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@ghutchis ghutchis released this 05 May 21:02
· 237 commits to master since this release
openbabel-3-1-0
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This version represents additional API and is backwards-compatible with the 3.0 release.

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, #2059)
  • 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)

Cast of contributors

adalke (Andrew Dalke), afonari (Alexandr Fonari), au1985 (Alex Ustinov), baoilleach (Noel O'Boyle), bbucior (Ben Bucior), dkoes (David Koes), e-kwsm (Eisuke Kawashima), fredrikw (Fredrik
Wallner), ghutchis (Geoff Hutchison), Kamil Rytarowski, khoran (Kevin Horan), mrakitin (Maksim Rakitin), n-yoshikawa (Naruki Yoshikawa), njzjz (Jinzhe Zeng), orex (Kirill Okhotnikov), ricrogz (Ric), rmeli (Rocco Meli), Roger Sayle, timvdm (Tim Vandermeersch), voidpin (pin) , wiedi (Sebastian Wiedenroth)

Assets 5