1. Signature Translator Download

The translator program translates various molecular file formats, in particular, it can be used to output a signature format. This program is provided as is and no responsibility will be taken from the author or Sandia National Labs. Bugs may be reported by e-mailing the author.The signature translator is a suite of codes (C, C++, and Perl), written for use on a Unix machine. This download contains the signature translator as well as a SMILES to signature converter.

Signature Translator (~2.0 MB)
READ-ME
 

Installation Instructions

Translator

  1. Change to the directory containing the translator.tar.gz archive. Unzip the file and type the following to un-tar the archive:
    2. tar -xf translator.tar
  2. Change to the subdirectory containing the source code:
    3. cd src
  3. Make the executables tra and convert2mol
    4. make
  4. Alternatively tra and convert2mol can be generated
    5. cd src/smilestra
    make
  5. Verify creation of the executables tra and convert2mol and install into the local search path
    6. ls ../bin

Additional Instructions for Converting from SMILES to Signature

  1. To translate a SMILES string into Signature:

    2. scan_smiles -s "smiles_string" signature_heightoutput_header

    Example: scan_smiles "c1ccccc1" 2 benzene

    The height-2 signature for benzene will be placed in the file benzene.scan2
  2. To translate a file containing a series of SMILES strings:

    3. scan_smiles [-m] input_file.smi signature_heightoutput_header

    Example: scan_smiles database.smi 1 esters

    The height-1 signature for the SMILES strings contained in database.smi will be output as a series of files esters.00000.scan1, esters.00001.scan1, ...
    Example: scan_smiles -m database.smi 1 esters  
    The height-1 signature for the SMILES strings contained in database.smi will be output as a series of files based on the molecule names specified in the input file: esters.aspirin.scan1, esters.butylbenzoate.scan1, ...
    The input file should contain 1 SMILES string per line with an optional molecule name following the SMILES string. Comments and blank lines are not allowed (except at the end of the file). The input file must have the .smi extension. For detailed instruction on SMILES conversion, see the convert2mol man page in the doc directory.

2. Molecular Canonizer Download

The same translator program can also be used to canonize molecular structures. Download and install the following code and read the README.canonize file.

Signature Translator (~2.0 MB)


3. Protein Signature Products and Protein-Protein Interaction Prediction Download

Protein signature and Protein-Protein Interaction Predictor


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jfaulon@sandia.gov
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