Mercurial > repos > deepakjadmin > mayatool3_test2
diff docs/scripts/txt/InfoSDFiles.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/txt/InfoSDFiles.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,102 @@ +NAME + InfoSDFiles.pl - List information about SDFile(s) + +SYNOPSIS + InfoSDFile.pl SDFile(s)... + + InfoSDFile.pl [-a --all] [-c --count] [--chiral] [--datacheck] [-d + --detail infolevel] [-e --empty] [-f, --fields] [-h, --help] [-i, + --invalidatomnumbers] [-m, --mismatch] [-s, --salts] [-u, + --unknownatoms] [-w, --workingdir dirname] SDFile(s)... + +DESCRIPTION + List information about *SDFile(s)* contents: number of compounds, empty + records and so on. Multiple SDFile names are separated by spaces. The + valid file extensions are *.sdf* and *.sd*. All other file names are + ignored. All the SD files in a current directory can be specified either + by **.sdf* or the current directory name. + +OPTIONS + -a, --all + List all the available information. + + -c, --count + List number of compounds. This is default behavior. + + --chiral + List number of empty atom/bond blocks for compounds with chiral flag + set in count line. + + -d, --detail *infolevel* + Level of information to print. Default: 1. Possible values: *1, 2, + or 3*. + + --datacheck + List number of numerical and non-numerical values for each data + field. + + -e, --empty + List number of empty atom/bond blocks and data fields for compounds. + + -f, --fields + List data field labels present for compounds. + + -h, --help + Print this help message. + + -i, --invalidatomnumbers + List number of bond blocks for compounds which contain invalid atom + numbers. + + -m, --mismatch + List number of atom/bond blocks for compounds which don't match with + counts line information in header block. + + -s, --salts + List number of atom blocks for compounds which contain salts + identified as disconnected structural units. + + -u, --unknownatoms + List number of atom blocks for compounds which contain special atom + symbols such as L, Q, * ,LP, X, R#, or any other non periodic table + symbols. + + -w, --workingdir *dirname* + Location of working directory. Default: current directory. + +EXAMPLES + To count compounds in SD file(s), type: + + % InfoSDFiles.pl Sample1.sdf + % InfoSDFiles.pl Sample1.sdf Sample2.sdf + % InfoSDFiles.pl *.sdf + + To list all available information for SD file(s), type: + + % InfoSDFiles.pl -a *.sdf + + To list all data fields present in sample.sdf, type: + + % InfoSDFiles.pl -f Sample.sdf + + To count number of compounds which contain salts and list associated + structural data, type: + + % InfoSDFiles.pl -s -d 3 Sample.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + ExtractFromSDFiles.pl, FilterSDFiles.pl, MergeTextFilesWithSD.pl + +COPYRIGHT + Copyright (C) 2015 Manish Sud. All rights reserved. + + This file is part of MayaChemTools. + + MayaChemTools is free software; you can redistribute it and/or modify it + under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation; either version 3 of the License, or (at + your option) any later version. +