File: ChangeLog

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2008-07-03  Noel O'Boyle  <baoilleach@gmail.com>

	* windows-vc2005/OBPythonOBF/setup.py: Update setup.py to include
	forcefield files when installing

2008-07-03  Michael Banck  <mbanck@gmx.net>

	* scripts/Makefile.am (dist-hook): Do not fail if make distclean does
	not succeed in the perl and ruby directories.
	* scripts/Makefile.in: Regenerated.

	* data/Makefile.am (table_DATA): Added plugindefines.txt.
	* data/Makefile.in: Regenerated.
	* data/CMakelists.txt: Removed space-groups.xsl from to_install.

	* test/cmlreadfile.cpp: Read files from TESTDATADIR, not relative to
	current directory.
	* test/wrapper.sh: Use ${srcdir}, not ${top_srcdir} to set
	$BABEL_DATADIR.
	* test/wrapper.sh: Run inchi tests from source directory if ${srcdir}
	is non-empty.  Set and export TESTDATADIR.

2008-07-03  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/ruby/README: Updated build instructions

2008-07-03  Michael Banck  <mbanck@gmx.net>

	* src/CMakelists.txt (LIBRARY_VERSION): New variable.
	* src/CMakelists.txt (BABEL_LIBRARY): Set VERSION property to
	${LIBRARY_VERSION}.
	
2008-07-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/Makefile.am, src/CMakeLists.txt: Update SONAME to 3 for
	version 2.2.0 release.

2008-07-03  Marcus D. Hanwell  <marcus@cryos.org>

	* CMakeLists.txt: Relaxed the CMake requirement to 2.4.7.

	* include/openbabel/griddata.h, src/griddata.cpp: Added three new
	getter functions to get the x, y and z axes.

	* src/CMakeLists.txt: Updated to use SONAME 3.

	* include/openbabel/mol.h, src/mol.cpp: Added extra arguments to
	GetMolWt, GetExactMass and GetSpacedFormula to optionally disable
	implicit hydrogens. Defaults to preserve existing behaviour.

	* src/grid.cpp: Fixed the Init function to apply padding correctly.

2008-07-02  Marcus D. Hanwell  <marcus@cryos.org>

	* include/openbabel/grid.h, src/grid.cpp: Updated the documentation
	and a few fixes to the function prototypes.

        * include/openbabel/griddata.h, src/griddata.cpp: Updates to the
	documentation, added a GetMaxVector function and made SetLimits const
	fixes for the vector3 form.

	* CMakeLists.txt, src/CMakeLists.txt, src/formats/CMakeLists.txt:
	Reduce the number of version variables floating around to only those
	that are used...

	* CMakeLists.txt, src/formats/CMakeLists.txt: Use a versioned plugin
	directory as autotools does.

2008-07-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/locale.cpp: Add string.h header, from patch by Marcus
	Hufgard. Allows compilation with GCC 4.3.1 on Linux:
	PR#2008642.

	* src/formats/gausszmatformat.cpp: Add definition of
	strcasestr if not defined. Solves compile problems on Cygwin.

	* configure.in, src/config.h.in, configure: Check for
	rpc/xdr.h needed for xtcformat.

	* src/formats/xtcformat.cpp: Use new HAVE_RPC_XDR_H #define.

	* src/formats/smilesformat.cpp: Bring back FIX format, killed
	during merger of canonical and standard smiles.

	* src/rotamer.cpp, src/locale.cpp, src/base.cpp,
	include/openbabel/atom.h, include/openbabel/locale.h,
	include/openbabel/forcefield.h,
	include/openbabel/pointgroup.h,
	include/openbabel/fingerprint.h: Doxygen updates for 2.2.0.

2008-07-02  Chris Morley

	* src/descriptor.cpp(PredictandSave): don't duplicate an existing
	OBPairData. Was crashing when adding a property that was already
	present. 
	 
	* src/formats/smilesformat.cpp(StandardLabels): A couple of vectors now
	have 2147483647 pushed when the atom is H, to match the situation with
	canonical ordering, rather than ending up with a size smaller than the
	number of atoms. I assume 2147483647 = 2^31-1 is just a big number?
	Fixes bug 1999348.

2008-07-01  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/kekulize.cpp (expandcycle): Add more flexible API for
	expandcycle.

	* scripts/perl/Makefile.PL: Update from Noel for PR#2007797.

	* Makefile.*, configure.*: Update for 2.2.0 release.

2008-07-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/atomrecord.cpp: Fix bug where arginine hydrogen atoms
	where read as dummy Xx atoms. (#2002557)

	* src/formats/pdbformat.cpp: 1) Write the chain number. 2) Don't
	rearrange atom ids when writing. (see chains item 2)

	* src/chains.cpp: 1) Serine OG is now given the correct atom id.
	2) produce correctly ordered atom ids (see pdbformat item 2)
	3) fix for cyclic peptides (have no NTer)
	4) water, ions and ligands are all placed in the ' ' chain now and get
	unique residue numbers.
	5) partially identified residues are merged with the atoms not used to
	identify them and the resids is set to UNK (hetflags is also set to
	true) (e.g. CSD in 1LWF = CYS with two O's on S )

2008-07-01  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/python/pybel.py: Make pybel use CloneData instead of SetData
	
2008-07-01  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/openbabel-python.i: Make the BFS Iterator return two values,
	the Atom and the depth
	
2008-07-01  Chris Morley

	* data/atomtyp.txt: remove IMPVAL entry for silicon to fix
	bug #1911590. (I thought I had already done this.)
	
	* windows-vc2005/babelconfig.h: add macro which apparently
	disables native tr1 in recent VC++ 2008, so that boost version
	will be used. Step towards getting tit to compile on this
	platform but probably not there yet. Not critical for v2.2.0
	release, since Windows compilation should be done from SVN.

2008-06-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Makefile.am: Move cmake to EXTRA_DIST (4 Makefiles for one
	file?)
	* Makefile.in: Regenerated.

	* include/openbabel/base.h, src/base.cpp: New CloneData()
	method to solve PR#2004495 for scripting interfaces.

	* src/Makefile.am, src/Makefile.in: Bump library version for
	2.2 release.

	* src/formats/smilesformat.cpp: Minor fix relating to
	PR#1999348.

	* src/patty.cpp, src/forcefield.cpp, src/oberror.cpp, 
	src/generic.cpp, src/canon.cpp, src/dlhandler_unix.cpp, 
	src/data.cpp, src/grid.cpp, src/mol.cpp: Minor fixes from
	static code analysis. Test for empty() instead of size().


