Hello community, here is the log from the commit of package openbabel for openSUSE:Factory checked in at Mon Jul 27 22:39:06 CEST 2009. -------- --- KDE/openbabel/openbabel.changes 2008-07-22 14:16:44.000000000 +0200 +++ openbabel/openbabel.changes 2009-07-27 22:37:35.812720000 +0200 @@ -1,0 +2,34 @@ +Sat Jul 25 23:48:41 CEST 2009 - beineri@opensuse.org + +- update to OpenBabel 2.2.2: + * Fixed many stereochemistry errors when reading/writing SMILES. + * Significantly improved aromaticity and Kekule bond assignment. + * Improved 2D -> 3D coordinate generation + * Improved coordinate generation using --gen3d command-line operation + * Improved performance for coordinate generation. + * New --fillUC command-line operation for babel. + * Fixes to pH-dependent hydrogen addition. + * Added support for reading vibrational data from Molden, Molpro, + and NWChem output files. + * Updated atomic radii from recent theoretical calculations. + * Fixed bug when reading gzip-compressed Mol2 or XML files. + * Close files after an error. Fixes a bug with Pybel where files + would remain open. + * New File Formats Import & Export: + - Molpro input and output. + -VASP coordinate files (CONTCAR and POSCAR). + +- update to OpenBabel 2.2.1: + * Added support for MACCS fingerprints. + * Many fixes and enhancements to the force field code. + * Improved 3D coordinate generation, particularly with ring fragments. + * Fixed a variety of PDB import errors with atom types. + * Added support for reading charges and radii from PQR file formats. + * Added support for reading and writing unit cells in PDB formats. + * New "output" file format for taking generic ".out", ".log", and + ".dat" files and reading with appropriate file type based on contents. + * Added improved error handling/reporting when unable to load file formats. + * Improved CIF file format support. + * Generic "output" format for reading from quantum chemistry files. + +------------------------------------------------------------------- calling whatdependson for head-i586 Old: ---- openbabel-2.2.0-crippled.tar.bz2 New: ---- openbabel-2.2.2-crippled.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ openbabel.spec ++++++ --- /var/tmp/diff_new_pack.CvIFDe/_old 2009-07-27 22:37:53.000000000 +0200 +++ /var/tmp/diff_new_pack.CvIFDe/_new 2009-07-27 22:37:53.000000000 +0200 @@ -1,5 +1,5 @@ # -# spec file for package openbabel (Version 2.2.0) +# spec file for package openbabel (Version 2.2.2) # # Copyright (c) 2009 SUSE LINUX Products GmbH, Nuernberg, Germany. # @@ -18,8 +18,8 @@ Name: openbabel -Version: 2.2.0 -Release: 29 +Version: 2.2.2 +Release: 1 License: GPL v2 only BuildRoot: %{_tmppath}/%{name}-%{version}-build BuildRequires: gcc-c++ libxml2-devel swig zlib-devel @@ -118,8 +118,7 @@ %files -n libopenbabel-devel %defattr(-,root,root,-) %{_libdir}/pkgconfig/openbabel-2.0.pc -%dir /usr/include/inchi -/usr/include/inchi/inchi_api.h +/usr/include/inchi102 %dir %{_includedir}/openbabel-2.0 %{_includedir}/openbabel-2.0/openbabel/ %{_libdir}/*.so ++++++ build-checks.diff ++++++ --- /var/tmp/diff_new_pack.CvIFDe/_old 2009-07-27 22:37:53.000000000 +0200 +++ /var/tmp/diff_new_pack.CvIFDe/_new 2009-07-27 22:37:53.000000000 +0200 @@ -1,82 +1,30 @@ ---- src/forcefield.cpp -+++ src/forcefield.cpp -@@ -1240,7 +1240,7 @@ namespace OpenBabel - - bool OBForceField::SystematicRotorSearchNextConformer(unsigned int