A major new update to OpenBabel has been released, version 2.4.0 is a significant change and is highly recommended.

New file formats

• DALTON output files (read only) and DALTON input files (read/write) (Casper Steinmann)
• JSON format used by ChemDoodle (read/write) (Matt Swain)
• JSON format used by PubChem (read/write) (Matt Swain)
• LPMD's atomic configuration file (read/write) (Joaquin Peralta)
• The format used by the CONTFF and POSFF files in MDFF (read/write) (Kirill Okhotnikov)
• ORCA output files (read only) and ORCA input files (write only) (Dagmar Lenk)
• ORCA-AICCM's extended XYZ format (read/write) (Dagmar Lenk)
• Painter format for custom 2D depictions (write only) (Noel O'Boyle)
• Siesta output files (read only) (Patrick Avery)
• Smiley parser for parsing SMILES according to the OpenSMILES specification (read only) (Tim Vandermeersch)
• STL 3D-printing format (write only) (Matt Harvey)
• Turbomole AOFORCE output (read only) (Mathias Laurin)
• A representation of the VDW surface as a point cloud (write only) (Matt Harvey)

New file format capabilities and options

• AutoDock PDBQT: Options to preserve hydrogens and/or atom names (Matt Harvey)
• CAR: Improved space group support in .car files (kartlee)
• CDXML: Read/write isotopes (Roger Sayle)
• CIF: Extract charges (Kirill Okhotnikov)
• CIF: Improved support for space-groups and symmetries (Alexandr Fonari)
• DL_Poly: Cell information is now read (Kirill Okhotnikov)
• Gaussian FCHK: Parse alpha and beta orbitals (Geoff Hutchison)
• Gaussian out: Extract true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and more (David van der Spoel)
• MDL Mol: Read in atom class information by default and optionally write it out (Roger Sayle)
• MDL Mol: Support added for ZBO, ZCH and HYD extensions (Matt Swain)
• MDL Mol: Implement the MDL valence model on reading (Roger Sayle)
• MDL SDF: Option to write out an ASCII depiction as a property (Noel O'Boyle)
• mmCIF: Improved mmCIF reading (Patrick Fuller)
• mmCIF: Support for atom occupancy and atom_type (Kirill Okhotnikov)
• Mol2: Option to read UCSF Dock scores (Maciej Wójcikowski)
• MOPAC: Read z-matrix data and parse (and prefer) ESP charges (Geoff Hutchison)
• NWChem: Support sequential calculations by optionally overwriting earlier ones (Dmitriy Fomichev)
• NWChem: Extract info on MEP(IRC), NEB and quadrupole moments (Dmitriy Fomichev)
• PDB: Read/write PDB insertion codes (Steffen Möller)
• PNG: Options to crop the margin, and control the background and bond colors (Fredrik Wallner)
• PQR: Use a stored atom radius (if present) in preference to the generic element radius (Zhixiong Zhao)
• PWSCF: Extend parsing of lattice vectors (David Lonie)
• PWSCF: Support newer versions, and the 'alat' term (Patrick Avery)
• SVG: Option to avoid addition of hydrogens to fill valence (Lee-Ping)
• SVG: Option to draw as ball-and-stick (Jean-Noël Avila)
• VASP: Vibration intensities are calculated (Christian Neiss, Mathias Laurin)
• VASP: Custom atom element sorting on writing (Kirill Okhotnikov)

Other new features and improvements

• 2D layout: Improved the choice of which bonds to designate as hash/wedge bonds around a stereo center (Craig James)
• 3D builder: Use bond length corrections based on bond order from Pyykko and Atsumi (http://dx.doi.org/10.1002/chem.200901472) (Geoff Hutchison)
• 3D generation: "--gen3d", allow user to specify the desired speed/quality (Geoff Hutchison)
• Aromaticity: Improved detection (Geoff Hutchison)
• Canonicalisation: Changed behaviour for multi-molecule SMILES. Now each molecule is canonicalized individually and then sorted. (Geoff Hutchison/Tim Vandermeersch)
• Charge models: "--print" writes the partial charges to standard output after calculation (Geoff Hutchison)
• Conformations: Confab, the systematic conformation generator, has been incorporated into Open Babel (David Hall/Noel O'Boyle)
• Conformations: Initial support for ring rotamer sampling (Geoff Hutchison)
• Conformer searching: Performance improvement by avoiding gradient calculation and optimising the default parameters (Geoff Hutchison)
• EEM charge model: Extend to use additional params from http://dx.doi.org/10.1186/s13321-015-0107-1 (Tomáš Raček)
• FillUnitCell operation: Improved behavior (Patrick Fuller)
• Find duplicates: The "--duplicate" option can now return duplicates instead of just removing them (Chris Morley)
• GAFF forcefield: Atom types updated to match Wang et al. J. Comp. Chem. 2004, 25, 1157 (Mohammad Ghahremanpour)
• New charge model: EQeq crystal charge equilibration method (a speed-optimized crystal-focused charge estimator, http://pubs.acs.org/doi/abs/10.1021/jz3008485) (David Lonie)
• New charge model: "fromfile" reads partial charges from a named file (Matt Harvey)
• New conversion operation: "changecell", for changing cell dimensions (Kirill Okhotnikov)
• New command-line utility: "obthermo", for extracting thermochemistry data from QM calculations (David van der Spoel)
• New fingerprint: ECFP (Geoff Hutchison/Noel O'Boyle/Roger Sayle)
• OBConversion: Improvements and API changes to deal with a long-standing memory leak (David Koes)
• OBAtom::IsHBondAcceptor(): Definition updated to take into account the atom environment (Stefano Forli)
• Performance: Faster ring-finding algorithm (Roger Sayle)
• Performance: Faster fingerprint similarity calculations if compiled with -DOPTIMIZE_NATIVE=ON (Noel O'Boyle/Jeff Janes)
• SMARTS matching: The "-s" option now accepts an integer specifying the number of matches required (Chris Morley)
• UFF: Update to use traditional Rappe angle potential (Geoff Hutchison)

Language bindings

• Bindings: Support compiling only the bindings against system libopenbabel (Reinis Danne)
• Java bindings: Add example Scala program using the Java bindings (Reinis Danne)
• New bindings: PHP (Maciej Wójcikowski)
• PHP bindings: BaPHPel, a simplified interface (Maciej Wójcikowski)
• Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
• Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick Fuller, Björn Grüning)
• Python bindings, Pybel: compress output if filename ends with .gz (Maciej Wójcikowski)
• Python bindings, Pybel: Residue support (Maciej Wójcikowski)

Development/Build/Install Improvements

• Version control: move to git and GitHub from subversion and SourceForge
• Continuous integration: Travis for Linux builds and Appveyor for Windows builds (David Lonie and Noel O'Boyle)
• Python installer: Improvements to the Python setup.py installer and "pip install openbabel" (David Hall, Matt Swain, Joshua Swamidass)
• Compilation speedup: Speed up compilation by combining the tests (Noel O'Boyle)
• MacOSX: Support compiling with libc++ on MacOSX (Matt Swain)