Subject: CVS commit: pkgsrc/biology/openbabel
From: Makoto Fujiwara
Date: 2014-11-20 10:05:56
Message id: 20141120090556.DF1E298@cvs.netbsd.org

Log Message:
(upstream) update 2.3.0 to 2.3.2

(ChangeLog)
2012-08-20  Paolo Tosco <paolo.tosco@unito.it>
        * src/formats/mol2format.cpp: added a check for N.4 nitrogens
        (fixes PR#3557898)

2012-06-09  Paolo Tosco <paolo.tosco@unito.it>
        * src/kekulize.cpp: reverted the r4862 patch to kekulize.cpp;
        the incorrect aromaticity perception of oxonium salts concerned
        only the MOL2 format, so the fix was applied to mol2format.cpp
        instead
        * src/formats/mol2format.cpp: added a check to improve downstream
        aromaticity perception on charged molecules containing oxygen

2012-06-07  Paolo Tosco <paolo.tosco@unito.it>
        * include/openbabel/atom.h: added protos for CountFreeSulfurs() and
        IsThiocarboxylSulfur() functions which are equivalent to
        CountFreeOxygens() and IsCarboxylOxygen() and address
        (di)thiocarboxyl groups
        * src/atom.cpp: added the CountFreeSulfurs() and
        IsThiocarboxylSulfur() functions
        * src/forcefields/forcefieldmmff94.cpp: added some additional
        checks to make MMFF94 atom type assignment more robust
        * src/formats/mol2format.cpp: added some checks to improve downstream
        aromaticity perception on charged molecules containing nitrogen,
        oxygen and sulfur
        * src/kekulize.cpp: added a check to fix incorrect perception of
        aromatic oxonium and thionium cations

(NEWS)
Open Babel 2.3.1 (2011-10-14)

This release represents a major bug-fix release and is a stable
upgrade, strongly recommended for all users of Open Babel. Many bugs
and enhancements have been added since the 2.3.0 release.

Citation:

Please consider citing this work if you publish work which used Open Babel:
Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim
Vandermeersch  and Geoffrey R. Hutchison. "Open Babel: An open
chemical toolbox." Journal of Cheminformatics 2011, 3:33.

http://dx.doi.org/10.1186/1758-2946-3-33

Files:
RevisionActionfile
1.23modifypkgsrc/biology/openbabel/Makefile
1.2modifypkgsrc/biology/openbabel/PLIST
1.5modifypkgsrc/biology/openbabel/distinfo
1.4modifypkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt
1.2modifypkgsrc/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h