CVS commit: pkgsrc/biology/openbabel

["Kamil Rytarowski" <kamil%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   kamil
Date:           Wed Nov 20 17:02:13 UTC 2019

Modified Files:
        pkgsrc/biology/openbabel: Makefile PLIST buildlink3.mk distinfo
        pkgsrc/biology/openbabel/patches: patch-doc_CMakeLists.txt
Added Files:
        pkgsrc/biology/openbabel/patches: patch-src_conformersearch.cpp
            patch-src_formats_confabreport.cpp
Removed Files:
        pkgsrc/biology/openbabel: PLIST.Linux PLIST.SunOS
        pkgsrc/biology/openbabel/patches:
            patch-include_openbabel_obmolecformat.h
            patch-include_openbabel_shared__ptr.h patch-src_ops_unique.cpp

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:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#migrating-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: https://doi.org/10.1186/s13321-019-0372-5
    (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)
https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob300.html
https://github.com/openbabel/openbabel/releases

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 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 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 (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 (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, 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 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 Wojcikowski)
    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 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)

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


To generate a diff of this commit:
cvs rdiff -u -r1.34 -r1.35 pkgsrc/biology/openbabel/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/openbabel/PLIST \
    pkgsrc/biology/openbabel/buildlink3.mk
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/openbabel/PLIST.Linux \
    pkgsrc/biology/openbabel/PLIST.SunOS
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/openbabel/distinfo
cvs rdiff -u -r1.4 -r1.5 \
    pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt
cvs rdiff -u -r1.1 -r0 \
    pkgsrc/biology/openbabel/patches/patch-include_openbabel_obmolecformat.h
cvs rdiff -u -r1.2 -r0 \
    pkgsrc/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h \
    pkgsrc/biology/openbabel/patches/patch-src_ops_unique.cpp
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/openbabel/patches/patch-src_conformersearch.cpp \
    pkgsrc/biology/openbabel/patches/patch-src_formats_confabreport.cpp

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/openbabel/Makefile
diff -u pkgsrc/biology/openbabel/Makefile:1.34 pkgsrc/biology/openbabel/Makefile:1.35
--- pkgsrc/biology/openbabel/Makefile:1.34      Sun Jul 21 22:24:29 2019
+++ pkgsrc/biology/openbabel/Makefile   Wed Nov 20 17:02:12 2019
@@ -1,22 +1,34 @@
-# $NetBSD: Makefile,v 1.34 2019/07/21 22:24:29 wiz Exp $
+# $NetBSD: Makefile,v 1.35 2019/11/20 17:02:12 kamil Exp $
 #
 
-DISTNAME=      openbabel-2.3.2
-PKGREVISION=   9
+GITHUB_PROJECT=        openbabel
+DISTNAME=      openbabel-${RELVERSION:S/-/./g}
 CATEGORIES=    biology
-MASTER_SITES=  ${MASTER_SITE_SOURCEFORGE:=openbabel/}
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=openbabel/}
+GITHUB_TAG=    ${PKGBASE}-${RELVERSION}
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 HOMEPAGE=      http://openbabel.org/
 COMMENT=       Chemistry file translation program
 LICENSE=       gnu-gpl-v2
 
-USE_LANGUAGES= c c++03
+RELVERSION=    3-0-0
+
+USE_LANGUAGES= c gnu++11
 USE_TOOLS+=    pkg-config
 USE_CMAKE=     yes
 
 .include "options.mk"
 
+CONFIGURE_DIRS=                ${WRKDIR}/build
+CMAKE_ARG_PATH=                ${WRKSRC}
+
+CMAKE_ARGS+=   -DLLVM_CONFIG=${LLVM_CONFIG_PATH:Q}
+
+post-extract:
+       ${MKDIR} ${WRKDIR}/build
+
+.include "../../graphics/cairo/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../math/eigen2/buildlink3.mk"
 .include "../../textproc/libxml2/buildlink3.mk"