2008-06-30  Michael Banck  <mbanck@gmx.net>
	
	* src/Makefile.am (EXTRA_DIST): Added config.h.cmake.
	* src/Makefile.in: Regenerated.

	* Makefile.am (SUBDIRS): Added cmake.
	* Makefile.in: Regenerated.
	* cmake/Makefile.am: New file.
	* cmake/Makefile.in: New file.
	* cmake/modules/Makefile.am: Likewise.	
	* cmake/modules/Makefile.in: Likewise.	
	* configure.in (AC_OUTPUT): Added cmake/Makefile and
	cmake/modules/Makefile.
	* configure: Regenerated.
	* acinclude (AM_PATH_XML2): New macro, copied from aclocal.m4.

2008-06-29  Marcus D. Hanwell  <marcus@cryos.org>

	* include/openbabel/math/vector3.h,
	include/openbabel/math/matrix3x3.h: Made the destructors non-virtual,
	fixes Avogadro bug 2005984.

2008-06-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/obiter.h, src/obiter.cpp: Fix
	PR#1901348. Add support for BFS iteration from arbitrary
	atoms.

	* include/openbabel/math/*.h, src/math/*.cpp: Updates to fix
	some GCC warnings.

	* include/openbabel/bond.h, src/bond.cpp: Patch from Steven
	Constable, PR#2004391. Adds SetLength() to move both atoms.

	* include/openbabel/mol.h: Fix for ReserveAtoms() suggested by
	Andrew Dalke.

	* src/formats/mdlformat.cpp: Fix for SKP records, suggested by
	Andrew.

	* src/formats/pdbformat.cpp: Fix for CONECT records for atoms
	with > 4 records (PR#1711154).

2008-06-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/parsmart.cpp: Add support for Isotopes in SMARTS. Fixes
	PR#1987729.

	* test/files/nci.smi: Add tests for matching isotopic
	SMILES/SMARTS.

2008-06-23  Chris Morley

	* test/inchiwrite.cpp: add -xn option so that the tests are done without
	the 'recommended' InChI options. wInChI.exe is not yet available
	for InChI 1.02. Needs revisting when it is.

	* src/fingerprint.cpp(FastSearchIndexer): ensure fpid is terminated
	when copied to guard against theoretical problem pointed out
	by Andrew Dalke.

2008-06-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/chains.cpp: Assign HOH and ligands to separate residues.
	(#1774776)

2008-06-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/atomrecord.cpp: Keep original chain ID (#1760959).

2008-06-21  Carsten Niehaus  <cniehaus@kde.org>

	* src/obutil.cpp: Typo fixes.

	* src/forcefields/[forcefielduff.cpp,forcefieldmmff94.cpp]: Typo fixes

	* src/formats/[mpdformat.cpp,xtcformat.cpp]: Typo fixes
	
	* src/forcefields/*.h: Make ctor explicit.
	
2008-06-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obutil.cpp (CartesianToInternal): Fix PR#1923896 for
	Fenske-Hall z-matrix format. When looking for non-linear
	atoms, don't pick non-bonded >10.0 Angstroms, which cause
	problems with FH (and other) fixed format z-matrices.

	* src/mol.cpp (ConnectTheDots): Fix for PR#1813502 for
	existing bonds getting deleted by ConnectTheDots. Make sure to
	preserve all original connections from PDB.

	* src/formats/pdbformat.cpp (ReadMolecule): Fix for PR#1985681
	with virtual bonds still built into a PDB file.

2008-06-20  Chris Morley

	* include/openbabel/locale.h, src/locale.cpp: extra #includes
	
	* windows-vc2005/babelconfig.h: define strdup. Version to 2.2.0
	
	* include/openbabel/obiter.h: trivial change to avoid compiler warning
	
	* src/fingerprints/finger3.cpp: do singel SMARTS match, as suggested by
	Ernst-Georg Schmid

	* windows-vc2005/OBError/OBError.vcproj: add locale.cpp

2008-06-20  Noel O'Boyle  <baoilleach@gmail.com>

	* Revert of r2347: I had set eol:native instead of eol-style native.

2008-06-19  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/fingerprint.cpp: Contribution from Andrew Dalke for
	improved speed using GCC.

2008-06-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/locale.h, src/locale.cpp: New OBLocale class
	to centralize calls to setlocale/uselocale. Should solve strange
	segfault on Linux with freelocale.

	* include/openbabel/obiter.h, src/obiter.cpp: Add depth tracking
	for DFS and BFS iterators. Addresses PR#1901348.

2008-06-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/*.cpp: Checked all files for their use of tokenize().
	All added lines are like:
	
	if (vs.size() < 1) return false; // timvdm 18/06/2008 

	* include/openbabel/obiter.h, src/obiter.cpp: Reimplement
	FOR_PAIRS_OF_MOL. Do not build a list of all pairs in the constructor,
	but find the pairs while iterating. This is faster and requires less
	memory.

	* include/openbabel/forcefield.cpp: Add SetParameterFile().

	* src/forcefields/forcefieldmmff94.*: Use the new SetParameterFile().
	Add a global definition for MMFF94s.

	* data/*: Add MMFF94s parameters.

	MMFF94s: Same functional form, only torsion and oop parameters are
	different. To see the difference, you can try to minimize alanine with
	both force fields, MMFF94s will give a planar nitrogen while MMFF94
	will not.

2008-06-17  Noel O'Boyle  <baoilleach@gmail.com>

	* Reverted r2535 except for changes to scripts/perl/Makefile.PL
	* scripts/openbabel-python.i: Updated SWIG interface file to ignore 21
	methods of each std::vector created. This should substantially reduce
	the size of the wrapper code.

2008-06-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/xtcformat.cpp: make confs a std::vector too. Was double
	*confs = new double[natoms * 3].

2008-06-16  Chris Morley

	* include/openbabel/oberror.h, src/oberror.cpp:
	add a parameter to ThrowError to allow error messages to be 
	output only once (although they are all logged.). The default
	behaviour is as at present.
	
	* src/formats/inchiformat.cpp: default output uses the "recommended"
	set of InChi options. -xn option uses no options as at present.
	
	Add -xl option to output the InChI log - only once for multiple
	molecules.
	
	* include/openbabel/fingerprint.h, src/formats/fingerprintformat.cpp:
	Make DescribeBits error message appear only once.
	
