1babel(1)                    User's Reference Manual                   babel(1)
2

NAME

4     babel, obabel — a converter for chemistry and molecular modeling data
5     files
6

SYNOPSIS

8     babel [-H help-options]
9     babel [OPTIONS] [-i input-type] infile [-o output-type] outfile
10
11     obabel [-H help-options]
12     obabel [OPTIONS] [-i input-type | -: "SMILES-string"] infile
13           [-o output-type] -O outfile
14

DESCRIPTION

16     babel is a cross-platform program designed to interconvert between many
17     file formats used in molecular modeling and computational chemistry and
18     related areas.
19
20     obabel and babel are slightly different. The first is closer to the nor‐
21     mal Unix convention for commandline programs and more flexible when the
22     user needs to specify parameter values on options. With babel this only
23     works when the option is the last on the line; with obabel no such
24     restriction applies. It further has a shortcut for entering SMILES
25     strings, which can be used in place of an input file.
26
27     Open Babel is also a complete programmers toolkit for developing chem‐
28     istry software. For more information, se the Open Babel web pages
29     <http://openbabel.org/>.
30

OPTIONS

32     If only input and output files are given, Open Babel will guess the file
33     type from the filename extension.
34
35     -: "SMILES-string"
36           Enter SMILES string and use it in place of an input file. The
37           SMILES string should be enclosed in quotation marks. More than one
38           can be used, and a molecule title can be included if enclosed in
39           quotes.
40
41     -a options
42           Format-specific input options. See -H format-ID for options allowed
43           by a particular format
44
45     --addtotitle
46           Append text to the current molecule title
47
48     --addformula
49           Append the molecular formula after the current molecule title
50
51     -b    Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
52
53     -c    Center atomic coordinates at (0,0,0)
54
55     -C    Combine molecules in first file with others having the same name
56
57     -e    Continue after errors
58
59     -d    Delete Hydrogens
60
61     ---errorlevel 2
62           Filter the level of errors and warnings displayed:
63                  1 = critical errors only
64                  2 = include warnings too (default)
65                  3 = include informational messages too
66                  4 = include "audit log" messages of changes to data
67                  5 = include debugging messages too
68
69     -f #  For multiple entry input, start import with molecule # as the first
70           entry
71
72     -F    Output the available fingerprint types
73
74     -h    Add hydrogens
75
76     -H    Output usage information
77
78     -H format-ID
79           Output formatting information and options for format specified
80
81     -Hall
82           Output formatting information and options for all formats
83
84     -i<format-ID>
85           Specifies input format, see below for the available formats
86
87     -j
88
89     --join
90           Join all input molecules into a single output molecule entry
91
92     -k    Translate computational chemistry modeling keywords (e.g., GAMESS
93           and Gaussian)
94
95     -m    Produce multiple output files, to allow:
96                 -   Splitting one input file - put each molecule into consec‐
97                     utively numbered output files
98                 -   Batch conversion - convert each of multiple input files
99                     into a specified output format
100
101     -l #  For multiple entry input, stop import with molecule # as the last
102           entry
103
104     -o format-ID
105           Specifies output format, see below for the available formats
106
107     -O outfile
108           Specify the output file. This option applies to obabel only.
109
110     -p    Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
111
112     --property
113           Add or replace a property (e.g., in an MDL SD file)
114
115     -s SMARTS
116           Convert only molecules matching the SMARTS pattern specified
117
118     --separate
119           Separate disconnected fragments into individual molecular records
120
121     -t    All input files describe a single molecule
122
123     --title title
124           Add or replace molecular title
125
126     -x options
127           Format-specific output options. See -H format-ID for options
128           allowed by a particular format
129
130     -v SMARTS
131           Convert only molecules NOT matching SMARTS pattern specified
132
133     -V    Output version number and exit
134
135     -z    Compress the output with gzip
136

