CVS commit: pkgsrc/biology/openbabel

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Thu Nov 20 09:05:56 UTC 2014

Modified Files:
        pkgsrc/biology/openbabel: Makefile PLIST distinfo
        pkgsrc/biology/openbabel/patches: patch-doc_CMakeLists.txt
            patch-include_openbabel_shared__ptr.h

Log Message:
(upstream) update 2.3.0 to 2.3.2

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

2012-06-09  Paolo Tosco <paolo.tosco%unito.it@localhost>
        * 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@localhost>
        * 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


To generate a diff of this commit:
cvs rdiff -u -r1.22 -r1.23 pkgsrc/biology/openbabel/Makefile
cvs rdiff -u -r1.1.1.1 -r1.2 pkgsrc/biology/openbabel/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/openbabel/distinfo
cvs rdiff -u -r1.3 -r1.4 \
    pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h

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