Converting Names to Molecules

Converts a file of chemical names (specified by the -in option) of a specific language (-language option) into a file of chemical structures (specified by the -out option).

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> java Nam2Mol_example --help

will generate the following output:

Simple parameter list

  nam2mol
    I/O
      -in : Input filename
      -out : Output filename

    Lexichem
      -language : Language for input names.
      -tag : Set name as SD data with tag
      -empty : Output an empty molecule for unparseable names
      -charset : Choose charset/encoding for input names.

Code

Download code

Nam2Mol_example.java and Nam2Mol_example.txt interface file