1babel(1) User's Reference Manual babel(1)
2
4 babel — a converter for chemistry and molecular modeling data files
5
7 babel [-H help-options]
8 babel [OPTIONS] [-i input-type] infile [-o output-type] outfile
9
11 Babel is a cross-platform program designed to interconvert between many
12 file formats used in molecular modeling and computational chemistry and
13 related areas.
14 Open Babel is also a complete programmers toolkit for developing chem‐
16 istry software. For more information, se the Open Babel web pages
17 <http://openbabel.sourceforge.net/>.
18
20 If only input and ouput files are given, Open Babel will guess the file
21 type from the filename extension.
22 -a options
24 Format-specific input options. See -H format-ID for options allowed
25 by a particular format
26 --addtotitle
28 Append text to the current molecule title
29 --addformula
31 Append the molecular formula after the current molecule title
32 -b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
34 -c Center atomic coordinates at (0,0,0)
36 -C Combine molecules in first file with others having the same name
38 -e Continue after errors
40 -d Delete Hydrogens
42 ---errorlevel 2
44 Filter the level of errors and warnings displayed:
45 1 = critical errors only
46 2 = include warnings too (default)
47 3 = include informational messages too
48 4 = include "audit log" messages of changes to data
49 5 = include debugging messages too
50 -f # For multiple entry input, start import with molecule # as the first
52 entry
53 -F Output the available fingerprint types
55 -h Add hydrogens
57 -H Output usage information
59 -H format-ID
61 Output formatting information and options for format specified
62 -Hall
64 Output formatting information and options for all formats
65 -i<format-ID>
67 Specifies input format, see below for the available formats
68 -j
70 --join
72 Join all input molecules into a single output molecule entry
73 -k Translate computational chemistry modeling keywords (e.g., GAMESS
75 and Gaussian)
76 -m Produce multiple output files, to allow:
78 - Splitting one input file - put each molecule into consec‐
79 utively numbered output files
80 - Batch conversion - convert each of multiple input files
81 into a specified output format
82 -l # For multiple entry input, stop import with molecule # as the last
84 entry
85 -o format-ID
87 Specifies output format, see below for the available formats
88 -p Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
90 --property
92 Add or replace a property (e.g., in an MDL SD file)
93 -s SMARTS
95 Convert only molecules matching the SMARTS pattern specified
96 --separate
98 Separate disconnected fragments into individual molecular records
99 -t All input files describe a single molecule
101 --title title
103 Add or replace molecular title
104 -x options
106 Format-specific output options. See -H format-ID for options
107 allowed by a particular format
108 -v SMARTS
110 Convert only molecules NOT matching SMARTS pattern specified
111 -V Output version number and exit
113 -z Compress the output with gzip
115
117 The following formats are currently supported by Open Babel:
118 acr -- Carine ASCI Crystal
119 alc -- Alchemy format
120 arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
121 bgf -- MSI BGF format
122 box -- Dock 3.5 Box format
123 bs -- Ball and Stick format
124 c3d1 -- Chem3D Cartesian 1 format
125 c3d2 -- Chem3D Cartesian 2 format
126 caccrt -- Cacao Cartesian format
127 cache -- CAChe MolStruct format [Write-only]
128 cacint -- Cacao Internal format [Write-only]
129 can -- Canonical SMILES format
130 car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
131 ccc -- CCC format [Read-only]
132 cdx -- ChemDraw binary format [Read-only]
133 cdxml -- ChemDraw CDXML format
134 cht -- Chemtool format [Write-only]
135 cif -- Crystallographic Information File
136 cml -- Chemical Markup Language
137 cmlr -- CML Reaction format
138 com -- Gaussian 98/03 Cartesian Input [Write-only]
139 copy -- Copies raw text [Write-only]
140 crk2d -- Chemical Resource Kit 2D diagram format
141 crk3d -- Chemical Resource Kit 3D format
142 csr -- Accelrys/MSI Quanta CSR format [Write-only]
143 cssr -- CSD CSSR format [Write-only]
144 ct -- ChemDraw Connection Table format
145 dmol -- DMol3 coordinates format
146 ent -- Protein Data Bank format
147 fa -- FASTA format [Write-only]
