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

Uploaded

0:73ae111cf86f

.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.ie \nF \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    nr % 0
.    rr F
.\}
.el \{\
.    de IX
..
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.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.