Index: pkgsrc/biology/openbabel/PLIST
diff -u pkgsrc/biology/openbabel/PLIST:1.3 pkgsrc/biology/openbabel/PLIST:1.4
--- pkgsrc/biology/openbabel/PLIST:1.3  Thu Nov 20 09:10:32 2014
+++ pkgsrc/biology/openbabel/PLIST      Wed Nov 20 17:02:12 2019
@@ -1,106 +1,118 @@
-@comment $NetBSD: PLIST,v 1.3 2014/11/20 09:10:32 mef Exp $
-${PLIST.wx-gui}bin/obgui
-bin/babel
+@comment $NetBSD: PLIST,v 1.4 2019/11/20 17:02:12 kamil Exp $
 bin/obabel
-bin/obchiral
 bin/obconformer
 bin/obenergy
 bin/obfit
+bin/obfitall
 bin/obgen
 bin/obgrep
 bin/obminimize
+bin/obmm
 bin/obprobe
 bin/obprop
 bin/obrotamer
 bin/obrotate
 bin/obspectrophore
+bin/obsym
+bin/obtautomer
+bin/obthermo
 bin/roundtrip
 include/inchi/inchi_api.h
-include/openbabel-2.0/openbabel/alias.h
-include/openbabel-2.0/openbabel/atom.h
-include/openbabel-2.0/openbabel/atomclass.h
-include/openbabel-2.0/openbabel/babelconfig.h
-include/openbabel-2.0/openbabel/base.h
-include/openbabel-2.0/openbabel/bitvec.h
-include/openbabel-2.0/openbabel/bond.h
-include/openbabel-2.0/openbabel/bondtyper.h
-include/openbabel-2.0/openbabel/builder.h
-include/openbabel-2.0/openbabel/canon.h
-include/openbabel-2.0/openbabel/chains.h
-include/openbabel-2.0/openbabel/chargemodel.h
-include/openbabel-2.0/openbabel/chemdrawcdx.h
-include/openbabel-2.0/openbabel/chiral.h
-include/openbabel-2.0/openbabel/conformersearch.h
-include/openbabel-2.0/openbabel/data.h
-include/openbabel-2.0/openbabel/descriptor.h
-include/openbabel-2.0/openbabel/dlhandler.h
-include/openbabel-2.0/openbabel/fingerprint.h
-include/openbabel-2.0/openbabel/forcefield.h
-include/openbabel-2.0/openbabel/format.h
-include/openbabel-2.0/openbabel/generic.h
-include/openbabel-2.0/openbabel/graphsym.h
-include/openbabel-2.0/openbabel/grid.h
-include/openbabel-2.0/openbabel/griddata.h
-include/openbabel-2.0/openbabel/groupcontrib.h
-include/openbabel-2.0/openbabel/inchiformat.h
-include/openbabel-2.0/openbabel/internalcoord.h
-include/openbabel-2.0/openbabel/isomorphism.h
-include/openbabel-2.0/openbabel/kinetics.h
-include/openbabel-2.0/openbabel/lineend.h
-include/openbabel-2.0/openbabel/locale.h
-include/openbabel-2.0/openbabel/math/align.h
-include/openbabel-2.0/openbabel/math/erf.h
-include/openbabel-2.0/openbabel/math/matrix3x3.h
-include/openbabel-2.0/openbabel/math/spacegroup.h
-include/openbabel-2.0/openbabel/math/transform3d.h
-include/openbabel-2.0/openbabel/math/vector3.h
-include/openbabel-2.0/openbabel/matrix.h
-include/openbabel-2.0/openbabel/mcdlutil.h
-include/openbabel-2.0/openbabel/mol.h
-include/openbabel-2.0/openbabel/molchrg.h
-include/openbabel-2.0/openbabel/obconversion.h
-include/openbabel-2.0/openbabel/oberror.h
-include/openbabel-2.0/openbabel/obiter.h
-include/openbabel-2.0/openbabel/obmolecformat.h
-include/openbabel-2.0/openbabel/obutil.h
-include/openbabel-2.0/openbabel/op.h
-include/openbabel-2.0/openbabel/optransform.h
-include/openbabel-2.0/openbabel/parsmart.h
-include/openbabel-2.0/openbabel/patty.h
-include/openbabel-2.0/openbabel/phmodel.h
-include/openbabel-2.0/openbabel/plugin.h
