Subject: CVS commit: pkgsrc/biology/openbabel
From: Kamil Rytarowski
Date: 2019-11-20 18:02:13
Message id:

Log Message:
openbabel: Upgrade to 3.0.0

Upstream changelog

Open Babel 3.0.0

@ghutchis ghutchis released this on 10 Oct - 29 commits to master since this release

This release represents a major update and is strongly recommended for all users.

It also removes deprecated components and breaks the API in a few places. For \ 
information on migrating from the previous version, please see: … ing-to-3-0

We intend to move to semi-annual releases in Spring and Fall, with bug fix \ 
releases as needed.

A sample of major new features:

    Code for handling implicit hydrogens and kekulization has been entirely \ 
replaced. As well as being accurate, the new approach is much faster.
    Speed of reading and writing SMILES has been improved by more than 50-fold.
    Removal of the old 'babel' binary in favor of the newer 'obabel' \ 
command-line tool.
    New improved fragment-based 3D coordinate generation code as part of Google \ 
Summer of code 2018/2019. Significantly faster and more accurate: \
    (Please cite J. Cheminf. (2019) v11, article 49 if you use the new 3D \ 
coordinate generation.)
    New API for handling reactions stored as molecules (e.g. Reaction InChI, etc.)
    New API for copying part of an OBMol as a substructure
    Support for Maestro file format, contributed by Patrick Lorton of Schrodinger

There are an incredible number of improvements, minor features and many bug fixes.

For a full list of changes and to download source packages (and eventually binaries) … ob300.html

Thanks to a cast of many for this release, particularly including Noel O'Boyle;
aandi, adalke (Andrew Dalke), adamjstewart (Adam J. Stewart), afonari (Alexandr \ 
Fonari), artoria2e5 (Mingye Wang), baoilleach (Noel O'Boyle), barrymoo (Barry \ 
Moore), bbucior (Ben Bucior), boryszef (Borys Szefczyk), camannguyen (An \ 
Nguyen), cmanion (Charles A. Manion), cowsandmilk (David Hall), cstein (Casper \ 
Steinmann), derekharmon (Derek Harmon), djhogan (Daniel Hogan), dkoes (David \ 
Koes), e-kwsm (Eisuke Kawashima), eloyfelix (Eloy Felix), fredrikw (Fredrik \ 
Wallner), ghutchis (Geoff Hutchison), hille721 (Christoph Hille), hseara (Hector \ 
Martinez-Seara), jasonychuang (Jason Huang), jeffjanes (Jeff Janes), johnmay \ 
(John Mayfield), katrinleinweber (Katrin Leinweber), keipertk (Kristopher \ 
Keipert), kyle-roberts-arzeda, langner (Karol M. Langner), lorton (Pat Lorton), \ 
mcs07 (Matt Swain), merkys (Andrius Merkys), mkrykunov, mmghahremanpour \ 
(Mohammad Ghahremanpour), mwojcikowski (Maciej Wojcikowski), n-yoshikawa (Naruki \ 
Yoshikawa), nakatamaho (Nakata Maho), nsoranzo (Nicola Soranzo
), oititov (Titov Oleg), orex (Kirill Okhotnikov), pbecherer (Paul Becherer), \ 
peawagon (Jen), philthiel (Philipp Thiel), psavery (Patrick Avery), rmeli (Rocco \ 
Meli), serval2412 (Julien Nabet), sunoru, susilehtola (Susi Lehtola), tgaudin \ 
(Theophile Gaudin), theavey (Thomas Heavey), timvdm (Tim Vandermeersch), \ 
torcolvin (Tor Colvin), wojdyr (Marcin Wojdyr), xomachine (Dmitriy Fomichev), \ 
yishutu (Yi-Shu Tu)

Open Babel 2.4.0 (2016-9-21)

This release represents a major update and should be a stable upgrade, strongly \ 
recommended for all users.

Note that this release deprecates the babel executable in favor of obabel. A \ 
future release will remove babel entirely. For information on the differences, \ 
please see the documentation.
New file formats

    DALTON output files (read only) and DALTON input files (read/write) (Casper \ 
    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 \ 
    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 Wojcikowski)
    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 Moller)
    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-Noel 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 ( (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 \ 
    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 \ (Tomas Racek)
    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, \ (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 Wojcikowski)
    PHP bindings: BaPHPel, a simplified interface (Maciej Wojcikowski)
    Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
    Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick \ 
Fuller, Bjorn Gruning)
    Python bindings, Pybel: compress output if filename ends with .gz (Maciej \ 
    Python bindings, Pybel: Residue support (Maciej Wojcikowski)

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 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)

Cast of contributors

Alexandr Fonari, Anders Steen Christensen, Andreas Kempe, arkose, Benoit \ 
Leblanc, Bjorn Gruning, Casper Steinmann, Chris Morley, Christoph Willing, Craig \ 
James, Dagmar Lenk, David Hall, David Koes, David Lonie, David van der Spoel, \ 
Dmitriy Fomichev, Fulvio Ciriaco, Fredrik Wallner, Geoff Hutchison, Heiko \ 
Becker, Itay Zandbank, Jean-Noel Avila, Jeff Janes, Joaquin Peralta, Joshua \ 
Swamidass, Julien Nabet, Karol Langner, Karthik Rajagopalan, Katsuhiko Nishimra, \ 
Kevin Horan, Kirill Okhotnikov, Lee-Ping, Matt Harvey, Maciej Wojcikowski, \ 
Marcus Hanwell, Mathias Laurin, Matt Swain, Mohamad Mohebifar, Mohammad \ 
Ghahremanpour, Noel O'Boyle, Patrick Avery, Patrick Fuller, Paul van Maaren, \ 
Peng Bai, Philipp Thiel, Reinis Danne, Roger Sayle, Ronald Cohen, Scott \ 
McKechnie, Stefano Forli, Steve Roughley, Steffen Moeller, Tim Vandermeersch, \ 
Tomas Racek, Tomas Trnka, Tor Colvin, Torsten Sachse, Yi-Shu Tu, Zhixiong Zhao