2.1 Command Line Interface

A description of the command line interface can be obtained by executing mdl2sma with no arguments.

prompt> mdl2sma

will generate the following output:

MDL2SMA v1.1  Query Format Conversion
OpenEye Scientific Software, December 2005

usage:  mdl2sma [options] <infile> [<outfile>]

options: -a  Aromatic atoms and bonds must be aromatic
         -A  Aliphatic atoms must be aliphatic
         -B  Aliphatic bonds must be aliphatic
         -r  Only ring bonds can match in rings
         -i  Allow matching of implicit hydrogens

Command line options are distinguished from filenames by having a `-' prefix. Options can appear anywhere on the command line, i.e. before, after or in between filenames. When incompatible options are specified the last one given on the command line takes effect.

The first filename given on the command line is taken to be the input MDL query file, and the optional second filename is treated as the output SMARTS file. A minus character may be used in place of the input filename to specify that the input is to be read from standard input, stdin, and in place of the output filename to specify that the output is to be written to standard output, stdout. If only one filename is specified on the command line, the output is written to stdout by default.

-a: This option requires that atoms and bonds that are aromatic in the input file, must be aromatic in the matched molecule. Because a substructure query only specifies part of a molecule, a Kekulé substructure that is aromatic in the query may match molecules in which that substructure is aliphatic, typically by substitution or non-neutral charge states.
-A: This option requires that atoms that are non-aromatic in the query, must be non-aromatic in the matched molecule. Because a substructure query only specifies part of a molecule, a Kekulé substructure that is not aromatic in the query may match molecules in which that substructure is aromatic, typically by substitution or non-neutral charge states.
-B: This option requires that bonds that are non-aromatic in the query, must be non-aromatic in the matched molecule.
-r: This option requires that acyclic bonds in the query must be acyclic in the matched molecule.

				SMACK Substructure Query Conversion Tools

				SMACK Substructure Query Conversion Tools