mol2nam

OpenEye Scientific Software’s mol2nam application converts molecular structures into reasonable chemical names.

Command Line Interface

A description of the command line interface can be obtained by executing mol2nam with the -help option.

prompt> mol2nam --help

will generate the following output:

mol2nam - Structure to Name Conversion
OpenEye Scientific Software
   Version: 2.1.0
   Built: <build date>
   Platform: <platform>

Help functions:
  mol2nam --help simple      : Get a list of simple parameters
  mol2nam --help all         : Get a complete list of parameters
  mol2nam --help defaults    : List the defaults for all parameters
  mol2nam --help <parameter> : Get detailed help on a parameter
  mol2nam --help html        : Create an html help file for this program

Required Parameters

-in <filename>

The input file can be in any of a number of popular connection table formats. If no output file is specified, the program writes one name per line, for each connection table in the input file, to standard output (stdout). If an output file is specified with -out, it is treated as the output molecule file, and each of the input molecules are written to it, with the title of each record set to the assigned name.

The file format of the input 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

To read from stdin (via a pipe), use the file extension that corresponds to the input stream. For example, to pipe in SMILES, use: -in .smi.

Command Line Options

-out <filename>
Output molecule file. The title of each molecule will be set to the generated name. Output formats are the same as available for -in.
-style <name style>

Determines the name style of generated names. By default, mol2nam uses the OpenEye name style. Styles include:

autonom
Attempt to generate MDL/Beilstein AutoNom-like names. MDL’s AutoNom normally generates capitalized names, which can be controlled via the -capitalize command line option.
cas
Attempt to generate CAS-like names, as used by the Chemical Abstracts Service (CAS).
casidx
Attempt to generate CAS permuted index-like names, as used by the Chemical Abstracts Service (CAS).
iupac
Attempt to generate the Preferred IUPAC Name (PIN) of a compound as defined by the IUPAC2005 standard.
iupac79
Attempt to generate an IUPAC 1979-style name.
iupac93
Attempt to generate an IUPAC 1993-style name.
openeye
Attempt to generate an OpenEye-style name. [default]
traditional
Attempt to generate traditional, common or archaic names for a compound.
systematic
Attempt to generate (fully) systematic names.

[default = openeye]

-capitalize

Capitalize the appropriate letter of the generated name.

[default = false]

-language <lang>

Determines the output language of generated names. 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]

-charset <charset>
-encoding <charset>
ascii
Encode the output using ASCII.
eucjp
Encode the output using EUC-JP to represent Japanese characters. This is normally used in conjunction with the -language japanese command line option.
html
Encode the output using HTML markup to represent Greek characters, foreign characters and superscripts.
sjis
Encode the output using Shift-JIS to represent Japanese characters. This is normally used in conjunction with the -language japanese command line option.
utf8
Encode the output using UTF-8.

[default = ascii]

-delim
By default, the connection tables written to the output file have their title replaced with the generated compound name. However, if the -delim option is given followed by a delimiter string, the name is appended to the original title separated by the specified delimiter.
-tag
When the output file is to be written in MDL SD file format, also write the compound name in the specified data tag.

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