NAME
    RDKitConvertFileFormat.py - Convert between molecular file formats

SYNOPSIS
    RDKitConvertFileFormat.py [--infileParams <Name,Value,...>] [
    --outfileParams <Name,Value,...> ] [--overwrite] [-w <dir>] -i <infile>
    -o <outfile>

    RDKitConvertFileFormat.py -h | --help | -e | --examples

DESCRIPTION
    Convert between molecular file formats.

    The supported input file formats are: Mol (.mol), SD (.sdf, .sd), SMILES
    (.smi, .txt, .csv, .tsv), MOL2 (.mol2), PDB (.pdb)

    The supported output file formats are: SD (.sdf, .sd), SMILES (.smi),
    PDB (.pdb)

OPTIONS
    -e, --examples
        Print examples.

    -h, --help
        Print this help message.

    -i, --infile <infile>
        Input file name.

    --infileParams <Name,Value,...> [default: auto]
        A comma delimited list of parameter name and value pairs for reading
        molecules from files. The supported parameter names for different
        file formats, along with their default values, are shown below:

            SD, MOL: removeHydrogens,yes,sanitize,yes,strictParsing,yes
            MOL2: removeHydrogens,yes,sanitize,yes
            SMILES: smilesColumn,1,smilesNameColumn,2,smilesDelimiter,space,
                smilesTitleLine,auto,sanitize,yes
            PDB: removeHydrogens,yes,sanitize,yes

        Possible values for smilesDelimiter: space, comma or tab.

    -o, --outfile <outfile>
        Output file name.

    --outfileParams <Name,Value,...> [default: auto]
        A comma delimited list of parameter name and value pairs for writing
        molecules to files. The supported parameter names for different file
        formats, along with their default values, are shown below:

            SD: compute2DCoords,auto,kekulize,no
            SMILES: kekulize,no,smilesDelimiter,space, smilesIsomeric,yes,
                smilesTitleLine,yes

        Default value for compute2DCoords: yes for SMILES input file; no for
        all other file types.

    --overwrite
        Overwrite existing files.

    -w, --workingdir <dir>
        Location of working directory which defaults to the current
        directory.

EXAMPLES
    To convert a SD file into a isomeric SMILES file, type:

        % RDKitConvertFileFormat.py -i Sample.sdf -o SampleOut.smi

    To convert a SD file into a non isomeric SMILES file, type

        % RDKitConvertFileFormat.py --outfileParams "smilesIsomeric,no"
          -i Sample.sdf -o SampleOut.smi

    To convert a SMILES file into a SD file along with calculation of 2D
    coordinates, type:

        % RDKitConvertFileFormat.py -i Sample.smi -o SampleOut.sdf

    To convert a MDL MOL file into a PDB file, type:

        % RDKitConvertFileFormat.py -i Sample.mol -o SampleOut.pdb

    To convert a CSV SMILES file with column headers, SMILES strings in
    column 1, and name in column 2 into a SD file containing 2D coordinates,
    type:

        % RDKitConvertFileFormat.py --infileParams "smilesDelimiter,comma,
          smilesTitleLine,yes,smilesColumn,1,smilesNameColumn,2" -i Sample.csv
          -o SampleOut.sdf

AUTHOR
    Manish Sud(msud@san.rr.com)

SEE ALSO
    RDKitDrawMolecules.py, RDKitRemoveDuplicateMolecules.py,
    RDKitSearchFunctionalGroups.py, RDKitSearchSMARTS.py

COPYRIGHT
    Copyright (C) 2018 Manish Sud. All rights reserved.

    The functionality available in this script is implemented using RDKit,
    an open source toolkit for cheminformatics developed by Greg Landrum.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.