-include/openbabel-2.0/openbabel/pointgroup.h
-include/openbabel-2.0/openbabel/query.h
-include/openbabel-2.0/openbabel/rand.h
-include/openbabel-2.0/openbabel/reaction.h
-include/openbabel-2.0/openbabel/residue.h
-include/openbabel-2.0/openbabel/ring.h
-include/openbabel-2.0/openbabel/rotamer.h
-include/openbabel-2.0/openbabel/rotor.h
-include/openbabel-2.0/openbabel/shared_ptr.h
-include/openbabel-2.0/openbabel/spectrophore.h
-include/openbabel-2.0/openbabel/stereo/bindings.h
-include/openbabel-2.0/openbabel/stereo/cistrans.h
-include/openbabel-2.0/openbabel/stereo/squareplanar.h
-include/openbabel-2.0/openbabel/stereo/stereo.h
-include/openbabel-2.0/openbabel/stereo/tetrahedral.h
-include/openbabel-2.0/openbabel/stereo/tetranonplanar.h
-include/openbabel-2.0/openbabel/stereo/tetraplanar.h
-include/openbabel-2.0/openbabel/text.h
-include/openbabel-2.0/openbabel/tokenst.h
-include/openbabel-2.0/openbabel/typer.h
-include/openbabel-2.0/openbabel/xml.h
-lib/cmake/openbabel2/OpenBabel2Config.cmake
-lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake
-lib/cmake/openbabel2/OpenBabel2_EXPORTS-relwithdebinfo.cmake
-lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake
+include/openbabel3/openbabel/alias.h
+include/openbabel3/openbabel/atom.h
+include/openbabel3/openbabel/babelconfig.h
+include/openbabel3/openbabel/base.h
+include/openbabel3/openbabel/bitvec.h
+include/openbabel3/openbabel/bond.h
+include/openbabel3/openbabel/bondtyper.h
+include/openbabel3/openbabel/builder.h
+include/openbabel3/openbabel/canon.h
+include/openbabel3/openbabel/chains.h
+include/openbabel3/openbabel/chargemodel.h
+include/openbabel3/openbabel/chemdrawcdx.h
+include/openbabel3/openbabel/conformersearch.h
+include/openbabel3/openbabel/data.h
+include/openbabel3/openbabel/data_utilities.h
+include/openbabel3/openbabel/depict/asciipainter.h
+include/openbabel3/openbabel/depict/cairopainter.h
+include/openbabel3/openbabel/depict/commandpainter.h
+include/openbabel3/openbabel/depict/depict.h
+include/openbabel3/openbabel/depict/painter.h
+include/openbabel3/openbabel/depict/svgpainter.h
+include/openbabel3/openbabel/descriptor.h
+include/openbabel3/openbabel/distgeom.h
+include/openbabel3/openbabel/dlhandler.h
+include/openbabel3/openbabel/elements.h
+include/openbabel3/openbabel/fingerprint.h
+include/openbabel3/openbabel/forcefield.h
+include/openbabel3/openbabel/format.h
+include/openbabel3/openbabel/generic.h
+include/openbabel3/openbabel/graphsym.h
+include/openbabel3/openbabel/grid.h
+include/openbabel3/openbabel/griddata.h
+include/openbabel3/openbabel/groupcontrib.h
+include/openbabel3/openbabel/inchiformat.h
+include/openbabel3/openbabel/internalcoord.h
+include/openbabel3/openbabel/isomorphism.h
+include/openbabel3/openbabel/json.h
+include/openbabel3/openbabel/kekulize.h
+include/openbabel3/openbabel/kinetics.h
+include/openbabel3/openbabel/lineend.h
+include/openbabel3/openbabel/locale.h
+include/openbabel3/openbabel/math/align.h
+include/openbabel3/openbabel/math/erf.h
+include/openbabel3/openbabel/math/matrix3x3.h
