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NAME

MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)

SYNOPSIS

MolFilesToSD.pl MDLMOLFile(s)...

MolFilesToSD.pl [-c, --compoundid usefileprefix | idlabel] [-d, --datafieldlabel fieldlabel] [-h, --help] [-m, --mode molnameline | datafield | both | none] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] MDLMOLFile(s)...

DESCRIPTION

Generate a SD file from MDLMOL File(s). Multiple file names are separated by spaces. The valid file extension is .mol. All other file names are ignored. All the files in a current directory can be specified by *.mol, or the current directory name.

OPTIONS

-c, --compoundid usefileprefix | idlabel

Specify how to generate compound IDs: use MOL filename prefix or generate a new compound ID by combining idlabel with compound number. Possible values: usefileprefix | idlabel. By default, Cmd is used as a idlabel to generate these types of compound IDs: Cmpd1, Cmpd2 and so on.

Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on, specify "MolID" value for this option.

-d, --datafieldlabel fieldlabel

Specify data field label for adding compound ID field into SD file during datafield | both values of -m, --mode option. Default: <Cmpd_ID>.

-h, --help

Print this help message.

-m, --mode molnameline | datafield | both | none

Specify how to add compopund ID into SD file: relplace the molname line, add a new data field, replace the molname line and add data field, or do nothing. Possible values: molnameline | datafield | both | none. Default: nothing.

Use -c, --compoundid to specify compound ID generation process.

-o, --overwrite

Overwrite existing files.

-r, --root rootname

New SD file name is generated using the root: <Root>.sdf. Default new file name: <InitialMOLFileName>1To<Count>.sdf.

-w, --workingdir dirname

Location of working directory. Default: current directory.

EXAMPLES

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

% MolFilesToSD.pl -r NewSample -o Sample*.mol

To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in MolName line and Cmpd_ID datafield from Sample*.mol files, type:

% MolFilesToSD.pl -r NewSample -m both -o Sample*.mol

AUTHOR

Manish Sud

SEE ALSO

InfoSDFiles.plSDToMolFiles.pl

COPYRIGHT

Copyright (C) 2017 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.

 

 

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