	* src/mol.cpp(GetTitle): make variable title static to avoid returning
	a pointer to a temporary variable. But this might cause problems with
	multiple molecules unless the title is captured in the calling code 
	before getting the next. Until this is done properly, add a
	test so that the problem can only occur with multi-line titles.

	* src/formats/smilesformat.cpp: add option to output explicit hydrogen
	form like [CH3][CH3].
	**** The SMILES output currently crashes with  Nc1nc(O)c2nc[nH]c2n1
	but I haven't tracked this down.****
	
	* src/ops/addpolarh.cpp: add simple op for Feature Request #1995162 
	
	* windows-vc2005/gen3D/gen3D.vcproj,
	windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj: update

2008-06-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/cssrformat.cpp, src/formats/MCDLformat.cpp,
	src/formats/mmcifformat.cpp, src/formats/balstformat.cpp,
	src/formats/chemdrawcdx.cpp, src/formats/boxformat.cpp,
	src/formats/unichemformat.cpp, src/formats/yasaraformat.cpp,
	src/formats/zindoformat.cpp, src/formats/gromos96format.cpp,
	src/formats/xedformat.cpp: sprintf --> snprintf

	* src/chains.cpp, src/pointgroup.cpp, src/rotor.cpp: Some more sprintf
	-> snprintf (I don't expect any problems here, but just in case...)

	* include/openbabel/forcefield.cpp, src/forcefield.cpp,
	src/forcefields/*: Replace sprintf(_logbuf, ...) with
	snprintf(_logbuf, BUFF_SIZE). 

2008-06-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/chain.h, src/chain.cpp: Replace:
	1) malloc/free with new/delete
	2) new T[n] with std::vector (where possible)
	Original code still there as comments, can be removed once reviewed.

	* src/parsmarts.cpp: Replace malloc/free with new/delete.
	Replace realloc(array, size) with:
	  T *tmp = new T[size];
	  copy(array, array + old_size, tmp);
	  delete [] array;
	  array = tmp;


2005-06-14  Marcus D. Hanwell  <marcus@cryos.org>

	* src/formats/xtcformat.cpp: Some modifications to the xtc format to
	use C++ structures.

	* CMakeLists.txt, src/formats/CMakeLists.txt: Some build system
	updates to build format plugins as modules.

	* src/ops/loader.cpp: GCC 4.3 fix - cstdlib needed for free calls.

2008-06-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/atom.h, src/atom.cpp: Add OBAtom::Duplcate()
	which will copy everything except the internal index.

	* include/openbabel/generic.h, src/generic.cpp: Add
	OBUnitCell::FillUnitCell() method to create space-group-defined
	atoms. Uses OBAtom::Duplicate.

2008-06-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.cpp: Change GetGradient(..., int terms
	= ...) to GetGradient(..., int /*terms*/ = ...). (comiler warning:
	unused parameter).

	* src/forcefields/*.cpp: Change i->Compute<gradients>() to i->template
	Compute<gradients>().

	* include/openbabel/builder.h, src/builder.cpp: Make most functions 
	static.

	* src/mol.cpp: Use OBBuilder::GetNewBondVector() in AddHydrogens(). 

2005-06-13  Marcus D. Hanwell  <marcus@cryos.org>

	* src/formats/mdlformat.cpp: Use static_cast in the min function.

2008-06-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/typer.cpp: Add a special case for guanidinium carbon
	atoms. (We may need additional special cases.)

	* data/atomtyp.txt, data/atomtyp.h: Change pattern for N3+ to
	match any 4-valent N, regardless of whether the formal charge has
	been set.
	
	* src/kekulize.cpp (NewPerceiveKekulizeBonds): Give up on
	kekulization when we find "cycles" with < 3 atoms. Sybyl mol2
	labels some atoms as aromatic that aren't in rings. Fixes
	PR#1965566 and PR#1784204.

	* include/openbabel/mol.h, src/mol.cpp (GetTitle): Add a parameter
	to replace newlines with spaces. Fixes PR#1984742.

	* configure.in: Check for xlocale.h, locale.h, and uselocale functions.

	* src/data.cpp, src/ops/loader.cpp, src/ops/optransform.cpp,
	src/descriptors/groupcontrib.cpp, src/builder.cpp,
	src/forcefields/forcefieldmm2.cpp,
	src/forcefields/forcefielduff.cpp,
	src/forcefields/forcefieldmmff94.cpp,
	src/forcefields/forcefieldghemical.cpp, src/obconversion.cpp:
	Change locale using uselocale if available and reset it to the
	afterwards. Update of previous change, suggested by Benoit.

	* include/openbabel/bond.h, include/openbabel/atom.h,
	src/bond.cpp: Fixes for "const" correctness. It's now possible to
	get the bond length of a const OBBond.
	
2008-06-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/data.cpp, src/ops/loader.cpp, src/ops/optransform.cpp,
	src/descriptors/groupcontrib.cpp, src/builder.cpp,
	src/forcefields/forcefieldmm2.cpp,
	src/forcefields/forcefielduff.cpp,
	src/forcefields/forcefieldmmff94.cpp,
	src/forcefields/forcefieldghemical.cpp, src/obconversion.cpp:
	Change locale before parsing files to use "C" numeric locale and
	reset it to the original state afterwards. Should solve PR#1785463.

	* src/obiter.cpp: Fixes from Izhar for DFS and BFS iterators.

	* src/mol.cpp, include/openbabel/mol.h: Added iterative
	GetFragment method to augment Separate(), contributed by Izhar.

2008-06-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/phmodel.cpp (OBPhModel::CorrectForPH): Fix PR#1835204. Allow
	SMILES to have pH-correction. (i.e., only check for automatic
	formal charges for molecules with dimension > 0).

	* src/formats/mdlformat.cpp: Add a check for EOF before reading,
	as suggested by Izhar.

	* src/formats/smilesformat.cpp: Add initial pass at "standard"
	SMILES labels.

	* Doxygen, include/*.h, src/*.cpp: Update doxygen documentation.

2008-06-07  Chris Morley

	* src/formats/fingerprintformat.cpp: correct folding error message
	and prevent description of bits when fingerprint is folded.
	
	* src/formats/smilesformat.cpp: change -xc to -xa (for atomclass)
	
	* windows-vc2005/OBFS/OBFS.vcproj,windows-vc2005/OpenBabelOBF.sln
	add dependency of OBCommon to Fastsearch project

2008-06-06  Chris Morley

	* src/formats/smilesformat.cpp: SMIFormat was being hidden because
	its constructor was being called again when its derived class
	CANSMIFormat was made. Now both derived from a base class with most
	of the functionality. 
	Modified Description() and made same for both.
	Removed DEFAULTFORMAT flag (MolFormat already is).
	
