view docs/scripts/txt/SDToMolFiles.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

NAME
    SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)

SYNOPSIS
    SDToMolFiles.pl SDFile(s)...

    SDToMolFiles.pl [-d, --DataField DataFieldName] [-m, --mode DataField |
    MolName | RootPrefix] [-h, --help] [-o, --overwrite] [-r, --root
    rootname] [-w, --workingdir dirname] SDFile(s)...

DESCRIPTION
    Generate MDLMOL file(s) from *SDFile(s)*. All header data labels and
    values in SDFile(s) are simply ignored; other appopriate data from
    SDFile(s) is transferred to MDLMOL files. Multiple *SDFile(s)* 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
    -d, --DataField *DataFieldName*
        Specify *SDFile(s)* datafield label name whose value is used for
        generation of MDLMOL file names. Default value: *None*.

    -h, --help
        Print this help message.

    -m, --mode *DataField | MolName | RootPrefix*
        Specify how to generate MDLMOL file names: use a *SDFile(s)*
        datafield value; use molname line from *SDFile(s)*; generate a
        sequential ID using root prefix specified by -r, --root option.

        Possible values: *DataField | MolName | RootPrefix | RootPrefix*.
        Default: *RootPrefix*.

        For empty *MolName* and *DataField* values during these specified
        modes, file name is automatically generated using *RootPrefix*.

        For *RootPrefix* value of -m, --mode option, MDLMOL file names are
        generated using by appending compound record number to value of -r,
        --root option. For example: *RootName*Cmd<RecordNumber>.mol.

        Allowed characters in file names are: a-zA-Z0-9_. All other
        characters in datafield values, molname line, and root prefix are
        ignore during generation of file names.

    -o, --overwrite
        Overwrite existing files.

    -r, --root *rootname*
        Specify root name to used during *RootPrefix* -m, --mode option
        value. New MDLMOL file names are generated using the root:
        <Root>Cmpd<RecordNumber>.mol Default for new file names:
        <InitialSDFileName>Cmpd<RecordNumber>.mol. This option is ignored
        for multiple input files.

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

EXAMPLES
    To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:

        % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd

    To generate Sample*.mol files from Sample1.sdf, type:

        % SDToMolFiles.pl -r Sample -o Sample1.sdf

    To generate MOL files from Sample1.sdf using molname line data for
    generating MOL file names, type:

        % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf

    To generate MOL files from Sample1.sdf using a specific data field
    values for generating MOL file names, type:

        % SDToMolFiles.pl -m DataField --DataField MolID -r Sample
          -o Sample1.sdf

AUTHOR
AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    InfoSDFiles.pl, MolFilesToSD.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.