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1 NAME
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2 InfoSDFiles.pl - List information about SDFile(s)
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3
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4 SYNOPSIS
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5 InfoSDFile.pl SDFile(s)...
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6
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7 InfoSDFile.pl [-a --all] [-c --count] [--chiral] [--datacheck] [-d
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8 --detail infolevel] [-e --empty] [-f, --fields] [-h, --help] [-i,
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9 --invalidatomnumbers] [-m, --mismatch] [-s, --salts] [-u,
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10 --unknownatoms] [-w, --workingdir dirname] SDFile(s)...
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11
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12 DESCRIPTION
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13 List information about *SDFile(s)* contents: number of compounds, empty
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14 records and so on. Multiple SDFile names are separated by spaces. The
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15 valid file extensions are *.sdf* and *.sd*. All other file names are
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16 ignored. All the SD files in a current directory can be specified either
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17 by **.sdf* or the current directory name.
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18
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19 OPTIONS
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20 -a, --all
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21 List all the available information.
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22
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23 -c, --count
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24 List number of compounds. This is default behavior.
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25
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26 --chiral
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27 List number of empty atom/bond blocks for compounds with chiral flag
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28 set in count line.
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29
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30 -d, --detail *infolevel*
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31 Level of information to print. Default: 1. Possible values: *1, 2,
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32 or 3*.
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33
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34 --datacheck
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35 List number of numerical and non-numerical values for each data
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36 field.
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37
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38 -e, --empty
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39 List number of empty atom/bond blocks and data fields for compounds.
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40
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41 -f, --fields
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42 List data field labels present for compounds.
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43
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44 -h, --help
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45 Print this help message.
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46
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47 -i, --invalidatomnumbers
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48 List number of bond blocks for compounds which contain invalid atom
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49 numbers.
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50
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51 -m, --mismatch
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52 List number of atom/bond blocks for compounds which don't match with
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53 counts line information in header block.
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54
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55 -s, --salts
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56 List number of atom blocks for compounds which contain salts
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57 identified as disconnected structural units.
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58
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59 -u, --unknownatoms
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60 List number of atom blocks for compounds which contain special atom
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61 symbols such as L, Q, * ,LP, X, R#, or any other non periodic table
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62 symbols.
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63
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64 -w, --workingdir *dirname*
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65 Location of working directory. Default: current directory.
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66
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67 EXAMPLES
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68 To count compounds in SD file(s), type:
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69
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70 % InfoSDFiles.pl Sample1.sdf
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71 % InfoSDFiles.pl Sample1.sdf Sample2.sdf
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72 % InfoSDFiles.pl *.sdf
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73
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74 To list all available information for SD file(s), type:
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75
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76 % InfoSDFiles.pl -a *.sdf
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77
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78 To list all data fields present in sample.sdf, type:
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79
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80 % InfoSDFiles.pl -f Sample.sdf
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81
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82 To count number of compounds which contain salts and list associated
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83 structural data, type:
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84
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85 % InfoSDFiles.pl -s -d 3 Sample.sdf
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86
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87 AUTHOR
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88 Manish Sud <msud@san.rr.com>
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89
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90 SEE ALSO
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91 ExtractFromSDFiles.pl, FilterSDFiles.pl, MergeTextFilesWithSD.pl
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92
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93 COPYRIGHT
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94 Copyright (C) 2015 Manish Sud. All rights reserved.
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95
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96 This file is part of MayaChemTools.
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97
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98 MayaChemTools is free software; you can redistribute it and/or modify it
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99 under the terms of the GNU Lesser General Public License as published by
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100 the Free Software Foundation; either version 3 of the License, or (at
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101 your option) any later version.
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102
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