1babel(1) User's Reference Manual babel(1)
2
4 babel, obabel — a converter for chemistry and molecular modeling data
5 files
6
8 babel [-H help-options]
9 babel [OPTIONS] [-i input-type] infile [-o output-type] outfile
10 obabel [-H help-options]
12 obabel [OPTIONS] [-i input-type | -: "SMILES-string"] infile
13 [-o output-type] -O outfile
14
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 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 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
32 If only input and output files are given, Open Babel will guess the file
33 type from the filename extension.
34 -: "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 -a options
42 Format-specific input options. See -H format-ID for options allowed
43 by a particular format
44 --addtotitle
46 Append text to the current molecule title
47 --addformula
49 Append the molecular formula after the current molecule title
50 -b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
52 -c Center atomic coordinates at (0,0,0)
54 -C Combine molecules in first file with others having the same name
56 -e Continue after errors
58 -d Delete Hydrogens
60 ---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 -f # For multiple entry input, start import with molecule # as the first
70 entry
71 -F Output the available fingerprint types
73 -h Add hydrogens
75 -H Output usage information
77 -H format-ID
79 Output formatting information and options for format specified
80 -Hall
82 Output formatting information and options for all formats
83 -i<format-ID>
85 Specifies input format, see below for the available formats
86 -j
88 --join
90 Join all input molecules into a single output molecule entry
91 -k Translate computational chemistry modeling keywords (e.g., GAMESS
93 and Gaussian)
94 -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 -l # For multiple entry input, stop import with molecule # as the last
102 entry
103 -o format-ID
105 Specifies output format, see below for the available formats
106 -O outfile
108 Specify the output file. This option applies to obabel only.
109 -p Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
111 --property
113 Add or replace a property (e.g., in an MDL SD file)
114 -s SMARTS
116 Convert only molecules matching the SMARTS pattern specified
117 --separate
119 Separate disconnected fragments into individual molecular records
120 -t All input files describe a single molecule
122 --title title
124 Add or replace molecular title
125 -x options
127 Format-specific output options. See -H format-ID for options
128 allowed by a particular format
129 -v SMARTS
131 Convert only molecules NOT matching SMARTS pattern specified
132 -V Output version number and exit
134 -z Compress the output with gzip
136
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
242 Individual file formats may have additional formatting options.
243 Input format options are preceded by 'a', e.g. -as
245 Output format options are preceded by 'x', e.g. -xn
247 For further specific information and options, use -H<format-type>
249 e.g., -Hcml
250
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
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
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 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 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.
282Open Babel 2.2 July 4, 2008 Open Babel 2.2