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comparison docs/scripts/txt/InfoSDFiles.txt @ 0:4816e4a8ae95 draft default tip
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author | deepakjadmin |
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date | Wed, 20 Jan 2016 09:23:18 -0500 |
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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 |