comparison docs/scripts/txt/InfoSDFiles.txt @ 0:4816e4a8ae95 draft default tip

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