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diff docs/scripts/man1/SplitSDFiles.1 @ 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/man1/SplitSDFiles.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,264 @@ +.\" 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++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +SplitSDFiles.pl \- Split SDFile(s) into multiple SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +SplitSDFiles.pl SDFile(s)... +.PP +SplitSDFiles.pl [\fB\-c, \-\-CmpdsMode\fR DataField | MolName | RootPrefix] +[\fB\-d, \-\-DataField\fR DataFieldName] [\fB\-h, \-\-help\fR] [\fB\-m, \-\-mode\fR Cmpds | Files] +[\fB\-n, \-\-numfiles\fR number] [\fB\-\-numcmpds\fR number] [\fB\-o, \-\-overwrite\fR] +[\fB\-r, \-\-root\fR rootname] [\fB\-w,\-\-workingdir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Split \fISDFile(s)\fR into multiple \s-1SD\s0 files. Each new SDFile contains a compound +subset of similar size from the initial file. Multiple \fISDFile(s)\fR names are separated +by space. 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\-c, \-\-CmpdsMode\fR \fIDataField | MolName | RootPrefix\fR" 4 +.IX Item "-c, --CmpdsMode DataField | MolName | RootPrefix" +This option is only used during \fICmpds\fR value of <\-m, \-\-mode> option with +specified \fB\-\-numcmpds\fR value of 1. +.Sp +Specify how to generate new file names during \fICmpds\fR value of <\-m, \-\-mode> +option: use \fISDFile(s)\fR datafield value or molname line for a specific compound; +generate a sequential \s-1ID\s0 using root prefix specified by \fB\-r, \-\-root\fR option. +.Sp +Possible values: \fIDataField | MolName | RootPrefix | RootPrefix\fR. +Default: \fIRootPrefix\fR. +.Sp +For empty \fIMolName\fR and \fIDataField\fR values during these specified modes, file +name is automatically generated using \fIRootPrefix\fR. +.Sp +For \fIRootPrefix\fR value of \fB\-c, \-\-CmpdsMode\fR option, new file names are +generated using by appending compound record number to value of \fB\-r, \-\-root\fR option. +For example: \fIRootName\fRCmd<RecordNumber>.sdf. +.Sp +Allowed characters in file names are: a\-zA\-Z0\-9_. All other characters in datafield +values, molname line, and root prefix are ignore during generation of file names. +.IP "\fB\-d, \-\-DataField\fR \fIDataFieldName\fR" 4 +.IX Item "-d, --DataField DataFieldName" +This option is only used during \fIDataField\fR value of <\-c, \-\-CmpdsMode> option. +.Sp +Specify \fISDFile(s)\fR datafield label name whose value is used for generation of new file +for a specific compound. Default value: \fINone\fR. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-m, \-\-mode\fR \fICmpds | Files\fR" 4 +.IX Item "-m, --mode Cmpds | Files" +Specify how to split \fISDFile(s)\fR: split into files with each file containing specified +number of compounds or split into a specified number of files. +.Sp +Possible values: \fICmpds | Files\fR. Default: \fIFiles\fR. +.Sp +For \fICmpds\fR value of \fB\-m, \-\-mode\fR option, value of \fB\-\-numcmpds\fR option +determines the number of new files. And value of \fB\-n, \-\-numfiles\fR option is +used to figure out the number of new files for \fIFiles\fR value of \fB\-m, \-\-mode\fR option. +.IP "\fB\-n, \-\-numfiles\fR \fInumber\fR" 4 +.IX Item "-n, --numfiles number" +Number of new files to generate for each \fISDFile(s)\fR. Default: \fI2\fR. +.Sp +This value is only used during \fIFiles\fR value of \fB\-m, \-\-mode\fR option. +.IP "\fB\-\-numcmpds\fR \fInumber\fR" 4 +.IX Item "--numcmpds number" +Number of compounds in each new file corresponding to each \fISDFile(s)\fR. +Default: \fI1\fR. +.Sp +This value is only used during \fICmpds\fR value of \fB\-m, \-\-mode\fR option. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New \s-1SD\s0 file names are generated using the root: <Root>Part<Count>.sdf. +Default new file names: <InitialSDFileName> Part<Count>.sdf. This option +is ignored for multiple input files. +.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 split each \s-1SD\s0 file into 5 new \s-1SD\s0 files, type: +.PP +.Vb 2 +\& % SplitSDFiles.pl \-n 5 \-o Sample1.sdf Sample2.sdf +\& % SplitSDFiles.pl \-n 5 \-o *.sdf +.Ve +.PP +To split Sample1.sdf into 10 new NewSample*.sdf files, type: +.PP +.Vb 1 +\& % SplitSDFiles.pl \-m Files \-n 10 \-r NewSample \-o Sample1.sdf +.Ve +.PP +To split Sample1.sdf into new NewSample*.sdf files containing maximum of 5 compounds +in each file, type: +.PP +.Vb 1 +\& % SplitSDFiles.pl \-m Cmpds \-\-numcmpds 5 \-r NewSample \-o Sample1.sdf +.Ve +.PP +To split Sample1.sdf into new \s-1SD\s0 files containing one compound each with new file +names corresponding to molname line, type: +.PP +.Vb 1 +\& % SplitSDFiles.pl \-m Cmpds \-\-numcmpds 1 \-c MolName \-o Sample1.sdf +.Ve +.PP +To split Sample1.sdf into new \s-1SD\s0 files containing one compound each with new file +names corresponding to value of datafield MolID, type: +.PP +.Vb 2 +\& % SplitSDFiles.pl \-m Cmpds \-\-numcmpds 1 \-c DataField \-d MolID +\& \-o Sample1.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoSDFiles.pl, JoinSDFiles.pl, MolFilesToSD.pl, SDToMolFiles.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.