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1 NAME
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2 MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)
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3
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4 SYNOPSIS
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5 MolFilesToSD.pl MDLMOLFile(s)...
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6
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7 MolFilesToSD.pl [-c, --compoundid usefileprefix | idlabel] [-d,
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8 --datafieldlabel fieldlabel] [-h, --help] [-m, --mode molnameline |
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9 datafield | both | none] [-o, --overwrite] [-r, --root rootname] [-w,
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10 --workingdir dirname] MDLMOLFile(s)...
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11
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12 DESCRIPTION
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13 Generate a SD file from *MDLMOL File(s)*. Multiple file names are
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14 separated by spaces. The valid file extension is *.mol*. All other file
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15 names are ignored. All the files in a current directory can be specified
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16 by **.mol*, or the current directory name.
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17
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18 OPTIONS
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19 -c, --compoundid *usefileprefix | idlabel*
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20 Specify how to generate compound IDs: use MOL filename prefix or
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21 generate a new compound ID by combining *idlabel* with compound
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22 number. Possible values: *usefileprefix | idlabel*. By default,
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23 *Cmd* is used as a *idlabel* to generate these types of compound
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24 IDs: Cmpd1, Cmpd2 and so on.
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25
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26 Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on,
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27 specify "MolID" value for this option.
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28
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29 -d, --datafieldlabel *fieldlabel*
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30 Specify data field label for adding compound ID field into SD file
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31 during *datafield | both* values of -m, --mode option. Default:
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32 <Cmpd_ID>.
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33
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34 -h, --help
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35 Print this help message.
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36
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37 -m, --mode *molnameline | datafield | both | none*
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38 Specify how to add compopund ID into SD file: relplace the molname
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39 line, add a new data field, replace the molname line and add data
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40 field, or do nothing. Possible values: *molnameline | datafield |
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41 both | none*. Default: *nothing*.
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42
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43 Use -c, --compoundid to specify compound ID generation process.
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44
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45 -o, --overwrite
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46 Overwrite existing files.
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47
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48 -r, --root *rootname*
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49 New SD file name is generated using the root: <Root>.sdf. Default
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50 new file name: <InitialMOLFileName>1To<Count>.sdf.
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51
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52 -w, --workingdir *dirname*
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53 Location of working directory. Default: current directory.
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54
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55 EXAMPLES
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56 To generate NewSample.sdf file from Sample*.mol files, type:
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57
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58 % MolFilesToSD.pl -r NewSample -o Sample*.mol
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59
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60 To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in
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61 MolName line and Cmpd_ID datafield from Sample*.mol files, type:
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62
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63 % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol
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64
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65 AUTHOR
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66 Manish Sud <msud@san.rr.com>
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67
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68 SEE ALSO
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69 InfoSDFiles.pl, SDToMolFiles.pl
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70
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71 COPYRIGHT
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72 Copyright (C) 2015 Manish Sud. All rights reserved.
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73
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74 This file is part of MayaChemTools.
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75
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76 MayaChemTools is free software; you can redistribute it and/or modify it
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77 under the terms of the GNU Lesser General Public License as published by
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78 the Free Software Foundation; either version 3 of the License, or (at
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79 your option) any later version.
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