1obabel(1) User's Reference Manual obabel(1)
2
4 obabel — a converter for chemistry and molecular modeling data files
5
7 obabel [-H help-options]
8 obabel [OPTIONS] [-i input-type | -: "SMILES-string"] infile
9 [-o output-type] -O outfile
10
12 obabel is a cross-platform program designed to interconvert between many
13 file formats used in molecular modeling and computational chemistry and
14 related areas.
15 Open Babel is also a complete programmers toolkit for developing chem‐
17 istry software. For more information, se the Open Babel web pages
18 <http://openbabel.org/>.
19
21 If only input and output files are given, Open Babel will guess the file
22 type from the filename extension.
23 -: "SMILES-string"
25 Enter SMILES string and use it in place of an input file. The
26 SMILES string should be enclosed in quotation marks. More than one
27 can be used, and a molecule title can be included if enclosed in
28 quotes.
29 -a options
31 Format-specific input options. See -H format-ID for options allowed
32 by a particular format
33 --addtotitle
35 Append text to the current molecule title
36 --addformula
38 Append the molecular formula after the current molecule title
39 -b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
41 -c Center atomic coordinates at (0,0,0)
43 -C Combine molecules in first file with others having the same name
45 -e Continue after errors
47 -d Delete Hydrogens
49 ---errorlevel 2
51 Filter the level of errors and warnings displayed:
52 1 = critical errors only
53 2 = include warnings too (default)
54 3 = include informational messages too
55 4 = include "audit log" messages of changes to data
56 5 = include debugging messages too
57 -f # For multiple entry input, start import with molecule # as the first
59 entry
60 -F Output the available fingerprint types
62 -h Add hydrogens
64 -H Output usage information
66 -H format-ID
68 Output formatting information and options for format specified
69 -Hall
71 Output formatting information and options for all formats
72 -i<format-ID>
74 Specifies input format, see below for the available formats
75 -j
77 --join
79 Join all input molecules into a single output molecule entry
80 -k Translate computational chemistry modeling keywords (e.g., GAMESS
82 and Gaussian)
83 -m Produce multiple output files, to allow:
85 - Splitting one input file - put each molecule into consec‐
86 utively numbered output files
87 - Batch conversion - convert each of multiple input files
88 into a specified output format
89 -l # For multiple entry input, stop import with molecule # as the last
91 entry
92 -o format-ID
94 Specifies output format, see below for the available formats
95 -O outfile
97 Specify the output file. This option applies to obabel only.
98 -p Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
100 --property
102 Add or replace a property (e.g., in an MDL SD file)
103 -s SMARTS
105 Convert only molecules matching the SMARTS pattern specified
106 --separate
108 Separate disconnected fragments into individual molecular records
109 -t All input files describe a single molecule
111 --title title
113 Add or replace molecular title
114 -x options
116 Format-specific output options. See -H format-ID for options al‐
117 lowed by a particular format
118 -v SMARTS
120 Convert only molecules NOT matching SMARTS pattern specified
121 -V Output version number and exit
123 -z Compress the output with gzip
125
127 The following formats are currently supported by Open Babel:
128 acr -- Carine ASCI Crystal
129 alc -- Alchemy format
130 arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
131 bgf -- MSI BGF format
132 box -- Dock 3.5 Box format
133 bs -- Ball and Stick format
134 c3d1 -- Chem3D Cartesian 1 format
135 c3d2 -- Chem3D Cartesian 2 format
136 caccrt -- Cacao Cartesian format
137 cache -- CAChe MolStruct format [Write-only]
138 cacint -- Cacao Internal format [Write-only]
139 can -- Canonical SMILES format
140 car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
141 ccc -- CCC format [Read-only]
142 cdx -- ChemDraw binary format [Read-only]
143 cdxml -- ChemDraw CDXML format
144 cht -- Chemtool format [Write-only]
145 cif -- Crystallographic Information File
146 cml -- Chemical Markup Language
147 cmlr -- CML Reaction format
148 com -- Gaussian Cartesian Input [Write-only]
149 copy -- Copies raw text [Write-only]
150 crk2d -- Chemical Resource Kit 2D diagram format
151 crk3d -- Chemical Resource Kit 3D format
152 csr -- Accelrys/MSI Quanta CSR format [Write-only]
