diff mayachemtools/docs/scripts/man1/InfoSDFiles.1 @ 0:73ae111cf86f draft

Uploaded

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+++ b/mayachemtools/docs/scripts/man1/InfoSDFiles.1	Wed Jan 20 11:55:01 2016 -0500
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+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "INFOSDFILES 1"
+.TH INFOSDFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+InfoSDFiles.pl \- List information about SDFile(s)
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+InfoSDFile.pl SDFile(s)...
+.PP
+InfoSDFile.pl [\fB\-a \-\-all\fR] [\fB\-c \-\-count\fR] [\fB\-\-chiral\fR] [\fB\-\-datacheck\fR]
+[\fB\-d \-\-detail\fR infolevel] [\fB\-e \-\-empty\fR] [\fB\-f, \-\-fields\fR] [\fB\-h, \-\-help\fR]
+[\fB\-i, \-\-invalidatomnumbers\fR] [\fB\-m, \-\-mismatch\fR] [\fB\-s, \-\-salts\fR] [\fB\-u, \-\-unknownatoms\fR]
+[\fB\-w, \-\-workingdir\fR dirname] SDFile(s)...
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+List information about \fISDFile(s)\fR contents: number of compounds, empty records
+and so on. Multiple SDFile names are separated by spaces. The valid file extensions
+are \fI.sdf\fR and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current
+directory can be specified either by \fI*.sdf\fR or the current directory name.
+.SH "OPTIONS"
+.IX Header "OPTIONS"
+.IP "\fB\-a, \-\-all\fR" 4
+.IX Item "-a, --all"
+List all the available information.
+.IP "\fB\-c, \-\-count\fR" 4
+.IX Item "-c, --count"
+List number of compounds. This is \fBdefault behavior\fR.
+.IP "\fB\-\-chiral\fR" 4
+.IX Item "--chiral"
+List number of empty atom/bond blocks for compounds with chiral flag set in
+count line.
+.IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
+.IX Item "-d, --detail infolevel"
+Level of information to print. Default: 1. Possible values: \fI1, 2, or 3\fR.
+.IP "\fB\-\-datacheck\fR" 4
+.IX Item "--datacheck"
+List number of numerical and non-numerical values for each data field.
+.IP "\fB\-e, \-\-empty\fR" 4
+.IX Item "-e, --empty"
+List number of empty atom/bond blocks and data fields for compounds.
+.IP "\fB\-f, \-\-fields\fR" 4
+.IX Item "-f, --fields"
+List data field labels present for compounds.
+.IP "\fB\-h, \-\-help\fR" 4
+.IX Item "-h, --help"
+Print this help message.
+.IP "\fB\-i, \-\-invalidatomnumbers\fR" 4
+.IX Item "-i, --invalidatomnumbers"
+List number of bond blocks for compounds which contain invalid atom numbers.
+.IP "\fB\-m, \-\-mismatch\fR" 4
+.IX Item "-m, --mismatch"
+List number of atom/bond blocks for compounds which don't match with counts
+line information in header block.
+.IP "\fB\-s, \-\-salts\fR" 4
+.IX Item "-s, --salts"
+List number of atom blocks for compounds which contain salts identified as
+disconnected structural units.
+.IP "\fB\-u, \-\-unknownatoms\fR" 4
+.IX Item "-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.
+.IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
+.IX Item "-w, --workingdir dirname"
+Location of working directory. Default: current directory.
+.SH "EXAMPLES"
+.IX Header "EXAMPLES"
+To count compounds in \s-1SD\s0 file(s), type:
+.PP
+.Vb 3
+\&    % InfoSDFiles.pl Sample1.sdf
+\&    % InfoSDFiles.pl Sample1.sdf Sample2.sdf
+\&    % InfoSDFiles.pl *.sdf
+.Ve
+.PP
+To list all available information for \s-1SD\s0 file(s), type:
+.PP
+.Vb 1
+\&    % InfoSDFiles.pl \-a *.sdf
+.Ve
+.PP
+To list all data fields present in sample.sdf, type:
+.PP
+.Vb 1
+\&    % InfoSDFiles.pl \-f Sample.sdf
+.Ve
+.PP
+To count number of compounds which contain salts and list associated structural
+data, type:
+.PP
+.Vb 1
+\&    % InfoSDFiles.pl \-s \-d 3 Sample.sdf
+.Ve
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+ExtractFromSDFiles.pl, FilterSDFiles.pl, MergeTextFilesWithSD.pl
+.SH "COPYRIGHT"
+.IX Header "COPYRIGHT"
+Copyright (C) 2015 Manish Sud. All rights reserved.
+.PP
+This file is part of MayaChemTools.
+.PP
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.