2.1 Command Line Interface

A description of the command line interface can be obtained by executing nam2mol with no arguments.

prompt> nam2mol

will generate the following output:

nam2mol v1.8  Name to Structure Conversion
OpenEye Scientific Software, May 2008

usage:  nam2mol [options] <namfile> [<outfile>]
        -empty: Output an empty molecule for unparseable names
        -depict: Generate 2D co-ordinates (if licensed)
        -tag: Set name as SD data with tag
        -de: Parse German compound names
        -es: Parse Spanish compound names
        -ja: Parse Japanese compound names
        -sv: Parse Swedish compound names

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 file on the command line is assumed to be compound name file in ASCII text format, and the optional second filename is treated as the output molecule 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.

The file format of the output file is automatically determined from the file extension. The extensions .smi, .can and .ism may be used to specify SMILES format, .sdf, .mdl and .mol can be used to specify MDL connection table file formats, .sln for Sybyl line notation, .mol2 for Tripos .mol2 files, .pdb for PDB format files, etc...

				Lexichem Chemical Name to Structure and Structure to Name Conversion