3.2 Example executions

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. drugs.smi will be mapped to the -in flag and drugs.oeb.gz will be mapped to the -out flag begin 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 a sd format file called "maybridge.05-1.sdf". That file is 'cat'ed and 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)]".

				FILTER Database preparation Property calculation

				FILTER Database preparation Property calculation