NAME
    FilterSDFiles.pl - Filter compounds from SDFile(s)

SYNOPSIS
    FilterSDFiles.pl SDFile(s)...

    FilterSDFiles.pl [-a, --all] [-e, --empty] [-c, --cleansalts] [-h,
    --help] [-k, --keep] [-m, --mismatch] [-o, --overwrite] [-r, --root
    *rootname*] [-s, --salts] [-u, --unknownatoms] [-w, --workingdir
    *dirname*] SDFile(s)...

DESCRIPTION
    Filter specific compounds from *SDFile(s)*. Available choices are: wash
    or remove compounds with salts; take out compounds with no structural
    data; remove compounds with mismatched atom/bond blocks data; remove
    compounds which contain uknown atoms and so on. Multiple SDFile names
    are separated by spaces. The valid file extensions are *.sdf* and *.sd*.
    All other file names are ignored. All the SD files in a current
    directory can be specified either by **.sdf* or the current directory
    name.

OPTIONS
    -a, --all
        Use all options to filter compounds.

    -e, --empty
        Filter compounds with empty atom/bond blocks. This is default
        behavior.

    -c, --cleansalts
        Wash compounds which contain salts identified as disconnected
        structural units. The largest fragment is kept.

    -h, --help
        Print this help message.

    -k, --keep
        Keep the compounds which were filtered in a separate file. Default:
        Just ignore these compounds. Option -r --root is used to generate
        the new file name: <Root>Ignored.sdf. Default file name:
        <SDFileName>Ignored.sdf.

    -m, --mismatch
        Remove compounds with mismatched atom/bond blocks and counts line
        information specified by header block.

    -o, --overwrite
        Overwrite existing files.

    -r, --root *rootname*
        New SD file name is generated using the root: <Root>.sdf. Default
        file name:<SDFileName>Filtered.sdf. This option is ignored for
        multiple input files.

    -s, --salts
        Remove compounds which contain salts identified as disconnected
        structural units.

    -u, --unknownatoms
        Remove compounds with atom blocks containing special atom symbols
        such as L, Q, * ,LP, X, R#, or any other non periodic table symbols.

    -w, --workingdir *dirname*
        Location of working directory. Default: current directory.

EXAMPLES
    To remove compounds from SD files which contain salts, unknown atoms, or
    mismatched atom/bonds block data or no structural data, type:

        % FilterSDFiles.pl -a -o Sample.sdf
        % FilterSDFiles.pl -a -o *.sdf

    And to generate a new NewSampleIgnored.sdf file for filtered compounds,
    type:

        % FilterSDFiles.pl -a -k -r NewSample -o Sample.sdf

    To wash compounds in order to get rid of all disconnected fragments
    except for the largest one, type:

        % FilterSDFiles.pl -c -o Sample.sdf

AUTHOR
    Manish Sud <msud@san.rr.com>

SEE ALSO
    ExtractFromSDFiles.pl, InfoSDFiles.pl, MergeTextFilesWithSD.pl

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    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.

