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Daniel Leidert
1deca607f1
doc/obfit.1, doc/obgen.1, doc/obgrep.1, doc/obminimize.1, doc/obprobe.1, doc/obprop.1, doc/obrotamer.1, doc/obrotate.1, doc/roundtrip.1: Prevent hyphenation of URLs. Fixed an mdoc issue.
93 lines
2.8 KiB
Groff
93 lines
2.8 KiB
Groff
.Dd July 4, 2008
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.Os "Open Babel" 2.2
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.Dt obgrep 1 URM
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.Sh NAME
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.Nm obgrep
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.Nd an advanced molecular search program using SMARTS
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.Sh SYNOPSIS
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.Nm
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.Op Ar OPTIONS
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.Ar 'SMARTS-pattern'
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.Ar filename
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.Sh DESCRIPTION
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The obgrep tool can be used to search for molecules inside
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multi-molecule database files (e.g., SMILES, SDF, etc.) or across
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multiple files.
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.Sh OPTIONS
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If only a filename is given, obgrep will attempt to guess the file
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type from the filename extension.
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.Bl -tag -width flag
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.It Fl c
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Print the number of matches
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.It Fl f
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Full match, print matching-molecules only when the number of heavy
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atoms is also equal to the number of atoms in the SMARTS pattern
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.It Fl i Ar format
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Specifies input and output format, see
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.Xr babel 1
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for available formats
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.It Fl n
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Only print the name of the molecules
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.It Fl t Ar #
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Print a molecule only if the pattern occurs # times inside the molecule
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.It Fl v
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Invert the matching, print non-matching molecules
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.El
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.Sh EXAMPLES
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Note that in all examples, the SMARTS pattern is enclosed in single
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quotes '...' to ensure it is not changed by the shell.
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.Pp
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Print all the molecules with a methylamine group:
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.Dl "obgrep 'CN' database.smi"
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.Pp
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Print all the molecules without a methylamine group:
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.Dl "obgrep -v 'CN' database.smi"
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.Pp
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Print the number of molecules without a methylamine group:
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.Dl "obgrep -v -c 'CN' database.smi"
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.Pp
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Print methylamine (if it exists in the file):
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.Dl "obgrep -f 'CN' database.smi"
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.Pp
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Print methylamine and/or methanol (if they exist):
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.Dl "obgrep -f 'C[N,O]' database.smi"
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Print all molecules with aromatic carbon in all SMILES files in the
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directory (i.e., *.smi)
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.Dl "obgrep 'c' *.smi"
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.Sh SEE ALSO
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.Xr babel 1 ,
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.Xr obfit 1 ,
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.Xr obrotate 1 .
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.Pp
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The web pages for Open Babel can be found at:
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\%<\fBhttp://openbabel.org/\fR>
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.Pp
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A guide for constructing SMARTS patterns can be found at:
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\%<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR>
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.Sh AUTHORS
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The obgrep program was contributed by
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.An Fabien Fontaine
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.Pp
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.An -nosplit
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Open Babel is developed by a cast of many, including currrent maintainers
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.An Geoff Hutchison ,
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.An Chris Morley ,
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.An Michael Banck ,
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and innumerable others who have contributed fixes and additions.
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For more contributors to Open Babel, see
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\%<\fBhttp://openbabel.org/wiki/THANKS\fR>
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.Sh COPYRIGHT
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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.br
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Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and
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other contributors.
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.Pp
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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.Pp
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This program is distributed in the hope that it will be useful, but
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WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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General Public License for more details.
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