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

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date Wed, 20 Jan 2016 09:23:18 -0500
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1 NAME
2 SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)
3
4 SYNOPSIS
5 SDToMolFiles.pl SDFile(s)...
6
7 SDToMolFiles.pl [-d, --DataField DataFieldName] [-m, --mode DataField |
8 MolName | RootPrefix] [-h, --help] [-o, --overwrite] [-r, --root
9 rootname] [-w, --workingdir dirname] SDFile(s)...
10
11 DESCRIPTION
12 Generate MDLMOL file(s) from *SDFile(s)*. All header data labels and
13 values in SDFile(s) are simply ignored; other appopriate data from
14 SDFile(s) is transferred to MDLMOL files. Multiple *SDFile(s)* names are
15 separated by spaces. The valid file extensions are *.sdf* and *.sd*. All
16 other file names are ignored. All the SD files in a current directory
17 can be specified either by **.sdf* or the current directory name.
18
19 OPTIONS
20 -d, --DataField *DataFieldName*
21 Specify *SDFile(s)* datafield label name whose value is used for
22 generation of MDLMOL file names. Default value: *None*.
23
24 -h, --help
25 Print this help message.
26
27 -m, --mode *DataField | MolName | RootPrefix*
28 Specify how to generate MDLMOL file names: use a *SDFile(s)*
29 datafield value; use molname line from *SDFile(s)*; generate a
30 sequential ID using root prefix specified by -r, --root option.
31
32 Possible values: *DataField | MolName | RootPrefix | RootPrefix*.
33 Default: *RootPrefix*.
34
35 For empty *MolName* and *DataField* values during these specified
36 modes, file name is automatically generated using *RootPrefix*.
37
38 For *RootPrefix* value of -m, --mode option, MDLMOL file names are
39 generated using by appending compound record number to value of -r,
40 --root option. For example: *RootName*Cmd<RecordNumber>.mol.
41
42 Allowed characters in file names are: a-zA-Z0-9_. All other
43 characters in datafield values, molname line, and root prefix are
44 ignore during generation of file names.
45
46 -o, --overwrite
47 Overwrite existing files.
48
49 -r, --root *rootname*
50 Specify root name to used during *RootPrefix* -m, --mode option
51 value. New MDLMOL file names are generated using the root:
52 <Root>Cmpd<RecordNumber>.mol Default for new file names:
53 <InitialSDFileName>Cmpd<RecordNumber>.mol. This option is ignored
54 for multiple input files.
55
56 -w, --workingdir *dirname*
57 Location of working directory. Default: current directory.
58
59 EXAMPLES
60 To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:
61
62 % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd
63
64 To generate Sample*.mol files from Sample1.sdf, type:
65
66 % SDToMolFiles.pl -r Sample -o Sample1.sdf
67
68 To generate MOL files from Sample1.sdf using molname line data for
69 generating MOL file names, type:
70
71 % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf
72
73 To generate MOL files from Sample1.sdf using a specific data field
74 values for generating MOL file names, type:
75
76 % SDToMolFiles.pl -m DataField --DataField MolID -r Sample
77 -o Sample1.sdf
78
79 AUTHOR
80 AUTHOR
81 Manish Sud <msud@san.rr.com>
82
83 SEE ALSO
84 InfoSDFiles.pl, MolFilesToSD.pl
85
86 COPYRIGHT
87 Copyright (C) 2015 Manish Sud. All rights reserved.
88
89 This file is part of MayaChemTools.
90
91 MayaChemTools is free software; you can redistribute it and/or modify it
92 under the terms of the GNU Lesser General Public License as published by
93 the Free Software Foundation; either version 3 of the License, or (at
94 your option) any later version.
95