+include/openbabel3/openbabel/math/spacegroup.h
+include/openbabel3/openbabel/math/transform3d.h
+include/openbabel3/openbabel/math/vector3.h
+include/openbabel3/openbabel/matrix.h
+include/openbabel3/openbabel/mcdlutil.h
+include/openbabel3/openbabel/mol.h
+include/openbabel3/openbabel/molchrg.h
+include/openbabel3/openbabel/obconversion.h
+include/openbabel3/openbabel/oberror.h
+include/openbabel3/openbabel/obfunctions.h
+include/openbabel3/openbabel/obiter.h
+include/openbabel3/openbabel/obmolecformat.h
+include/openbabel3/openbabel/obutil.h
+include/openbabel3/openbabel/op.h
+include/openbabel3/openbabel/optransform.h
+include/openbabel3/openbabel/parsmart.h
+include/openbabel3/openbabel/patty.h
+include/openbabel3/openbabel/phmodel.h
+include/openbabel3/openbabel/plugin.h
+include/openbabel3/openbabel/pointgroup.h
+include/openbabel3/openbabel/query.h
+include/openbabel3/openbabel/reaction.h
+include/openbabel3/openbabel/reactionfacade.h
+include/openbabel3/openbabel/residue.h
+include/openbabel3/openbabel/ring.h
+include/openbabel3/openbabel/rotamer.h
+include/openbabel3/openbabel/rotor.h
+include/openbabel3/openbabel/shared_ptr.h
+include/openbabel3/openbabel/spectrophore.h
+include/openbabel3/openbabel/stereo/bindings.h
+include/openbabel3/openbabel/stereo/cistrans.h
+include/openbabel3/openbabel/stereo/squareplanar.h
+include/openbabel3/openbabel/stereo/stereo.h
+include/openbabel3/openbabel/stereo/tetrahedral.h
+include/openbabel3/openbabel/stereo/tetranonplanar.h
+include/openbabel3/openbabel/stereo/tetraplanar.h
+include/openbabel3/openbabel/tautomer.h
+include/openbabel3/openbabel/text.h
+include/openbabel3/openbabel/tokenst.h
+include/openbabel3/openbabel/typer.h
+include/openbabel3/openbabel/xml.h
+lib/cmake/openbabel3/OpenBabel3Config.cmake
+lib/cmake/openbabel3/OpenBabel3ConfigVersion.cmake
+lib/cmake/openbabel3/OpenBabel3_EXPORTS-release.cmake
+lib/cmake/openbabel3/OpenBabel3_EXPORTS.cmake
 lib/libinchi.so
 lib/libinchi.so.0
 lib/libinchi.so.0.4.1
 lib/libopenbabel.so
-lib/libopenbabel.so.4
-lib/libopenbabel.so.4.0.2
-${PLIST.wx-gui}lib/openbabel/${PKGVERSION}/png2format.so
+lib/libopenbabel.so.6
+lib/libopenbabel.so.6.0.0
 lib/openbabel/${PKGVERSION}/APIInterface.so
 lib/openbabel/${PKGVERSION}/CSRformat.so
 lib/openbabel/${PKGVERSION}/MCDLformat.so
@@ -112,6 +124,7 @@ lib/openbabel/${PKGVERSION}/acrformat.so
 lib/openbabel/${PKGVERSION}/adfformat.so
 lib/openbabel/${PKGVERSION}/alchemyformat.so
 lib/openbabel/${PKGVERSION}/amberformat.so
+lib/openbabel/${PKGVERSION}/aoforceformat.so
 lib/openbabel/${PKGVERSION}/asciiformat.so
 lib/openbabel/${PKGVERSION}/balstformat.so
 lib/openbabel/${PKGVERSION}/bgfformat.so
@@ -123,6 +136,7 @@ lib/openbabel/${PKGVERSION}/castepformat
 lib/openbabel/${PKGVERSION}/cccformat.so
 lib/openbabel/${PKGVERSION}/cdxmlformat.so
 lib/openbabel/${PKGVERSION}/chem3dformat.so
+lib/openbabel/${PKGVERSION}/chemdoodlejsonformat.so
 lib/openbabel/${PKGVERSION}/chemdrawcdx.so
 lib/openbabel/${PKGVERSION}/chemdrawct.so
 lib/openbabel/${PKGVERSION}/chemkinformat.so
@@ -130,12 +144,16 @@ lib/openbabel/${PKGVERSION}/chemtoolform
