.Dd November 25, 2005
.Os "Open Babel" 2.0
.Dt babel 1 URM
.Sh NAME
.Nm babel
.Nd "a converter for chemistry and molecular modeling data files"
.Sh SYNOPSIS
.Nm
.Op Fl H Ar help-options
.Nm
.Op Ar OPTIONS
.Op Fl i Ar input-type
.Ar infile
.Op Fl o Ar output-type
.Ar outfile
.Sh DESCRIPTION
.Re
Open Babel is a cross-platform program designed to interconvert
between many file formats used in molecular modeling and computational
chemistry and related areas.
.Pp
Note that Open Babel can also be used as a library to interconvert
many file formats and to provide standard chemistry software
routines. See the Open Babel web pages
<\fBhttp://openbabel.sourceforge.net/\fR> for more information.
.Sh OPTIONS
.Re
If only input and ouput files are given, Open Babel will guess the
file type from the filename extension.
.Bl -tag -width flag
.It Fl --errorlevel Ar 2
Filter the level of errors and warnings displayed:
.br
       1 = critical errors only
       2 = include warnings too (default)
       3 = include informational messages too
       4 = include "audit log" messages of changes to data
       5 = include debugging messages too
.It Fl a Ar options
Format-specific input options. See 
.Fl H Ar format-ID 
for options allowed by a particular format
.It Fl b
Convert dative bonds (e.g., [N+]([O-])=) to N(=O)=O)
.It Fl c
Center atomic coordinates at (0,0,0) 
.It Fl d
Delete Hydrogens 
.It Fl f Ar #
For multiple entry input, start import with molecule # as the first entry
.It Fl F
Output the available fingerprint types
.It Fl h
Add hydrogens 
.It Fl H
Output usage information 
.It Fl H Ar format-ID
Output formatting information and options for format specified
.It Fl Hall
Output formatting information and options for all formats
.It Fl i<format-ID>
Specifies input format, see below for the available formats 
.It Fl j
Join all input molecules into a single output molecule entry
.It Fl m
Produce multiple output files, to allow:
.Bl -dash -offset indent -compact
.It
Splitting one input file - put each molecule into consecutively
numbered output files
.It
Batch conversion - convert each of multiple input files into a
specified output format
.El
.It Fl l Ar #
For multiple entry input, stop import with molecule # as the last entry
.It Fl o Ar format-ID
Specifies output format, see below for the available formats 
.It Fl p
Add Hydrogens appropriate for pH (use transforms in phmodel.txt) 
.It Fl s Ar SMARTS
Convert only molecules matching the SMARTS pattern specified 
.It Fl t
All input files describe a single molecule 
.It Fl x Ar options
Format-specific output options. See 
.Fl H Ar format-ID
for options allowed by a particular format
.It Fl v Ar SMARTS
Convert only molecules \fBNOT\fP matching SMARTS pattern specified 
.It Fl V
Output version number and exit 
.It Fl z
Compress the output with gzip
.El
.Sh "FILE FORMATS"
.RE
The following formats are currently supported by Open Babel: 
.Bl -item -offset indent -compact
.It
alc -- Alchemy format
.It
bgf -- MSI BGF format
.It
box -- Dock 3.5 Box format
.It
bs -- Ball and Stick format
.It
c3d1 -- Chem3D Cartesian 1 format
.It
c3d2 -- Chem3D Cartesian 2 format
.It
caccrt -- Cacao Cartesian format
.It
cache -- CAChe MolStruct format [Write-only]
.It
cacint -- Cacao Internal format [Write-only]
.It
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
.It
ccc -- CCC format [Read-only]
.It
cht -- Chemtool format [Write-only]
.It
cml --  Chemical Markup Language
.It
cmlr --  CML Reaction format
.It
com -- Gaussian 98/03 Cartesian Input [Write-only]
.It
copy -- Copies raw text [Write-only]
.It
crk2d -- Chemical Resource Kit 2D diagram format
