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1 NAME
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2 SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)
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3
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4 SYNOPSIS
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5 SDToMolFiles.pl SDFile(s)...
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6
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7 SDToMolFiles.pl [-d, --DataField DataFieldName] [-m, --mode DataField |
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8 MolName | RootPrefix] [-h, --help] [-o, --overwrite] [-r, --root
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9 rootname] [-w, --workingdir dirname] SDFile(s)...
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10
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11 DESCRIPTION
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12 Generate MDLMOL file(s) from *SDFile(s)*. All header data labels and
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13 values in SDFile(s) are simply ignored; other appopriate data from
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14 SDFile(s) is transferred to MDLMOL files. Multiple *SDFile(s)* names are
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15 separated by spaces. The valid file extensions are *.sdf* and *.sd*. All
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16 other file names are ignored. All the SD files in a current directory
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17 can be specified either by **.sdf* or the current directory name.
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18
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19 OPTIONS
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20 -d, --DataField *DataFieldName*
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21 Specify *SDFile(s)* datafield label name whose value is used for
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22 generation of MDLMOL file names. Default value: *None*.
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23
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24 -h, --help
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25 Print this help message.
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26
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27 -m, --mode *DataField | MolName | RootPrefix*
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28 Specify how to generate MDLMOL file names: use a *SDFile(s)*
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29 datafield value; use molname line from *SDFile(s)*; generate a
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30 sequential ID using root prefix specified by -r, --root option.
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31
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32 Possible values: *DataField | MolName | RootPrefix | RootPrefix*.
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33 Default: *RootPrefix*.
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34
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35 For empty *MolName* and *DataField* values during these specified
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36 modes, file name is automatically generated using *RootPrefix*.
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37
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38 For *RootPrefix* value of -m, --mode option, MDLMOL file names are
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39 generated using by appending compound record number to value of -r,
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40 --root option. For example: *RootName*Cmd<RecordNumber>.mol.
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41
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42 Allowed characters in file names are: a-zA-Z0-9_. All other
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43 characters in datafield values, molname line, and root prefix are
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44 ignore during generation of file names.
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45
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46 -o, --overwrite
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47 Overwrite existing files.
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48
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49 -r, --root *rootname*
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50 Specify root name to used during *RootPrefix* -m, --mode option
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51 value. New MDLMOL file names are generated using the root:
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52 <Root>Cmpd<RecordNumber>.mol Default for new file names:
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53 <InitialSDFileName>Cmpd<RecordNumber>.mol. This option is ignored
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54 for multiple input files.
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55
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56 -w, --workingdir *dirname*
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57 Location of working directory. Default: current directory.
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58
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59 EXAMPLES
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60 To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:
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61
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62 % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd
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63
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64 To generate Sample*.mol files from Sample1.sdf, type:
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65
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66 % SDToMolFiles.pl -r Sample -o Sample1.sdf
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67
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68 To generate MOL files from Sample1.sdf using molname line data for
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69 generating MOL file names, type:
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70
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71 % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf
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72
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73 To generate MOL files from Sample1.sdf using a specific data field
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74 values for generating MOL file names, type:
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75
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76 % SDToMolFiles.pl -m DataField --DataField MolID -r Sample
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77 -o Sample1.sdf
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78
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79 AUTHOR
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80 AUTHOR
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81 Manish Sud <msud@san.rr.com>
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82
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83 SEE ALSO
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84 InfoSDFiles.pl, MolFilesToSD.pl
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85
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86 COPYRIGHT
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87 Copyright (C) 2015 Manish Sud. All rights reserved.
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88
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89 This file is part of MayaChemTools.
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90
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91 MayaChemTools is free software; you can redistribute it and/or modify it
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92 under the terms of the GNU Lesser General Public License as published by
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93 the Free Software Foundation; either version 3 of the License, or (at
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94 your option) any later version.
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95
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