 lib/openbabel/${PKGVERSION}/cifformat.so
 lib/openbabel/${PKGVERSION}/cmlformat.so
 lib/openbabel/${PKGVERSION}/cmlreactformat.so
+lib/openbabel/${PKGVERSION}/cofformat.so
+lib/openbabel/${PKGVERSION}/confabreport.so
 lib/openbabel/${PKGVERSION}/copyformat.so
 lib/openbabel/${PKGVERSION}/crkformat.so
 lib/openbabel/${PKGVERSION}/crystal09format.so
 lib/openbabel/${PKGVERSION}/cssrformat.so
+lib/openbabel/${PKGVERSION}/daltonformat.so
 lib/openbabel/${PKGVERSION}/dlpolyformat.so
 lib/openbabel/${PKGVERSION}/dmolformat.so
+lib/openbabel/${PKGVERSION}/exyzformat.so
 lib/openbabel/${PKGVERSION}/fastaformat.so
 lib/openbabel/${PKGVERSION}/fastsearchformat.so
 lib/openbabel/${PKGVERSION}/fchkformat.so
@@ -158,6 +176,8 @@ lib/openbabel/${PKGVERSION}/hinformat.so
 lib/openbabel/${PKGVERSION}/inchiformat.so
 lib/openbabel/${PKGVERSION}/jaguarformat.so
 lib/openbabel/${PKGVERSION}/lmpdatformat.so
+lib/openbabel/${PKGVERSION}/lpmdformat.so
+lib/openbabel/${PKGVERSION}/mdffformat.so
 lib/openbabel/${PKGVERSION}/mdlformat.so
 lib/openbabel/${PKGVERSION}/mmcifformat.so
 lib/openbabel/${PKGVERSION}/mmodformat.so
@@ -173,7 +193,9 @@ lib/openbabel/${PKGVERSION}/msmsformat.s
 lib/openbabel/${PKGVERSION}/nulformat.so
 lib/openbabel/${PKGVERSION}/nwchemformat.so
 lib/openbabel/${PKGVERSION}/opendxformat.so
+lib/openbabel/${PKGVERSION}/orcaformat.so
 lib/openbabel/${PKGVERSION}/outformat.so
+lib/openbabel/${PKGVERSION}/painterformat.so
 lib/openbabel/${PKGVERSION}/pcmodelformat.so
 lib/openbabel/${PKGVERSION}/pdbformat.so
 lib/openbabel/${PKGVERSION}/pdbqtformat.so
@@ -182,18 +204,25 @@ lib/openbabel/${PKGVERSION}/plugin_descr
 lib/openbabel/${PKGVERSION}/plugin_fingerprints.so
 lib/openbabel/${PKGVERSION}/plugin_forcefields.so
 lib/openbabel/${PKGVERSION}/plugin_ops.so
+lib/openbabel/${PKGVERSION}/png2format.so
 lib/openbabel/${PKGVERSION}/pngformat.so
+lib/openbabel/${PKGVERSION}/pointcloudformat.so
 lib/openbabel/${PKGVERSION}/posformat.so
 lib/openbabel/${PKGVERSION}/povrayformat.so
 lib/openbabel/${PKGVERSION}/pqrformat.so
 lib/openbabel/${PKGVERSION}/pubchem.so
+lib/openbabel/${PKGVERSION}/pubchemjsonformat.so
 lib/openbabel/${PKGVERSION}/pwscfformat.so
 lib/openbabel/${PKGVERSION}/qchemformat.so
 lib/openbabel/${PKGVERSION}/reportformat.so
+lib/openbabel/${PKGVERSION}/rinchiformat.so
 lib/openbabel/${PKGVERSION}/rsmiformat.so
 lib/openbabel/${PKGVERSION}/rxnformat.so
 lib/openbabel/${PKGVERSION}/shelxformat.so
+lib/openbabel/${PKGVERSION}/siestaformat.so
 lib/openbabel/${PKGVERSION}/smilesformat.so
+lib/openbabel/${PKGVERSION}/smileyformat.so
+lib/openbabel/${PKGVERSION}/stlformat.so
 lib/openbabel/${PKGVERSION}/svgformat.so
 lib/openbabel/${PKGVERSION}/textformat.so
 lib/openbabel/${PKGVERSION}/thermoformat.so
@@ -209,11 +238,12 @@ lib/openbabel/${PKGVERSION}/xsfformat.so
 lib/openbabel/${PKGVERSION}/xyzformat.so
 lib/openbabel/${PKGVERSION}/yasaraformat.so
 lib/openbabel/${PKGVERSION}/zindoformat.so
-lib/pkgconfig/openbabel-2.0.pc
+lib/pkgconfig/openbabel-3.pc
 man/man1/babel.1
 man/man1/obabel.1
