./biology/openbabel, Chemistry file translation program

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Branch: CURRENT, Version: 3.1.1nb5, Package name: openbabel-3.1.1nb5, Maintainer: pkgsrc-users

Open Babel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing
anyone to search, convert, analyze, or store data from molecular
modeling, chemistry, solid-state materials, biochemistry, or related

Required to run:
[textproc/libxml2] [graphics/cairo] [devel/boost-libs]

Required to build:
[pkgtools/x11-links] [devel/boost-headers] [x11/xcb-proto] [math/eigen3] [pkgtools/cwrappers] [x11/xorgproto]

Master sites:

SHA1: 22d5eea2492d4ea55fd29f9dcea34fd972af2a27
RMD160: 74c74c3129d47ecf70f37d17c1caa42693f6be28
Filesize: 35828.612 KB

Version history: (Expand)

CVS history: (Expand)

   2021-03-17 19:58:57 by Patrick Welche | Files touched by this commit (3)
Log message:
openbabel: make buildlink3.mk match Makefile and require eigen3
The dependency is visible for packages using the LBFGS solver.
   2021-01-01 09:24:59 by Ryo ONODERA | Files touched by this commit (266)
Log message:
*: Recursive revbump from boost-1.75.0
   2020-11-05 10:09:30 by Ryo ONODERA | Files touched by this commit (1814)
Log message:
*: Recursive revbump from textproc/icu-68.1
   2020-11-04 20:54:12 by Benny Siegert | Files touched by this commit (4)
Log message:
openbabel: do not download dependencies during build

Explicitly depend against maeparser, coordgenlibs and rapidjson, so that
the build does not download the current version from github (!).

Also fix the coordgenlibs detection logic -- this is also submitted

Fixes PR pkg/55755
   2020-11-02 00:06:39 by Makoto Fujiwara | Files touched by this commit (1)
Log message:
(biology/openbabel) Regen PLIST
   2020-08-17 22:20:41 by Leonardo Taccari | Files touched by this commit (2202)
Log message:
*: revbump after fontconfig bl3 changes (libuuid removal)
   2020-06-29 14:40:02 by Ryo ONODERA | Files touched by this commit (1)
Log message:
openbabel: Fix PLIST
   2020-06-29 14:10:34 by Ryo ONODERA | Files touched by this commit (9) | Package removed
Log message:
openbabel: Update to 3.1.1

* Depends on boost. If you have boost, cmake detects boost and it causes
  build failure.

This version primarily reflects fixes for packaging on Linux and FreeBSD
relative to 3.1.0. No features or significant bug fixes were involved.

This version represents additional API and is backwards-compatible with the 3.0 \ 

Significant features and fixes

    Fixed tautomer code (by timvdm #2171)
    New functionality: Support for periodic boundary conditions. See additional \ 
option -p for MMCIF format, and write option 'g' for CIF. (by bbucior, #1853)
    New functionality: Add distance geometry method (by n-yoshikawa, #1875, by \ 
timvdm #2158)
    Fixed crashes with new 3D coordinate generation (by timvdm #2149 and \ 
ghutchis #2150)

New features and improvements

    New file format: Wiswesser Line Notation reader from Roger Sayle (by \ 
baoilleach, #2084)
    New option: Add the --neutralize operation to convert charged atoms to \ 
neutral (by baoilleach, #2109)
    Update GAS CONSTANT to 2018 CODATA recommended value (by e-kwsm, #2045)
    Support #0 in SMARTS so that asterisks can be matched (by baoilleach, #2079)
    Bring back support for lowercase elements and D/T in GetAtomicNum(). (by \ 
baoilleach, #2100)
    Change docstrings of add/delete hydrogens to better reflect their \ 
functionality (by baoilleach, #2110)
    Support kekulization of aromatic sulfoxides (by baoilleach, #2121)
    Enable casting to StereoBase in the Python bindings (by baoilleach, #2124)
    OBBuilder: Add error message for ring/rigid fragments with all zero coords. \ 
(by timvdm, #2149)
    R script updates (by khoran, #2145)
    Be more strict when parsing charges in SMILES (by baoilleach, #2132)
    Improve tools/obconformer.cpp (by e-kwsm, #2154)

Bug fixes

    Fix CMake error with R and C# bindings (by ghutchis, #2051)
    Rename MAESTRO extensions from uppercase to lowercase (by baoilleach, #2053)
    Fix file format docstrings that were causing problems with Sphinx or GUI (by \ 
baoilleach, #2054)
    Fix BUILD_SHARED=OFF (by dkoes, #2056)
    Fix import of openbabel (by e-kwsm, #2058)
    Update for Open Babel 3 (by e-kwsm, #2060)
    Fix maeparser compile error with some Boost configs (by fredrikw, #2076)
    Find or build maeparser & coordgen libraries (by ricrogz, #2064)
    Fix issue #2095, caused by incorrect application of protonated SMARTS (by \ 
au1985, #2102)
    Fix issue #1794, UFF atom typing for deuterium (by ghutchis, #2114)
    Fix segfault on SMI to InChI conversion when using "-d" (by \ 
timvdm, #2115)
    Correct the path to the openbabel-python.cpp (by baoilleach, #2119)
    Remove fragments with zero coordinates - fixes #2144. (by ghutchis, #2150)
    Fix issue #2125 - Zero occupancy in cif file treated as 1.0. (by orex, #2136)
    Fix #2071 - obrms parser segmentation fault (by e-kwsm, #2073)
    Fix #2098 - OBDistanceGeometry is unavailable to users (by n-yoshikawa, #2105)
    Set MAEPARSER_BUILD_SHARED_LIBS (fix #2089) (by e-kwsm, #2155)
    Fix the import of Tkinter in Python 3+ (by mrakitin, #2157)
    Fix for segault (with regression test) (by dkoes, #2162)
    Follow-up with missing spelling fixes from #2163 (by mrakitin, #2166)
    Prefer std::fabs resolves build problem on mac-current (by ghutchis, #2168)
    Fix distance geometry stereo issues (by timvdm, #2158)
    Merge of "Improve OBConversion::WriteString() and WriteFile() \ 
initialization" (adalke) #1923 (by baoilleach, #2176)
    Fix output format in the cifformat writer (by afonari, #2170)

Development/Build/Install improvements

    Avoid using namespace in headers (by e-kwsm, #2055)
    Remove babel doc (by e-kwsm, #2057)
    Do not hard-code Open Babel major version for include directory (by e-kwsm, \ 
    Patched to build on NetBSD (by voidpin, #2093)
    Update download link (by njzjz, #2094)
    Fix GitHub ISSUE_TEMPLATE (by RMeli, #2082)
    Define OpenBabel3_LIBRARY (by dkoes, #2086)
    Initial GitHub action - misspell-fixer (by ghutchis, #2163)
    Automated GitHub builds (by ghutchis, #2165)