	* include/openbabel/mol.h: add back #include <float.h> which was
	somehow removed in the last commit and is need for Windows build.
	
	* windows-vc2005/OBCommonFormats/OBCommonFormats.vcproj: remove
	cansmilesformat.cpp
	
2008-06-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/phmodel.h, src/phmodel.cpp: Changes to OBPhModel, 
	use the	Henderson-Hasselbalch formula to determine protonation states.
	Updated doxygen documentation to give some info about the method.

	* include/openbabel/mol.h, src/mol.cpp: Use it.
	OBMol::AddHydrogens(bool polar=false, bool correctForPH=true, double
	pH=7.4)

	* data/phmodel.txt: Add extra column with pKa values.

	* test/phmodel.cpp: Unit test for the new phmodel. The two errors are
	Glutamate (4.0 used, should be 4.3) and Lysine (10.0 used, should be
	10.1). I'll probably have to add a visited list so we can only
	transform an atom once, transformations would then have to be ordered
	by decreasing complexity. But the errors are very small and this is a
	major improvement compared to what we had.

2008-06-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/openbabel-python*, scripts/python/*: Split the python
	bindings into three pieces for improved compilation. Should solve
	PR#1905826.

	* src/obconversion.cpp: Add stdlib.h to hopefully solve
	PR#1985717.

	* configure.in, configure: Update to build libinchi by default.

	* src/formats/smilesformat.cpp: Incorporate cansmilesformat
	code. Now all SMILES export goes through Craig's cleaner,
	less-buggy code. Currently all SMILES are canonically
	ordered. Need to add code to provide non-canonical ordering for "regular."
	
	* src/formats/Makefile.* src/formats/CMakeLists.txt: Update for above.

2008-06-05 Chris Morley

	* src/obconversion.cpp(Convert): test for Cntl Z to terminate
	commandline input rather than \n (a blank line).
	Fixes bug 1984660: piping with titleless mol files.
	Commandline data input always was clunky and is even clunkier now.
	Being able to pipe is more important. 
	
	* src/forcefield.cpp:In line 2535 replace 'dafault:' by 'default:' 
	This may have a real effect and needs to be checked.
	
	* include/openbabel/bitvec.h, src/canon.cpp,src/dlhandler_win32.cpp,
	src/forcefield.cpp, src/formats/cansmilesformat.cpp,
	src/formats/gamessformat.cpp, src/formats/gaussformat.cpp,
	src/formats/KFReader.c,src/formats/mol2format.cpp,
	src/formats/msmsformat.cpp, src/pointgroup.cpp,
	src/tokenst.cpp:
	Tidy to reduce compiler warnings: remove or comment out unreferenced
	variables; size_t decalation replaces some int or unsigned;
	!=NULL added to avoid implict const char* to bool conversion 
	
	* windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj: change to
	project build order as pointed out by peterennis bug #1985163


2008-06-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/mopacformat.cpp: Fix for PR#1978982 with reading
	Mopac 2007 force calculations.

	* src/formats/atomrecord.cpp: Fix SetAtomID as reported in
	PR#1838095. Thanks to Marc Lasson for bug report and fix.

	* src/formats/adfformat.cpp, src/formats/Makefile.am: Add KFReader
	and ArrayList code contributed under LGPL by SCM, Inc. for
	improved ADF binary support.

2008-06-04 Chris Morley

	* include/openbabel/mol.h: include float.h so that isinfinite
	is handled properly in Windows
	
	Deficiencies raised by Andrew Dalke
	
	* src/fingerprint.cpp: Error message if attempting to fold to 
	less than size of unsigned int.
	
	* src/formats/fingerprintformat.cpp(WriteMolecule) Error message 
	when parameter of -xN option (fold) is negative.
	
	* src/formats/fastsearchformat.cpp(WriteChem Object):
	Error message if more than one input file.
	
	Delete the outputstream after deleting the index, which is when
	it is written. Sometimes a fs file made without a specified name 
	was empty.
	
	* tools/babel.cpp: change indentation on help text
	
	* windows-vc2005/OpenBabelOBF.sln: another go at getting debug and
	release configurations right. The scripting interfaces need to be
	explicitly enabled before building if they are required. (I get
	tired of waiting for them.)

2008-06-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/residue.cpp (GetResidueNumber): Fix bug reported by Izhar
	Wallach.

	* src/forcefields/forcefielduff.cpp: Fix error reported by Chris
	Morley with Microsoft compiler -- don't duplicate loop variable names.

2008-06-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/atomtyp.txt, data/atomtyp.h: Add hybridization rules for
	Si, Al, Ge, As, Se, and Te. (Atom typing and valence rules need to
	be generalized.) Fixes problems with adding hydrogens to Si
	uncovered in Avogadro.

2005-06-02  Marcus D. Hanwell  <marcus@cryos.org>

	* src/atom.cpp, src/mol.cpp: Added extra checks in AddHydrogens for
	finite hydrogen coordinates. Also added some extra checks in the
	GetNewBondVector function to check for sane numbers.

2008-06-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Makefile.am, Makefile.in: Correct small automake typo with
	"autoconf" libtool macro directory.

	* configure: Regenerated using autogen.sh.

	* include/openbabel/grid.h: Fix compiler warning -- make sure to
	return values in all methods.

	* src/forcefield.cpp: Fix compiler warning "default" not "dafault"
	in switch statements.

	* src/formats/qchemformat.cpp, src/formats/gamessformat.cpp,
	src/formats/gaussformat.cpp, src/formats/fchkformat.cpp: Add
	support for reading dipole moments using OBVectorData.

2008-06-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/atomrecord.cpp: Call OBAtom::ForceImplH() for all atoms.
	Loading a pdb file and calling OBMol::AddHydrogens() added only on
	hydrogen.

2005-05-31  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/openbabel-csharp.i: Fixed two of the three remaining
	std::vectors based on examples found in Krugle code search

2005-05-30  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/openbabel-csharp.i: Fixed most of the std::vectors by using
	weird macro described in std_vector.i in the SWIG distribution

2005-05-30  Marcus D. Hanwell  <marcus@cryos.org>

	* configure, configure.in: Stop the wx-config test being called when
	the wx-gui is not enabled - bug 1979603.