 man/man1/obchiral.1
 man/man1/obconformer.1
+man/man1/obdistgen.1
 man/man1/obenergy.1
 man/man1/obfit.1
 man/man1/obgen.1
@@ -222,24 +252,32 @@ man/man1/obgui.1
 man/man1/obminimize.1
 man/man1/obprobe.1
 man/man1/obprop.1
+man/man1/obrms.1
 man/man1/obrotamer.1
 man/man1/obrotate.1
 man/man1/obspectrophore.1
+man/man1/obsym.1
+man/man1/obtautomer.1
+man/man1/obthermo.1
 man/man1/roundtrip.1
 share/openbabel/${PKGVERSION}/MACCS.txt
 share/openbabel/${PKGVERSION}/SMARTS_InteLigand.txt
 share/openbabel/${PKGVERSION}/UFF.prm
-share/openbabel/${PKGVERSION}/aromatic.txt
+share/openbabel/${PKGVERSION}/atomization-energies.txt
 share/openbabel/${PKGVERSION}/atomtyp.txt
 share/openbabel/${PKGVERSION}/babel_povray3.inc
 share/openbabel/${PKGVERSION}/bondtyp.txt
-share/openbabel/${PKGVERSION}/element.txt
-share/openbabel/${PKGVERSION}/fragments.txt
+share/openbabel/${PKGVERSION}/eem.txt
+share/openbabel/${PKGVERSION}/eem2015ba.txt
+share/openbabel/${PKGVERSION}/eem2015bm.txt
+share/openbabel/${PKGVERSION}/eem2015bn.txt
+share/openbabel/${PKGVERSION}/eem2015ha.txt
+share/openbabel/${PKGVERSION}/eem2015hm.txt
+share/openbabel/${PKGVERSION}/eem2015hn.txt
+share/openbabel/${PKGVERSION}/eqeqIonizations.txt
 share/openbabel/${PKGVERSION}/gaff.dat
 share/openbabel/${PKGVERSION}/gaff.prm
 share/openbabel/${PKGVERSION}/ghemical.prm
-share/openbabel/${PKGVERSION}/isotope-small.txt
-share/openbabel/${PKGVERSION}/isotope.txt
 share/openbabel/${PKGVERSION}/logp.txt
 share/openbabel/${PKGVERSION}/mmff94.ff
 share/openbabel/${PKGVERSION}/mmff94s.ff
@@ -257,6 +295,7 @@ share/openbabel/${PKGVERSION}/mmffs_tor.
 share/openbabel/${PKGVERSION}/mmffstbn.par
 share/openbabel/${PKGVERSION}/mmfftor.par
 share/openbabel/${PKGVERSION}/mmffvdw.par
+share/openbabel/${PKGVERSION}/mpC.txt
 share/openbabel/${PKGVERSION}/mr.txt
 share/openbabel/${PKGVERSION}/patterns.txt
 share/openbabel/${PKGVERSION}/phmodel.txt
@@ -264,10 +303,15 @@ share/openbabel/${PKGVERSION}/plugindefi
 share/openbabel/${PKGVERSION}/psa.txt
 share/openbabel/${PKGVERSION}/qeq.txt
 share/openbabel/${PKGVERSION}/resdata.txt
+share/openbabel/${PKGVERSION}/rigid-fragments-index.txt
+share/openbabel/${PKGVERSION}/rigid-fragments.txt
+share/openbabel/${PKGVERSION}/ring-fragments.txt
 share/openbabel/${PKGVERSION}/ringtyp.txt
 share/openbabel/${PKGVERSION}/space-groups.txt
 share/openbabel/${PKGVERSION}/splash.png
 share/openbabel/${PKGVERSION}/superatom.txt
 share/openbabel/${PKGVERSION}/svgformat.script
+share/openbabel/${PKGVERSION}/templates.sdf
 share/openbabel/${PKGVERSION}/torlib.txt
+share/openbabel/${PKGVERSION}/torsion.txt
 share/openbabel/${PKGVERSION}/types.txt
Index: pkgsrc/biology/openbabel/buildlink3.mk
diff -u pkgsrc/biology/openbabel/buildlink3.mk:1.3 pkgsrc/biology/openbabel/buildlink3.mk:1.4
--- pkgsrc/biology/openbabel/buildlink3.mk:1.3  Sun Jan  7 13:03:56 2018
+++ pkgsrc/biology/openbabel/buildlink3.mk      Wed Nov 20 17:02:12 2019
@@ -1,14 +1,15 @@
-# $NetBSD: buildlink3.mk,v 1.3 2018/01/07 13:03:56 rillig Exp $
+# $NetBSD: buildlink3.mk,v 1.4 2019/11/20 17:02:12 kamil Exp $
 
