|
1
|
1 NAME
|
|
|
2 MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)
|
|
|
3
|
|
|
4 SYNOPSIS
|
|
|
5 MolFilesToSD.pl MDLMOLFile(s)...
|
|
|
6
|
|
|
7 MolFilesToSD.pl [-c, --compoundid usefileprefix | idlabel] [-d,
|
|
|
8 --datafieldlabel fieldlabel] [-h, --help] [-m, --mode molnameline |
|
|
|
9 datafield | both | none] [-o, --overwrite] [-r, --root rootname] [-w,
|
|
|
10 --workingdir dirname] MDLMOLFile(s)...
|
|
|
11
|
|
|
12 DESCRIPTION
|
|
|
13 Generate a SD file from *MDLMOL File(s)*. Multiple file names are
|
|
|
14 separated by spaces. The valid file extension is *.mol*. All other file
|
|
|
15 names are ignored. All the files in a current directory can be specified
|
|
|
16 by **.mol*, or the current directory name.
|
|
|
17
|
|
|
18 OPTIONS
|
|
|
19 -c, --compoundid *usefileprefix | idlabel*
|
|
|
20 Specify how to generate compound IDs: use MOL filename prefix or
|
|
|
21 generate a new compound ID by combining *idlabel* with compound
|
|
|
22 number. Possible values: *usefileprefix | idlabel*. By default,
|
|
|
23 *Cmd* is used as a *idlabel* to generate these types of compound
|
|
|
24 IDs: Cmpd1, Cmpd2 and so on.
|
|
|
25
|
|
|
26 Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on,
|
|
|
27 specify "MolID" value for this option.
|
|
|
28
|
|
|
29 -d, --datafieldlabel *fieldlabel*
|
|
|
30 Specify data field label for adding compound ID field into SD file
|
|
|
31 during *datafield | both* values of -m, --mode option. Default:
|
|
|
32 <Cmpd_ID>.
|
|
|
33
|
|
|
34 -h, --help
|
|
|
35 Print this help message.
|
|
|
36
|
|
|
37 -m, --mode *molnameline | datafield | both | none*
|
|
|
38 Specify how to add compopund ID into SD file: relplace the molname
|
|
|
39 line, add a new data field, replace the molname line and add data
|
|
|
40 field, or do nothing. Possible values: *molnameline | datafield |
|
|
|
41 both | none*. Default: *nothing*.
|
|
|
42
|
|
|
43 Use -c, --compoundid to specify compound ID generation process.
|
|
|
44
|
|
|
45 -o, --overwrite
|
|
|
46 Overwrite existing files.
|
|
|
47
|
|
|
48 -r, --root *rootname*
|
|
|
49 New SD file name is generated using the root: <Root>.sdf. Default
|
|
|
50 new file name: <InitialMOLFileName>1To<Count>.sdf.
|
|
|
51
|
|
|
52 -w, --workingdir *dirname*
|
|
|
53 Location of working directory. Default: current directory.
|
|
|
54
|
|
|
55 EXAMPLES
|
|
|
56 To generate NewSample.sdf file from Sample*.mol files, type:
|
|
|
57
|
|
|
58 % MolFilesToSD.pl -r NewSample -o Sample*.mol
|
|
|
59
|
|
|
60 To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in
|
|
|
61 MolName line and Cmpd_ID datafield from Sample*.mol files, type:
|
|
|
62
|
|
|
63 % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol
|
|
|
64
|
|
|
65 AUTHOR
|
|
|
66 Manish Sud <msud@san.rr.com>
|
|
|
67
|
|
|
68 SEE ALSO
|
|
|
69 InfoSDFiles.pl, SDToMolFiles.pl
|
|
|
70
|
|
|
71 COPYRIGHT
|
|
|
72 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
73
|
|
|
74 This file is part of MayaChemTools.
|
|
|
75
|
|
|
76 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
77 under the terms of the GNU Lesser General Public License as published by
|
|
|
78 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
79 your option) any later version.
|
|
|
80
|