geomSteps) - { -- char _logbuf[100]; -+ char _logbuf[BUFF_SIZE]; - - if (_current_conformer >= _mol.NumConformers()) { // done - // Select conformer with lowest energy -@@ -1355,7 +1355,7 @@ namespace OpenBabel - - bool OBForceField::RandomRotorSearchNextConformer(unsigned int geomSteps) - { -- char _logbuf[100]; -+ char _logbuf[BUFF_SIZE]; - - if (_current_conformer >= _mol.NumConformers()) { // done - // Select conformer with lowest energy -@@ -1888,7 +1888,7 @@ namespace OpenBabel - - // output result of triangle smoothing - IF_OBFF_LOGLVL_LOW { -- char _logbuf[100]; -+ char _logbuf[BUFF_SIZE]; - - OBFFLog("RANDOM DISTANCE MATRIX BETWEEN LIMITS\n\n"); - for (i=0; i<N; i++) { -@@ -1912,7 +1912,7 @@ namespace OpenBabel - - // output metric matrix - IF_OBFF_LOGLVL_LOW { -- char _logbuf[100]; -+ char _logbuf[BUFF_SIZE]; +--- src/formats/smilesformat.cpp 2009/07/26 07:13:52 1.1 ++++ src/formats/smilesformat.cpp 2009/07/26 07:15:19 +@@ -347,6 +347,7 @@ + return result; + } - OBFFLog("METRIC MATRIX\n\n"); - for (i=0; i<N; i++) { -@@ -2403,7 +2403,7 @@ namespace OpenBabel - OBAtom *atom = new OBAtom; - vector3 grad; - double e_n1, e_n2; -- char _logbuf[100]; -+ char _logbuf[BUFF_SIZE]; - - atom->SetVector(9.0, 9.0, 0.0); - e_n1 = atom->x() * atom->x() + 2 * (atom->y() * atom->y()); -@@ -2447,7 +2447,7 @@ namespace OpenBabel - double e_n1, e_n2; - double g2g2, g1g1, g2g1; - bool firststep; -- char _logbuf[100]; -+ char _logbuf[BUFF_SIZE]; ++ return result; + } - firststep = true; - atom->SetVector(9.0, 9.0, 0.0); ---- src/forcefields/forcefieldmmff94.cpp -+++ src/forcefields/forcefieldmmff94.cpp -@@ -3853,7 +3853,7 @@ namespace OpenBabel - vector<int> types; - vector<double> fcharges, pcharges; - vector<double> bond_lengths; -- char buffer[150], _logbuf[100]; -+ char buffer[150], _logbuf[BUFF_SIZE]; - bool molfound, atomfound, bondfound, fchgfound, pchgfound; - double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; - double termcount; //1=bond, 2=angle, 3=strbnd, 4=torsion, 5=oop ---- src/formats/chemkinformat.cpp -+++ src/formats/chemkinformat.cpp -@@ -627,8 +627,10 @@ bool ChemKinFormat::ReadReactionQualifierLines(istream& ifs, OBReaction* pReact) - { - //not "END". Has an even number of tokens. - //3-body efficiencies -- for(int i=0;i<toks.size()-1;++i)//also incremented in body to retrieve id,val pairs -- pRD->SetEfficiency(toks[i++], atof(toks[i].c_str())); -+ for(int i=0;i<toks.size()-1;) { -+ pRD->SetEfficiency(toks[i], atof(toks[i+1].c_str())); -+ i += 2; -+ } + std::vector<unsigned long> OBTetraPlanarStereo::ToShape(const std::vector<unsigned long> &refs, +@@ -372,6 +373,7 @@ + return result; } + ++ return result; } - return ifs!=NULL; + + +--- src/fingerprints/finger3.cpp 2009/07/26 07:23:57 1.1 ++++ src/fingerprints/finger3.cpp 2009/07/26 07:24:39 +@@ -217,7 +217,8 @@ + int num = ppat->numbits, div = ppat->numoccurrences+1, ngrp; + while(num) //for each group of bits + { +- ngrp = (num + div -1)/div--; //rounds up ++ ngrp = (num + div -1)/div; //rounds up ++ div--; + num -= ngrp; + if(GetBit(fp, n) == bSet) + { ++++++ openbabel-2.2.0-crippled.tar.bz2 -> openbabel-2.2.2-crippled.tar.bz2 ++++++ ++++ 451563 lines of diff (skipped) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Remember to have fun... -- To unsubscribe, e-mail: opensuse-commit+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-commit+help@opensuse.org