 BUILDLINK_TREE+=       openbabel
 
 .if !defined(OPENBABEL_BUILDLINK3_MK)
 OPENBABEL_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.openbabel+=      openbabel>=2.3.0
-BUILDLINK_ABI_DEPENDS.openbabel?=      openbabel>=2.3.0nb4
+BUILDLINK_API_DEPENDS.openbabel+=      openbabel>=3.0.0
+BUILDLINK_ABI_DEPENDS.openbabel?=      openbabel>=3.0.0
 BUILDLINK_PKGSRCDIR.openbabel?=                ../../biology/openbabel
 
+.include "../../graphics/cairo/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../math/eigen2/buildlink3.mk"
 .include "../../textproc/libxml2/buildlink3.mk"

Index: pkgsrc/biology/openbabel/distinfo
diff -u pkgsrc/biology/openbabel/distinfo:1.7 pkgsrc/biology/openbabel/distinfo:1.8
--- pkgsrc/biology/openbabel/distinfo:1.7       Mon Nov  2 18:42:22 2015
+++ pkgsrc/biology/openbabel/distinfo   Wed Nov 20 17:02:12 2019
@@ -1,10 +1,9 @@
-$NetBSD: distinfo,v 1.7 2015/11/02 18:42:22 agc Exp $
+$NetBSD: distinfo,v 1.8 2019/11/20 17:02:12 kamil Exp $
 
-SHA1 (openbabel-2.3.2.tar.gz) = b8831a308617d1c78a790479523e43524f07d50d
-RMD160 (openbabel-2.3.2.tar.gz) = dc9aa026a81b987b08c60709a624a192418ee7fb
-SHA512 (openbabel-2.3.2.tar.gz) = d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919
-Size (openbabel-2.3.2.tar.gz) = 20509105 bytes
-SHA1 (patch-doc_CMakeLists.txt) = ce39c53c4edfec2f557e785f750e09a62a209d05
-SHA1 (patch-include_openbabel_obmolecformat.h) = e12a42b67106899d5285651f27e4830e0cc42fe2
-SHA1 (patch-include_openbabel_shared__ptr.h) = 92a16f7bcdd10cf44cf6c9302d80670563074c2c
-SHA1 (patch-src_ops_unique.cpp) = 80b9e7ca8a405ea7024bbca832b16a8013c12e18
+SHA1 (openbabel-3.0.0.tar.gz) = 8e1428127f00e39f5f05f58b9b186cd8e50f2486
+RMD160 (openbabel-3.0.0.tar.gz) = 333fd2af6dd6e59ca88258c2f228932a728321c6
+SHA512 (openbabel-3.0.0.tar.gz) = 94af7cffec7de3a7c9d18ea0e1f7b95b0fc64ec563ddb9d420bfb8e9dfa6ac2365338e55e0444e1f5aa2a9f35f5f53961212193c0fdb9d4fd348bd8f61a1684e
+Size (openbabel-3.0.0.tar.gz) = 36571060 bytes
+SHA1 (patch-doc_CMakeLists.txt) = c4a46fd0ddd253fb755680d7eb91799c74a6489d
+SHA1 (patch-src_conformersearch.cpp) = 0f16cc0d0a45e30c6bf00af3b67fac435013a337
+SHA1 (patch-src_formats_confabreport.cpp) = d9f81b6dfeff8ce7e94be5fdb375972ca8d422f2