2005-05-30  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/openbabel-csharp.i: Added header file to SWIG wrapper. Also
	removed several of the vector templates. These don't seem to be
	handled correctly by SWIG (should report bug to them).

2008-05-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: OBFFConstraints::Clear(), clear all the bitvecs.
	ConjugateGradientsTakeNSteps(), set _grad1[] to (0,0,0) when atom is
	fixed and not _gradientPtr (_grad1 is used for linesearch).
	Setup() & SetConstraints, check if SetupCalculations needs to be
	called. This is the case when the ignored bitvecs of both
	OBFFConstraints are different.

	* include/openbabel/forcefield.h: OBFFConstraints::GetIgnoredBitVec().
	Used in Setup() & SetConstraints().

2008-05-28 Chris Morley

	* windows-vc2005/OBCSharp/OBCSharp.vcproj,
	* windows-vc2005/OBJava/OBJava.vcproj,
	* windows-vc2005/OpenBabelOBF.sln
	Build release versions even in Debug mode.
	Use env var JAVABASE, e.g."C:\Program Files\Java\jdk1.6.0_03"
	so that there is no dependence in the code on the installed
	Java version. (Is there a standard variable for this?)
	
	* windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj:add adfformat

2008-05-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/openbabel-perl.i, scripts/perl/Makefile.PL: 
	Fix up Perl scripting. Now works on Mac OS X and appears to have
	clean converisons via "make test." Fixes PR#1795155 and 1881688.

	* src/formats/adfformat.cpp (OBT41Format::ReadMolecule): Convert
	from zyx format in ADF files to xyz in Open Babel for cubes. Only
	keep cubes which have actual data.

2005-05-28  Marcus D. Hanwell  <marcus@cryos.org>

	* src/formats/xml/cmlformat.cpp: Fixed PR 1975137 - atoi, strtol
	require null terminated strings.

2008-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/obiter.cpp: (same as Chris' commit, but let's do the same for angles)
	Make sure to always set _i, even when _vtorsion is empty.
	Otherwise OBMolTorsionIter::bool() will compare _i to _vtorsion.end() which
	caused a segfault on windows. Fixes Avogadro windows bug #1972244.

2008-05-27 Chris Morley

	* src/obiter.cpp(OBMolTorsionIter::OBMolTorsionIter):
	prevent crash when _vtorsion is empty. Was affecting builder
	with small molecules.

2008-05-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/Makefile.* src/formats/Makefile.*: Add versioned install
	directories for formats. Fixes PR#1905093.

	* src/formats/hinformat.cpp: Fix PR#1947913 with hang during HIN
	reading.

2005-05-26  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/openbabel-csharp.i: Creating SWIG wrapper for C#
	* windows-vc2005/OpenBabelOBF.sln, OBJava, OBCSharp: Creating projects
	for OBJava and OBCSharp

2008-05-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/builder.cpp: Fix bug. CorrectStereoAtoms was not checking the 
	size of refs, before doing refs[0]...refs[3] (thanks Noel)

2008-05-25 Chris Morley
	
	windows-vc2005/examples: new folder with an example project
	for OBF build. Will replace /template.

2008-05-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Setup(), delete TorsionData before using 
	FOR_TORSION_OF_MOL. (fixed #1954233)

	* windows-vc2005/OBCommonFormats/OBCommonFormats.vcproj: Correct
	location for obmolecformat.cpp

2005-05-24  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/java/README: Updated instructions for using Java bindings on
	Linux

2008-05-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* windows-vc2005/openbabel.sln: remove non-existing OBPython and test, 
	add template.

	* windows-vc2005/OpenBabelDLL/OpenBabelDLL.vcproj: move obmolecformats 
	from formats to sources.

	* windows-vc2005/template/*.*: Example of a C++ program using openbabel.

2005-05-23  Marcus D. Hanwell  <marcus@cryos.org>

	* include/openbabel/obconversion.h: Removed extra qualification on
	OpenInAndOutFiles which broke compilation here.

2008-05-23 Chris Morley

	* include/openbabel/obconversion.h, src/obconversion.cpp:
	Add OBConversion::OpenInAndOutFiles to aid scripting

2008-05-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp: SetTorsion(), move j=*i out of this for loop:
	for (i = atom.begin(), j = *i; ... ; i++, j = *i)
	This was causing weird results in windows (MSVC2005). Thanks 
	to Noel for reporting the bug, this also fixes #1954233 I believe.

2008-05-23 Chris Morley

	* src/formats/xml/cmlformat.cpp: Applied Jean Brefort's patch to fix
	leading spaces on atom refs bug #1965086
	

2005-05-23  Noel O'Boyle  <baoilleach@gmail.com>

	* Pybel: minor fix to test suite for running outside cinfony

2005-05-23  Noel O'Boyle  <baoilleach@gmail.com>

	* Pybel: Synching with cinfony, and getting ready for release as 1.3

2008-05-22 Chris Morley

	* data/atomtyp.txt: remove
	  IMPVAL  [N^2-,N^3-]		2
	and add
	  IMPVAL	[N-]			2
	so that O1S(=O)(=O)[N-]C(=O)C=C1C.[K+] is interpreted correctly.
 
	* src/formats/pngformat.cpp: minor documentation change

2005-05-22  Marcus D. Hanwell  <marcus@cryos.org>

	* CMakeLists.txt: Fixed version string in CMake. Also added policy
	stuff for CMake 2.6 and the option to set the library directory.

2008-05-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp: copy OBChiralData for all atoms in operator=.

	* include/openbabel/builder.h, src/builder.cpp: Added
	Swap(...) : swap the position of two substituents (can be used to
	invert chiral centers)
	CorrectAtomChirality(...) : use the (atomreftype) input references to
	make sure the molecule has the right chirality as specified by
	IsClockwise() / IsAntiClockwise().
	CorrectBondChirality(...) : use the IsUp() / IsDown() values to rotate
	the bonds if needed.

2008-05-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	Changes from avogadro win32 build:

	* include/openbabel/obutil.h: Change std::min(a,b) into std::min<const
	double>(a,b).

	* src/mol.cpp: OBMol::FindChildren was iterating over an atom's bonds
	in a wrong way.

2008-05-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: rename _T to
	_temp. (_T is more likely to be defined elsewhere compared to _temp).

2008-05-17  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/grid.h, src/grid.cpp,
	include/openbabel/griddata.h, src/griddata.cpp: Some 'const'
	updates.