.It
crk3d -- Chemical Resource Kit 3D format
.It
csr -- Accelrys/MSI Quanta CSR format [Write-only]
.It
cssr -- CSD CSSR format [Write-only]
.It
ct -- ChemDraw Connection Table format 
.It
dmol -- DMol3 coordinates format
.It
ent -- Protein Data Bank format
.It
feat -- Feature format
.It
fh -- Fenske-Hall Z-Matrix format [Write-only]
.It
fix -- SMILES FIX format [Write-only]
.It
fpt -- Fingerprint format [Write-only]
.It
fract -- Free Form Fractional format
.It
fs -- FastSearching
.It
g03 -- Gaussian98/03 Output [Read-only]
.It
g98 -- Gaussian98/03 Output [Read-only]
.It
gam -- GAMESS Output [Read-only]
.It
gamin -- GAMESS Input [Write-only]
.It
gamout -- GAMESS Output [Read-only]
.It
gau -- Gaussian 98/03 Cartesian Input [Write-only]
.It
gpr -- Ghemical format
.It
gr96 -- GROMOS96 format [Write-only]
.It
hin -- HyperChem HIN format
.It
inchi -- IUPAC InChI descriptor [Write-only]
.It
inp -- GAMESS Input [Write-only]
.It
ins -- ShelX format [Read-only]
.It
jin -- Jaguar input format [Write-only]
.It
jout -- Jaguar output format [Read-only]
.It
mdl -- MDL MOL format
.It
mmd -- MacroModel format
.It
mmod -- MacroModel format
.It
mol -- MDL MOL format
.It
mol2 -- Sybyl Mol2 format
.It
mopcrt -- MOPAC Cartesian format
.It
mopout -- MOPAC Output format [Read-only]
.It
mpd -- Sybyl descriptor format [Write-only]
.It
mpqc -- MPQC output format [Read-only]
.It
mpqcin -- MPQC simplified input format [Write-only]
.It
nw -- NWChem input format [Write-only]
.It
nwo -- NWChem output format [Read-only]
.It
pc --  PubChem format  [Read-only]
.It
pcm --  PCModel format
.It
pdb -- Protein Data Bank format
.It
pov -- POV-Ray input format [Write-only]
.It
pqs -- Parallel Quantum Solutions format
.It
prep -- Amber Prep format [Read-only]
.It
qcin -- Q-Chem input format [Write-only]
.It
qcout -- Q-Chem output format [Read-only]
.It
report -- Open Babel report format [Write-only]
.It
res -- ShelX format [Read-only]
.It
rxn -- MDL RXN format
.It
sd -- MDL MOL format
.It
sdf -- MDL MOL format
.It
smi -- SMILES format
.It
test -- Test format [Write-only]
.It
tmol -- TurboMole Coordinate format
.It
txyz -- Tinker MM2 format [Write-only]
.It
unixyz -- UniChem XYZ format
.It
vmol -- ViewMol format
.It
xed -- XED format [Write-only]
.It
xml --  General XML format [Read-only]
.It
xyz -- XYZ cartesian coordinates format
.It
yob -- YASARA.org YOB format
.It
zin -- ZINDO input format [Write-only]
.El
.Sh "FORMAT OPTIONS"
Individual file formats may have additional formatting options. 
.Pp
Input format options are preceded by 'a', e.g. -as 
.Pp
Output format options are preceded by 'x', e.g. -xn 
.Pp
For further specific information and options, use -H<format-type>
.br
 e.g., -Hcml
.Sh EXAMPLES
Standard conversion:
.Dl "babel -ixyz ethanol.xyz -opdb ethanol.pdb"
Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
.Dl "babel -ismi -omol2"
Split a multi-molecule file into new1.smi, new2.smi, etc.:
.Dl "babel infile.mol new.smi -m"
.Sh SEE ALSO
.Xr obfit 1 ,
.Xr obgrep 1 , 
.Xr obprop 1 , 
.Xr obrotate 1 
The web pages for Open Babel can be found at:
<\fBhttp://openbabel.sourceforge.net/\fR> 
.Sh AUTHORS
.An -nosplit
A cast of many, including currrent maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck , 
and innumerable others who have contributed fixes and additions. 
For more contributors to Open Babel, see 
<\fBhttp://openbabel.sourceforge.net/THANKS.shtml\fR>
.Sh COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison 
.Pp
 This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
.Pp
 This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.