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comparison docs/scripts/txt/MolFilesToSD.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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| -1:000000000000 | 0:4816e4a8ae95 |
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| 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 |