	* src/formats/adfformat.cpp: Update to use OBGridData rather than
	custom T41Data class.

2008-05-16  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/java/OBTest.java: Bring back test program.

	* scripts/openbabel-java.i, scripts/openbabel-perl.i,
	scripts/openbabel-ruby.i: Fix script bindings. Now compile
	cleanly. Perl still needs work to pass tests.

	* include/openbabel/math/spacegroup.h, include/openbabel/plugin.h:
	Minor updates for SWIG compatibility.

	* src/formats/Makefile.*: Add xtcformat.cpp.

	* src/formats/xtcformat.cpp: Add rpc/types.h for Mac
	compatibility.

2008-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Added functions
	to temporarily ignore or fix an atom. This allows interactive programs
	to use this while drawing (no repulsion between your new atom and the
	fragment you want to connect to. 

	* src/forcefields/forcefield*.cpp: Same

2008-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/CMakeList.txt: Add xtc format for non-WIN32 platforms.

2008-05-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/obconversion.cpp: save the filename in ReadFile (needed for xtc
	format).

2008-05-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/xtcformat.cpp: Portable compressed trajectory file
	format. Used by gromacs. Since there is no real API to handle
	trajectories at the moment, ReadMolecule is used. Instead of
	CastAndClear, the OBBase object is only cast to an OBMol object to
	which conformers are added for each frame. Box, step and time are
	currently ignored. Currently read only. (Avogadro implementation)

	* Makefiles: NOT updated yet, from looking at the gromacs source, it
	seems that the XDR stuff needs special handling on windows and I don't
	want to break OB now.

2008-05-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/atom.cpp: Replace implementation for 
	bool IsHbondDonor() { return MatchesSMARTS("[$([#8,#7H,#9;!H0])]"); }
	with C++ code for better performance.

2008-05-10  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/OBPythonOBF/setup.py: Adding missing oberror.dll.

2008-05-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/opendxformat.cpp: Bug fixing. Now roundtrips OpenDX
	data from APBS. The format will create an empty OBMol with
	attached OBGridData.

2008-05-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Regenerate autotools build system based on Daniel's updated autogen.

	* include/openbabel/mol.h, src/mol.cpp (DeleteAtom, DeleteBond,
	DeleteResidue): Update to allow the user to free an atom, bond or
	residue (i.e., just remove the atom or bond or residue from the molecule).

2008-05-07  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/pybel.py: Synch with cinfony.

2008-05-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: initialize static _constraints to a
	OBFFConstraints object.

2008-05-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/parsmarts.cpp: Add if(_pat) before _pat->...(). This was causing
	Avogadro to crash here sometimes.

2008-05-05  Daniel Leidert <daniel.leidert@wgdd.de>

	* autogen.sh: Force aclocal and autoheader to regenerate files to
	avoid timestamp issues (probably not necessary for automake and
	autoconf).

	* include/openbabel/Makefile.am: babelconfig.h is not removed
	automatically. Added it to DISTCLEANFILES.

2008-05-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/mol.cpp: Ensure energy is always 0.0.

	* src/formats/gaussformat.cpp: Prevent crash with incorrect partial charges.

	* include/openbabel/base.h, include/openbabel/generic.h: New class
	for 3x3 matrix data (e.g., quadrupole moments).

	* src/formats/adfformat.cpp, src/formats/t41data.h: Initial import
	of Molekel Tape41 support for ADF.

2005-05-04  Marcus D. Hanwell  <marcus@cryos.org>

	* configure.in, src/config.h.in, include/openbabel/forcefield.h: Fixed
	the babelconfig.h file - typo spotted...

2008-05-04  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/OBPythonOBF/setup.py: Minor changes to install the
	correct OBFs in the Python Windows install.

2008-05-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Make
	OBForceField::_constraints static.

	* include/openbabel/forcefield.h: Add virtual destructors to
	OBFFCalculation2-4.

2005-05-03  Marcus D. Hanwell  <marcus@cryos.org>

	* src/config.h.cmake: Fixed so that TIME_WITH_SYS_TIME is defined.

2008-05-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>
	
	* src/forcefields/forcefieldmmff94.*: Do the same for logging.

	* include/openbabel/forcefield.h, src/forcefields/forcefieldghemical.*,
	src/forcefields/forcefielduff.*,src/forcefields/forcefieldmmff94.*:
	OBFFCalculation has been replaced by OBFFCalculation2,
	OBFFCalculation3 and OBFFCalculation4. This makes the sizeof() smaller
	and improves performance.
	The OBFFCalculation::Compute(bool gradients) is now a template <bool
	gradients> Compute() function. The compiler will generate a Compute
	function with gradients and one without gradients. The E_Bond, ...
	functions are also template functions now. The old functions are still
	available as a wrapper for backwards compatibility. The template
	function is initialized in OBForceField::Energy(bool gradients) by
	calling E_Bond<true>() or E_Bond<false>().

2008-05-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* scripts/openbabel-python.i: Add OBBitVec.

2008-05-02  Marcus D. Hanwell  <marcus@cryos.org>

	* CMakeLists.txt: Fixed include directory order.

2008-05-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* data/atomtyp.*: Added amidine/guanidine IMPVAL rule (thanks to Steve
	Constable for reporting & fixing the bug).

2008-04-29  Marcus D. Hanwell  <marcus@cryos.org>

	* src/CMakeLists.txt, src/formats/CMakeLists.txt: Updates in order to
	build after obmolecformat.cpp was moved.

2008-04-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* autogen.sh, autoconf/: Add macros to work with new libtool 2.2.2.

	* configure.in, configure, aclocal.m4:  */Makefile.in: Use above.

	* src/obmolecformat.cpp: Move from src/formats to facilitate
	external programs creating OBMolecFormat subclasses.

	* src/formats/opendxformat.cpp: New format for OpenDX grids from
	APBS.

2008-04-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/mol.h: Add units to documentation for
	GetTorsion/SetTorsion.

	* tools/obrotate.cpp: Total review of the code. Thanks to Josep Maria
	and Noel for pointing out the problems.

	* src/mol.cpp: Added UnsetSSSRPerceived to all OBMol::Delete*()
	functions. (not DeleteConformer(int i), doesn't change rings... )

	* scripts/python/examples/*.py: Added some force field examples. More
	will follow.

	* include/openbabel/bond.h: Add some defensive checks to
	OBBond::GetBeginAtomIdx, OBBond::GetEndAtomIdx and
	OBBond::GetNbrAtomIdx. (closes #1953657)

	* scripts/openbabel-python.i: Added OBForceField::SetLogToStdOut() and
	OBForceField::SetLogToStdErr() to replace SetLogFile(std::ostream
	*pos) in python.