148 fasta -- FASTA format [Write-only]
149 fch -- Gaussian formatted checkpoint file format [Read-only]
150 fchk -- Gaussian formatted checkpoint file format [Read-only]
151 fck -- Gaussian formatted checkpoint file format [Read-only]
152 feat -- Feature format
153 fh -- Fenske-Hall Z-Matrix format [Write-only]
154 fix -- SMILES FIX format [Write-only]
155 fpt -- Fingerprint format [Write-only]
156 fract -- Free Form Fractional format
157 fs -- Open Babel FastSearching database
158 fsa -- FASTA format [Write-only]
159 g03 -- Gaussian 98/03 Output [Read-only]
160 g98 -- Gaussian 98/03 Output [Read-only]
161 gam -- GAMESS Output [Read-only]
162 gamin -- GAMESS Input [Write-only]
163 gamout -- GAMESS Output [Read-only]
164 gau -- Gaussian 98/03 Cartesian Input [Write-only]
165 gjc -- Gaussian 98/03 Cartesian Input [Write-only]
166 gjf -- Gaussian 98/03 Cartesian Input [Write-only]
167 gpr -- Ghemical format
168 gr96 -- GROMOS96 format [Write-only]
169 hin -- HyperChem HIN format
170 inchi -- IUPAC InChI [Write-only]
171 inp -- GAMESS Input [Write-only]
172 ins -- ShelX format [Read-only]
173 jin -- Jaguar input format [Write-only]
174 jout -- Jaguar output format [Read-only]
175 mdl -- MDL MOL format
176 mmd -- MacroModel format
177 mmod -- MacroModel format
178 mol -- MDL MOL format
179 mol2 -- Sybyl Mol2 format
180 molreport -- Open Babel molecule report [Write-only]
181 moo -- MOPAC Output format [Read-only]
182 mop -- MOPAC Cartesian format
183 mopcrt -- MOPAC Cartesian format
184 mopin -- MOPAC Internal
185 mopout -- MOPAC Output format [Read-only]
186 mpc -- MOPAC Cartesian format
187 mpd -- Sybyl descriptor format [Write-only]
188 mpqc -- MPQC output format [Read-only]
189 mpqcin -- MPQC simplified input format [Write-only]
190 nw -- NWChem input format [Write-only]
191 nwo -- NWChem output format [Read-only]
192 pc -- PubChem format [Read-only]
193 pcm -- PCModel format
194 pdb -- Protein Data Bank format
195 pov -- POV-Ray input format [Write-only]
196 pqs -- Parallel Quantum Solutions format
197 prep -- Amber Prep format [Read-only]
198 qcin -- Q-Chem input format [Write-only]
199 qcout -- Q-Chem output format [Read-only]
200 report -- Open Babel report format [Write-only]
201 res -- ShelX format [Read-only]
202 rxn -- MDL RXN format
203 sd -- MDL MOL format
204 sdf -- MDL MOL format
205 smi -- SMILES format
206 sy2 -- Sybyl Mol2 format
207 tdd -- Thermo format
208 test -- Test format [Write-only]
209 therm -- Thermo format
210 tmol -- TurboMole Coordinate format
211 txyz -- Tinker MM2 format [Write-only]
212 unixyz -- UniChem XYZ format
213 vmol -- ViewMol format
214 xed -- XED format [Write-only]
215 xml -- General XML format [Read-only]
216 xyz -- XYZ cartesian coordinates format
217 yob -- YASARA.org YOB format
218 zin -- ZINDO input format [Write-only]
219
221 Individual file formats may have additional formatting options.
222 Input format options are preceded by 'a', e.g. -as
224 Output format options are preceded by 'x', e.g. -xn
226 For further specific information and options, use -H<format-type>
228 e.g., -Hcml
229
231 Standard conversion:
232 babel -ixyz ethanol.xyz -opdb ethanol.pdb
233 Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
234 babel -ismi -omol2
235 Split a multi-molecule file into new1.smi, new2.smi, etc.:
236 babel infile.mol new.smi -m
237
239 obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1),
240 obrotamer(1). The web pages for Open Babel can be found at:
241 <http://openbabel.sourceforge.net/>
242
244 A cast of many, including the currrent maintainers Geoff Hutchison, Chris
245 Morley, Michael Banck, and innumerable others who have contributed fixes
246 and additions. For more contributors to Open Babel, see <http://openba‐
247 bel.sourceforge.net/wiki/THANKS>
248
250 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
251 Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison
252 This program is free software; you can redistribute it and/or modify it
254 under the terms of the GNU General Public License as published by the
255 Free Software Foundation version 2 of the License.
256 This program is distributed in the hope that it will be useful, but
258 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
259 ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
260 License for more details.
261Open Babel 2.1 April 7, 2007 Open Babel 2.1