OpenEye Scientific Software’s nam2mol application converts chemical compound names into molecular structures.

Command Line Interface

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

prompt> nam2mol --help

will generate the following output:

nam2mol - Name to Structure Conversion
OpenEye Scientific Software
   Version: 2.1.0
   Built: <build date>
   Platform: <platform>

Help functions:
  nam2mol --help simple      : Get a list of simple parameters
  nam2mol --help all         : Get a complete list of parameters
  nam2mol --help defaults    : List the defaults for all parameters
  nam2mol --help <parameter> : Get detailed help on a parameter
  nam2mol --help html        : Create an html help file for this program

Required Parameters

-in <filename>
The input file on the command line is assumed to be a compound name file in ASCII text format, and the optional output filename is treated as the output molecule file. If no output file is specified, molecules will be written to stdout in SMILES format.

Command Line Options

-out <filename>

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; .oeb for OEBinary; .mmod for Macromodel; .sln for Sybyl line notation; .mol2 for Tripos .mol2 files; .pdb for PDB format files, etc...

File type Extension
SMILES .smi .ism .can
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz
-language <lang>

Parse the input file based on the specified language. The default is English. Either the full name or synonym can be used. -language dutch and -language nl are equivalent.

Language Option Synonyms   Language Option Synonyms
English american english us   Italian italian it
British british uk   Japanese japanese jp ja
Chinese chinese zh cn   Polish polish pl
Danish danish dk da   Portuguese portuguese pt
Dutch dutch nl   Romanian romanian ro
French french fr   Russian russian ru
German german de   Slovak slovak sk
Greek greek el   Spanish spanish es
Hungarian hungarian hu   Swedish swedish se sv
Irish irish ie ga   Welsh welsh cy

[default = american]

Write an empty connection table whenever unable to parse an input line. This function is useful for keeping track of which names were converted, as the output file is guaranteed to have the same number of connection tables as there were lines in the input file.
Use dots to show program progress.
When writing output files that contain co-ordinates, this command line option can be used to generate suitable 2D co-ordinate depictions, provided that the OpenEye OEDepict toolkit is appropriately licensed.
Specify the tag field name to be used when writing MDL SD files. Normally, the original name is recorded in the title field of each output connection table. However, for MDL SD files the title is truncated to a maximum of 80 characters. This option allows the full name to additionally be written as a field to the file. For example, -tag name writes the name in the <name> data field.

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