2008-04-29  Marcus D. Hanwell  <marcus@cryos.org>

	* src/CMakeLists.txt, src/formats/CMakeLists.txt: Moved the
	obmolecformat.cpp linkage back to where it was - this works on both
	Windows and Linux and so seems the better solution.

2008-04-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Torsion constraints are working now.

2008-04-28  Marcus D. Hanwell  <marcus@cryos.org>

	* libavogadro/src/extensions/gaussianinputdialog.cpp: Removed trailing
	white space.

2008-04-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefielduff.cpp: Added groups and Ignore.

	* src/forcefields/forcefieldghemical.cpp: Added groups and Ignore.

	* src/forcefields/forcefieldmmff94.cpp: OpenMP version of MMFF94. Does
	not affect normal compilation. Only used with GCC options "-lgomp
	-fopenmp".

	* include/openbabel/forcefield.h: Changed _ncoords from int to
	unsigned int. (Fixes some compiler warnings)

2008-04-27 Chris Morley

	* include/openbabel/mol.h, src/mol.cpp(AssignSpinMultiplicity):
	added a parameter which forces no implicit hydrogen. The default
	is false and backward compatible.
	
	* src/mol.cpp(PerceiveBondOrders): added a call to
	AssignSpinMultiplicity which should prevent molecules from
	computational chemistry formats being given implicit hydrogen.

2008-04-25  Noel O'Boyle <baoilleach@gmail.com>

	* data/mr.txt: Based on a comparison with RDKit's Crippen parameter
	text file, identified a single error in the MR value for Me1 (see
	JCICS, 1999, 39, 868) 

2008-04-21 Chris Morley

	* src/descriptors/groupcontrib.cpp(Predict): Make a copy of
	the molecule and add hydrogens before calculating property.
	As recommended by Noel in his blog.

2008-04-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/xml/cmlformat.cpp: change line 1810 from 
	s = pUnitCell.GetSpaceGroupName();    to
	s = pUnitCell->GetSpaceGroupName(); 

2008-04-22  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/cmlformat.cpp: import/export crystal symmetry.
	* src/math/spacegroup.cpp: fixes a bug related to transform creation.

2008-04-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h: Documentation update.
	
	* src/forcefield.cpp: Fixed (X, Y, Z, XYZ) atoms are now checked in
	SteepestDescent and ConjugateGradients and works.
	Enable constraints again. Distance and angles work, torsion still
	needs some attention.

2008-04-21  Marcus D. Hanwell  <marcus@cryos.org>

	* include/openbabel/obconversion.h: Moved the Formatpos typedef
	outside of the class in order to preserve old API call.

2008-04-21 Chris Morley

	* include/openbabel/obconversion.h, src/obconversion.cpp:
	Reinstate a version of OBConversion::GetNextFormat() to prevent
	breaking xchemdraw. Formatpos is defined differently but would
	not be accessed in an application program.

	NEWS, windows-vc2005/OBPythonOBF/Readme.txt:
	Minor documentation changes

2008-04-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Added
	SetupPointer. Added Framework for specifying groups using OBBitVec for
	now until we have OBGroup/OBFragment. Documentation example using
	groups. 
	The *RotorSearch functions should call SetupPointers when they change
	conformer. This will update the pointers to the atom positions in the
	OBFFCalculation(s). This solves some weird results when the rotor
	search functions were used with MMFF94 or ghemical. UFF doesn't have
	this problem because it still uses the vector3 class.

	* src/forcefields/forcefieldmmff94.*: Added SetupPointer.
	SetupCalculations() now checks the intra and inter groups.

	* src/forcefields/forcefieldghemical.*: Added SetupPointer.

2008-04-19  Marcus D. Hanwell  <marcus@cryos.org>

	* include/openbabel/grid.h, src/grid.cpp,
	include/openbabel/griddata.h, src/griddata.cpp: Now using std::vector
	to store data internally. Made safer where possible.

	* src/formats/gausscubeformat.cpp: Cleaned up support for reading in
	multiple cubes - large cube files can now be read in.

	* src/formats/gausscubeformat.cpp: Worked on improvements to the cube
	writing function. It now staggers cubes in the z correctly and I think
	I got the rest of it lining up correctly now. Enabled.

	* configure.in, src/config.h.in: Updates to the auto* build tools,
	added HAVE_GCC_VISIBILITY logic and the defines to use it.

2008-04-15  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/OBPython: removed
	* windows-vc2005/OBPythonOBF: added setup.py,
	openbabel_postinstall.py, Readme.txt and logo.bmp

2008-04-15 Chris Morley

	* tools/obchiral.cpp, tools/obenergy.cpp, tools/obfit.cpp,
	tools/obminimize.cpp, tools/obmm.cpp, tools/obprobe.cpp,
	tools/obprop.cpp, tools/obsym.cpp:
	don't #include <#include <unistd.h> in Windows build
	
	* windows-vc2005/OBTools.sln, windows-vc2005/OBTools,
	windows-vc2005/OBTools/*.proj: New build files for tools exes

	* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi
	Add tools exe files to installer

2008-04-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/atomrecord.cpp: Fix from Louis Ricard to handle PDB
	files from platon. An example has been added to the test
	repository.

	* src/formats/gamessukformat.cpp: New format contributed by Jens
	Thomas to support the GAMESS-UK variant.

	* src/formats/moldenformat.cpp, src/formats/msmsformat.cpp: Ensure
	namespace is properly included.

	* tools/babel.cpp: Eliminate some GCC warnings.

	* ltmain.sh, configure.in, configure, */Makefile.*: Upgrade to
	libtool 2.2.x, which offers improved build speed and bug fixes.

2008-04-13  Marcus D. Hanwell  <marcus@cryos.org>

	* CMakeLists.txt, cmake/modules/MacroEnsureVersion.cmake,
	src/config.h.cmake: Added visibility support when using a recent GCC
	compiler.

	* src/CMakeLists.txt, src/formats/CMakeLists.txt,
	src/formats/inchi/CMakeLists.txt: Various fixes to ensure things are
	linked correctly.

	* include/openbabel/obmolecformat.h: Ensured this header includes the
	babelconfig.h header and exports its symbols.

	* src/formats/APIInterface.cpp: Export symbols.

