Mercurial > repos > deepakjadmin > mayatool3_test2
comparison docs/scripts/txt/SDToMolFiles.txt @ 0:4816e4a8ae95 draft default tip
Uploaded
author | deepakjadmin |
---|---|
date | Wed, 20 Jan 2016 09:23:18 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:4816e4a8ae95 |
---|---|
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 |