153 cssr -- CSD CSSR format [Write-only]
154 ct -- ChemDraw Connection Table format
155 dmol -- DMol3 coordinates format
156 ent -- Protein Data Bank format
157 fa -- FASTA format [Write-only]
158 fasta -- FASTA format [Write-only]
159 fch -- Gaussian formatted checkpoint file format [Read-only]
160 fchk -- Gaussian formatted checkpoint file format [Read-only]
161 fck -- Gaussian formatted checkpoint file format [Read-only]
162 feat -- Feature format
163 fh -- Fenske-Hall Z-Matrix format [Write-only]
164 fix -- SMILES FIX format [Write-only]
165 fpt -- Fingerprint format [Write-only]
166 fract -- Free Form Fractional format
167 fs -- Open Babel FastSearching database
168 fsa -- FASTA format [Write-only]
169 g03 -- Gaussian 98/03 Output [Read-only]
170 g98 -- Gaussian 98/03 Output [Read-only]
171 gam -- GAMESS Output [Read-only]
172 gamin -- GAMESS Input [Write-only]
173 gamout -- GAMESS Output [Read-only]
174 gau -- Gaussian Cartesian Input [Write-only]
175 gjc -- Gaussian Cartesian Input [Write-only]
176 gjf -- Gaussian Cartesian Input [Write-only]
177 gpr -- Ghemical format
178 gr96 -- GROMOS96 format [Write-only]
179 gzmat -- Gaussian Z-Matrix Input
180 hin -- HyperChem HIN format
181 inchi -- IUPAC InChI [Write-only]
182 inp -- GAMESS Input [Write-only]
183 ins -- ShelX format [Read-only]
184 jin -- Jaguar input format [Write-only]
185 jout -- Jaguar output format [Read-only]
186 mdl -- MDL MOL format
187 mmd -- MacroModel format
188 mmod -- MacroModel format
189 mol -- MDL MOL format
190 mol2 -- Sybyl Mol2 format
191 molreport -- Open Babel molecule report [Write-only]
192 moo -- MOPAC Output format [Read-only]
193 mop -- MOPAC Cartesian format
194 mopcrt -- MOPAC Cartesian format
195 mopin -- MOPAC Internal
196 mopout -- MOPAC Output format [Read-only]
197 mpc -- MOPAC Cartesian format
198 mpd -- Sybyl descriptor format [Write-only]
199 mpqc -- MPQC output format [Read-only]
200 mpqcin -- MPQC simplified input format [Write-only]
201 nw -- NWChem input format [Write-only]
202 nwo -- NWChem output format [Read-only]
203 pc -- PubChem format [Read-only]
204 pcm -- PCModel format
205 pdb -- Protein Data Bank format
206 pov -- POV-Ray input format [Write-only]
207 pqs -- Parallel Quantum Solutions format
208 prep -- Amber Prep format [Read-only]
209 qcin -- Q-Chem input format [Write-only]
210 qcout -- Q-Chem output format [Read-only]
211 report -- Open Babel report format [Write-only]
212 res -- ShelX format [Read-only]
213 rxn -- MDL RXN format
214 sd -- MDL MOL format
215 sdf -- MDL MOL format
216 smi -- SMILES format
217 sy2 -- Sybyl Mol2 format
218 tdd -- Thermo format
219 test -- Test format [Write-only]
220 therm -- Thermo format
221 tmol -- TurboMole Coordinate format
222 txyz -- Tinker MM2 format [Write-only]
223 unixyz -- UniChem XYZ format
224 vmol -- ViewMol format
225 xed -- XED format [Write-only]
226 xml -- General XML format [Read-only]
227 xyz -- XYZ cartesian coordinates format
228 yob -- YASARA.org YOB format
229 zin -- ZINDO input format [Write-only]
230
232 Individual file formats may have additional formatting options.
233 Input format options are preceded by 'a', e.g. -as
235 Output format options are preceded by 'x', e.g. -xn
237 For further specific information and options, use -H<format-type>
239 e.g., -Hcml
240
242 Standard conversion:
243 obabel ethanol.xyz -Oethanol.pdb
244 Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
245 obabel -ismi -omol2
246 Split a multi-molecule file into new1.smi, new2.smi, etc.:
247 obabel infile.mol -Onew.smi -m
248
250 obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1),
251 obrotamer(1). The web pages for Open Babel can be found at:
252 <http://openbabel.org/>
253
255 A cast of many, including the currrent maintainers Geoff Hutchison, Chris
256 Morley, Michael Banck, and innumerable others who have contributed fixes
257 and additions. For more contributors to Open Babel, see
258 <http://openbabel.org/wiki/THANKS>
259
261 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
262 Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison
263 This program is free software; you can redistribute it and/or modify it
265 under the terms of the GNU General Public License as published by the
266 Free Software Foundation version 2 of the License.
267 This program is distributed in the hope that it will be useful, but WITH‐
269 OUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
270 FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
271 more details.
272Open Babel 3.1 Oct 10, 2019 Open Babel 3.1