FILE FORMATS

138     The following formats are currently supported by Open Babel:
139           acr -- Carine ASCI Crystal
140           alc -- Alchemy format
141           arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
142           bgf -- MSI BGF format
143           box -- Dock 3.5 Box format
144           bs -- Ball and Stick format
145           c3d1 -- Chem3D Cartesian 1 format
146           c3d2 -- Chem3D Cartesian 2 format
147           caccrt -- Cacao Cartesian format
148           cache -- CAChe MolStruct format [Write-only]
149           cacint -- Cacao Internal format [Write-only]
150           can -- Canonical SMILES format
151           car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
152           ccc -- CCC format [Read-only]
153           cdx -- ChemDraw binary format [Read-only]
154           cdxml -- ChemDraw CDXML format
155           cht -- Chemtool format [Write-only]
156           cif -- Crystallographic Information File
157           cml --  Chemical Markup Language
158           cmlr --  CML Reaction format
159           com -- Gaussian 98/03 Cartesian Input [Write-only]
160           copy -- Copies raw text [Write-only]
161           crk2d -- Chemical Resource Kit 2D diagram format
162           crk3d -- Chemical Resource Kit 3D format
163           csr -- Accelrys/MSI Quanta CSR format [Write-only]
164           cssr -- CSD CSSR format [Write-only]
165           ct -- ChemDraw Connection Table format
166           dmol -- DMol3 coordinates format
167           ent -- Protein Data Bank format
168           fa -- FASTA format [Write-only]
169           fasta -- FASTA format [Write-only]
170           fch -- Gaussian formatted checkpoint file format [Read-only]
171           fchk -- Gaussian formatted checkpoint file format [Read-only]
172           fck -- Gaussian formatted checkpoint file format [Read-only]
173           feat -- Feature format
174           fh -- Fenske-Hall Z-Matrix format [Write-only]
175           fix -- SMILES FIX format [Write-only]
176           fpt -- Fingerprint format [Write-only]
177           fract -- Free Form Fractional format
178           fs -- Open Babel FastSearching database
179           fsa -- FASTA format [Write-only]
180           g03 -- Gaussian 98/03 Output [Read-only]
181           g98 -- Gaussian 98/03 Output [Read-only]
182           gam -- GAMESS Output [Read-only]
183           gamin -- GAMESS Input [Write-only]
184           gamout -- GAMESS Output [Read-only]
185           gau -- Gaussian 98/03 Cartesian Input [Write-only]
186           gjc -- Gaussian 98/03 Cartesian Input [Write-only]
187           gjf -- Gaussian 98/03 Cartesian Input [Write-only]
188           gpr -- Ghemical format
189           gr96 -- GROMOS96 format [Write-only]
190           hin -- HyperChem HIN format
191           inchi -- IUPAC InChI [Write-only]
192           inp -- GAMESS Input [Write-only]
193           ins -- ShelX format [Read-only]
194           jin -- Jaguar input format [Write-only]
195           jout -- Jaguar output format [Read-only]
196           mdl -- MDL MOL format
197           mmd -- MacroModel format
198           mmod -- MacroModel format
199           mol -- MDL MOL format
200           mol2 -- Sybyl Mol2 format
201           molreport -- Open Babel molecule report [Write-only]
202           moo -- MOPAC Output format [Read-only]
203           mop -- MOPAC Cartesian format
204           mopcrt -- MOPAC Cartesian format
205           mopin -- MOPAC Internal
206           mopout -- MOPAC Output format [Read-only]
207           mpc -- MOPAC Cartesian format
208           mpd -- Sybyl descriptor format [Write-only]
209           mpqc -- MPQC output format [Read-only]
210           mpqcin -- MPQC simplified input format [Write-only]
211           nw -- NWChem input format [Write-only]
212           nwo -- NWChem output format [Read-only]
213           pc --  PubChem format  [Read-only]
214           pcm --  PCModel format
215           pdb -- Protein Data Bank format
216           pov -- POV-Ray input format [Write-only]
217           pqs -- Parallel Quantum Solutions format
218           prep -- Amber Prep format [Read-only]
219           qcin -- Q-Chem input format [Write-only]
220           qcout -- Q-Chem output format [Read-only]
221           report -- Open Babel report format [Write-only]
222           res -- ShelX format [Read-only]
223           rxn -- MDL RXN format
224           sd -- MDL MOL format
225           sdf -- MDL MOL format
226           smi -- SMILES format
227           sy2 -- Sybyl Mol2 format
228           tdd -- Thermo format
229           test -- Test format [Write-only]
230           therm -- Thermo format
231           tmol -- TurboMole Coordinate format
232           txyz -- Tinker MM2 format [Write-only]
233           unixyz -- UniChem XYZ format
234           vmol -- ViewMol format
235           xed -- XED format [Write-only]
236           xml --  General XML format [Read-only]
237           xyz -- XYZ cartesian coordinates format
238           yob -- YASARA.org YOB format
239           zin -- ZINDO input format [Write-only]
240

FORMAT OPTIONS

242     Individual file formats may have additional formatting options.
243
244     Input format options are preceded by 'a', e.g. -as
245
246     Output format options are preceded by 'x', e.g. -xn
247
248     For further specific information and options, use -H<format-type>
249      e.g., -Hcml
250

EXAMPLES

252     Standard conversion:
253           babel -ixyz ethanol.xyz -opdb ethanol.pdb
254     Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
255           babel -ismi -omol2
256     Split a multi-molecule file into new1.smi, new2.smi, etc.:
257           babel infile.mol new.smi -m
258

SEE ALSO

260     obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1),
261     obrotamer(1).  The web pages for Open Babel can be found at:
262     <http://openbabel.org/>
263

AUTHORS

265     A cast of many, including the currrent maintainers Geoff Hutchison, Chris
266     Morley, Michael Banck, and innumerable others who have contributed fixes
267     and additions.  For more contributors to Open Babel, see
268     <http://openbabel.org/wiki/THANKS>
269
271     Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
272     Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison
273
274      This program is free software; you can redistribute it and/or modify it
275     under the terms of the GNU General Public License as published by the
276     Free Software Foundation version 2 of the License.
277
278      This program is distributed in the hope that it will be useful, but
279     WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
280     ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
281     License for more details.
282
283Open Babel 2.2                   July 4, 2008                   Open Babel 2.2
Impressum