gz. It also requires that molecules contain exactly one instance of the aniline substructure defined by the SMARTS pattern “[N;$(*-a)]”.