|
1
|
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
|