Index: pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt
diff -u pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt:1.4 pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt:1.5
--- pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt:1.4       Thu Nov 20 09:05:56 2014
+++ pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt   Wed Nov 20 17:02:12 2019
@@ -1,10 +1,10 @@
-$NetBSD: patch-doc_CMakeLists.txt,v 1.4 2014/11/20 09:05:56 mef Exp $
+$NetBSD: patch-doc_CMakeLists.txt,v 1.5 2019/11/20 17:02:12 kamil Exp $
 
-Fix man path.
-
---- doc/CMakeLists.txt.orig    2012-10-04 04:08:55.000000000 +0900
-+++ doc/CMakeLists.txt 2014-11-20 17:53:33.000000000 +0900
-@@ -1,5 +1,5 @@
+--- doc/CMakeLists.txt.orig    2019-10-07 16:39:17.000000000 +0000
++++ doc/CMakeLists.txt
+@@ -1,5 +1,7 @@
++include(GNUInstallDirs)
++
  file(GLOB man_1 *.1)
 -install(FILES ${man_1} DESTINATION share/man/man1)
 +install(FILES ${man_1} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)

Added files:

Index: pkgsrc/biology/openbabel/patches/patch-src_conformersearch.cpp
diff -u /dev/null pkgsrc/biology/openbabel/patches/patch-src_conformersearch.cpp:1.1
--- /dev/null   Wed Nov 20 17:02:13 2019
+++ pkgsrc/biology/openbabel/patches/patch-src_conformersearch.cpp      Wed Nov 20 17:02:12 2019
@@ -0,0 +1,12 @@
+$NetBSD: patch-src_conformersearch.cpp,v 1.1 2019/11/20 17:02:12 kamil Exp $
+
+--- src/conformersearch.cpp.orig       2019-10-07 16:39:17.000000000 +0000
++++ src/conformersearch.cpp
+@@ -23,6 +23,7 @@ GNU General Public License for more deta
+ #include <openbabel/elements.h>
+ #include <openbabel/bond.h>
+ #include "rand.h"
++#include <algorithm>
+ 
+ #if defined(_MSC_VER) && (_MSC_VER < 1800)
+  #define OB_ISNAN _isnan
Index: pkgsrc/biology/openbabel/patches/patch-src_formats_confabreport.cpp
diff -u /dev/null pkgsrc/biology/openbabel/patches/patch-src_formats_confabreport.cpp:1.1
--- /dev/null   Wed Nov 20 17:02:13 2019
+++ pkgsrc/biology/openbabel/patches/patch-src_formats_confabreport.cpp Wed Nov 20 17:02:12 2019
@@ -0,0 +1,17 @@
+$NetBSD: patch-src_formats_confabreport.cpp,v 1.1 2019/11/20 17:02:12 kamil Exp $
+
+--- src/formats/confabreport.cpp.orig  2019-10-07 16:39:17.000000000 +0000
++++ src/formats/confabreport.cpp
+@@ -33,6 +33,7 @@ as an example.
+ #include <openbabel/babelconfig.h>
+ #include <openbabel/obmolecformat.h>
+ #include <openbabel/math/align.h>
++#include <algorithm>
+ 
+ using namespace std;
+ namespace OpenBabel
+@@ -224,4 +225,3 @@ bool ConfabReport::WriteMolecule(OBBase*
+ }
+ 
+ } //namespace OpenBabel
+-