Open Babel Documentation Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) Mar 26, 2021 Contents 1 Introduction 3 1.1 Goals of the Open Babel project.....................................3 1.2 Frequently Asked Questions.......................................4 1.3 Thanks..................................................7 2 Install Open Babel 11 2.1 Install a binary package......................................... 11 2.2 Compiling Open Babel.......................................... 11 3 obabel - Convert, Filter and Manipulate Chemical Data 19 3.1 Synopsis................................................. 19 3.2 Options.................................................. 19 3.3 Examples................................................. 22 3.4 Format Options.............................................. 24 3.5 Append property values to the title.................................... 24 3.6 Generating conformers for structures.................................. 24 3.7 Filtering molecules from a multimolecule file.............................. 25 3.8 Substructure and similarity searching.................................. 28 3.9 Sorting molecules............................................ 28 3.10 Remove duplicate molecules....................................... 28 3.11 Aliases for chemical groups....................................... 29 3.12 Forcefield energy and minimization................................... 30 3.13 Aligning molecules or substructures................................... 30 3.14 Specifying the speed of 3D coordinate generation............................ 31 4 The Open Babel GUI 33 4.1 Basic operation.............................................. 33 4.2 Options.................................................. 33 4.3 Multiple input files............................................ 34 4.4 Wildcards in filenames.......................................... 34 4.5 Local input................................................ 35 4.6 Output file................................................ 35 4.7 Graphical display............................................. 35 4.8 Using a restricted set of formats..................................... 35 4.9 Other features.............................................. 35 4.10 Example files............................................... 36 5 Tutorial on using the GUI 37 5.1 Converting chemical file formats..................................... 37 i 5.2 Filtering structures............................................ 39 5.3 Substructure and similarity searching a large dataset.......................... 42 6 Molecular fingerprints and similarity searching 45 6.1 Fingerprint format............................................ 45 6.2 Spectrophores™............................................. 50 7 obabel vs Chemistry Toolkit Rosetta 55 7.1 Heavy atom counts from an SD file................................... 55 7.2 Convert a SMILES string to canonical SMILES............................. 55 7.3 Report how many SD file records are within a certain molecular weight range............. 56 7.4 Convert SMILES file to SD file..................................... 56 7.5 Report the similarity between two structures.............................. 56 7.6 Find the 10 nearest neighbors in a data set................................ 56 7.7 Depict a compound as an image..................................... 57 7.8 Highlight a substructure in the depiction................................. 57 7.9 Align the depiction using a fixed substructure.............................. 58 7.10 Perform a substructure search on an SDF file and report the number of false positives......... 59 7.11 Calculate TPSA............................................. 59 7.12 Working with SD tag data........................................ 60 7.13 Unattempted tasks............................................ 61 8 2D Depiction 63 8.1 Molecular graphics............................................ 64 9 3D Structure Generation 65 9.1 Generate a single conformer....................................... 65 9.2 Generate multiple conformers...................................... 67 10 Molecular Mechanics and Force Fields 71 10.1 Generalized Amber Force Field (gaff).................................. 71 10.2 Ghemical Force Field (ghemical).................................... 72 10.3 MMFF94 Force Field (mmff94)..................................... 72 10.4 Universal Force Field (uff)........................................ 73 11 Write software using the Open Babel library 75 11.1 The Open Babel API........................................... 75 11.2 C++.................................................... 76 11.3 Python.................................................. 79 11.4 Java.................................................... 96 11.5 Perl.................................................... 99 11.6 CSharp and OBDotNet.......................................... 102 11.7 Ruby................................................... 105 11.8 Updating to Open Babel 3.0 from 2.x.................................. 105 12 Cheminformatics 101 109 12.1 Cheminformatics Basics......................................... 109 12.2 Representing Molecules......................................... 111 12.3 Substructure Searching with Indexes.................................. 115 12.4 Molecular Similarity........................................... 117 12.5 Chemical Registration Systems..................................... 118 13 Stereochemistry 121 13.1 Accessing stereochemistry information................................. 121 13.2 The Config() object............................................ 122 ii 13.3 Modifying the stereochemistry...................................... 123 13.4 Stereo perception............................................. 124 13.5 Miscellaneous stereo functions in the API................................ 126 14 Handling of aromaticity 127 14.1 How is aromaticity information stored?................................. 127 14.2 Perception of aromaticity........................................ 127 14.3 SMILES reading and writing....................................... 128 14.4 Effect of modifying the structure..................................... 128 15 Radicals and SMILES extensions 131 15.1 The need for radicals and implicit hydrogen to coexist......................... 131 15.2 How Open Babel does it......................................... 131 15.3 In radicals either the hydrogen or the spin multiplicity can be implicit................. 132 15.4 SMILES extensions for radicals..................................... 133 15.5 Other Supported Extensions....................................... 133 16 Contributing to Open Babel 135 16.1 Overview................................................. 135 16.2 Developing Open Babel......................................... 136 16.3 Documentation.............................................. 140 16.4 Adding a new test............................................ 141 16.5 Software Archaeology.......................................... 145 17 Adding plugins 147 17.1 How to add a new file format...................................... 148 17.2 Adding new operations and options................................... 148 17.3 How to add a new descriptor....................................... 150 18 Supported File Formats and Options 153 18.1 Common cheminformatics formats................................... 154 18.2 Utility formats.............................................. 162 18.3 Other cheminformatics formats..................................... 170 18.4 Computational chemistry formats.................................... 173 18.5 Molecular fingerprint formats...................................... 184 18.6 Crystallography formats......................................... 187 18.7 Reaction formats............................................. 189 18.8 Image formats.............................................. 191 18.9 2D drawing formats........................................... 198 18.10 3D viewer formats............................................ 199 18.11 Kinetics and Thermodynamics formats................................. 201 18.12 Molecular dynamics and docking formats................................ 201 18.13 Volume data formats........................................... 205 18.14 JSON formats.............................................. 206 18.15 Miscellaneous formats.......................................... 207 18.16 Biological data formats.......................................... 207 18.17 Obscure formats............................................. 208 19 Descriptors 209 19.1 Numerical descriptors.......................................... 209 19.2 Textual descriptors............................................ 210 19.3 Descriptors for filtering......................................... 211 20 Charge models 213 20.1 Cheminformatics charge models..................................... 213 iii 20.2 Special charge models.......................................... 213 21 Release Notes 215 21.1 Open Babel 3.0.0............................................. 215 21.2 Open Babel 2.4.0............................................. 223 21.3 Open Babel 2.3.1............................................. 226 21.4 Open Babel 2.3.0............................................. 227 21.5 Open Babel 2.2.3............................................. 229 21.6 Open Babel 2.2.2............................................. 229 21.7 Open Babel 2.2.1............................................. 230 21.8 Open Babel 2.2.0............................................