	* src/formats/xml/cmlreactformat.cpp: Removed extra qualifier.

2008-04-10 Chris Morley
	
	* data/atomtyp.txt: revise IMPVAL entries for S. 
	Fixes bug #1938652. Patches a dilapidated program structure...
	
	* test/files/FormulaTest.smi: add S containing species to test above
	
	* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi:
	add help file and remove SetOutPath "$DESKTOP" which prevented
	shortcuts starting with the current directory being that of the
	exe file. Data files were not being found.

2008-04-09  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefielduff.cpp: Fix issue with C atoms not
	being set for OOP terms. Thanks to Bob Hanson for spotting this.

2008-04-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp: Remove inline declaration on constraints --
	prevents Python script bindings from compiling.

	* src/formats/hinformat.cpp: Read in partial charges. Fixes
	PR#1931260.

2008-04-01 Chris Morley

	* windows-vc2005/OBPythonOBF/OBPythonOBF.vcproj,
	* windows-vc2005/OpenBabelDLL/OpenBabelDLL.vcproj
	* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi
	Updated in minor ways
	
	* windows-vc2005/Projects in this workspace.txt: add OBF build

2008-04-01  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/python/setup.py: Error in my previous commit

2008-03-31  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Fix conjugate
	gradients. (my previous commit had a bug..)

2008-03-31  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/python/setup.py: Fix for MacOSX to allow compiling against
	the contents of the build tree rather than /usr/local

2008-03-31 Chris Morley

	* src/GUI/OBGUI.cpp, src/GUI/OBGUI.h: Click on menu item copies
	plugin id to clipboard
	
2008-03-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldghemical.cpp,
	src/forcefields/forcefielduff.cpp,
	src/forcefields/forcefieldmmff94.cpp: Don't use Cut-off when disabled.

2008-03-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Implement
	methods to handle cut-offs. Added SetLineSearchType().

	* src/forcefields/forcefieldghemical.*, src/forcefields/forcefielduff.*,
	src/forcefields/forcefieldmmff94.*: Use it.
	
	* tools/obminimize.cpp: Add new options to specify cut-off and linesearch.

2008-03-29 Chris Morley

	* src/formats/inchiformat.cpp: Add output options 
	"include fixed hydrogen layer" and "include bonds to metal"
	as shortcuts to NIST's InChI functionality.
	
	* include/openbabel/obconversion.h: Make default to OUTOPTIONS,
	as IsOptions does. Makes setting most options less cumbersome.


2008-03-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/UFF.prm: Improved N sp, sp2 atom typing, suggested by Bob Hanson.

	* src/forcefields/forcefielduff.*: Many bug fixes for angle and
	torsion terms, suggested by Bob Hanson (via Jmol implementation).

	* test/files/uffresults.txt: Updated for above changes.

	* configure, configure.in, */Makefile.in: Bump to 2.2.0b5 and
	update build files.

2008-03-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* test/files/uffresults.txt: Update UFF results for recent bug fixes.

2008-03-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Always call SetCoordinates in Setup.

2008-03-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Working
	Newton2NumLineSearch. Used only for SteepestDescent at the moment.

2008-03-26 Chris Morley

	* include/openbabel/parsmart.h, src/parsmart.cpp:
	Fix bug #1906462. If SMARTS pattern contains [H], the matching
	now is done on n explicit hydrogen copy of the molecules. Extra bool
	in struct Pattern and mods to AllocPattern, SMARTSParser, Match.
	Have to be careful with the mods: Match is called more than
	420 times in doing a smi to smi conversion with a SMARTS filter!

2008-03-25  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefielduff.cpp: changed anglecalc.zi = ..[0] to
	... [5]. This bug was reported by Bob Hanson in mail.

2008-03-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Fix LineSearch(*,*) to respect fixed atoms.
	Don't calculate gradient in NumericalDerivative.

2008-03-24 Chris Morley

	* src/formats/gaussformat.cpp: Fix bug #1924342 by looking for
	"Multiplicity" as suggested by Richard West

2008-03-24  Noel O'Boyle  <baoilleach@gmail.com>
	
	* windows-vc2005/OBPython/openbabel.py: Removed from SVN (it is
	created with SWIG as part of the build process)

2008-03-24  Noel O'Boyle  <baoilleach@gmail.com>
	
	* scripts/openbabel-python.i: Added griddata.h

2008-03-23  Noel O'Boyle  <baoilleach@gmail.com>
	
	* scripts/python/pybel.py: First attempts at incorporating the recent
	work by Tim, Geoff and others on geometry optimisation and 3D
	coordinate generation.

2008-03-23  Noel O'Boyle  <baoilleach@gmail.com>

	* scripts/openbabel-python.i: Fix for bug reported by Florian Nigsch.
	The Python iterators didn't correctly handle the case where there was
	nothing to iterate over.

2008-03-22 Chris Morley

	* src/builder.cpp: Slightly cleaner version of yesterdays's change.
	Load data when _fragments is empty.

	* src/formats/gausscubeformat.cpp, src/formats/gausszmatformat.cpp,
	src/formats/mmcifformat.cpp, src/formats/moldenformat.cpp,
	src/formats/msmsformat.cpp:
	Add some flags for Read or Write only, remove duplicate registration
	statements(IDs are not case sensitive), edit Description so options
	appear properly in GUI.
	
	* src/formats/acrformat.cpp, src/formats/chemdrawcdx.cpp,
	src/formats/qchemformat.cpp, src/formats/xml/cdxmlformat.cpp,
	src/formats/mopacformat.cpp, src/formats/msiformat.cpp: 
	Reduce compiler warnings by commenting out unused variables.
	
	* src/obutil.cpp: Remove OBAPI from definitions; only needed in 
	declarations

	* src/ops/gen3d.cpp: Remove error wrap statements (no cerr calls in
	OBBuilder now)
	
	* src/plugin.cpp(Display): remove tab character which was giving error
	messages in wxWidgets menus.
	* windows-vc2005/OBPythonOBF: New project to build Python for OBF
	(multi-DLL) build.
	
	Update Windows OBF build files.

2008-03-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Move GetGrid to
	OBForceField to implement it for all force fields at once.

	* src/forcefields/forcefieldmmff94.*: Remove GetGrid.

	* tools/obprobe.cpp: Implement the obprobe program.

2008-03-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp,
	src/forcefields/forcefieldmmff94.*: Add GetGrid probe method.

	* tools/Makefile.*, tools/obprobe.cpp: Add obprobe tool, still needs
	to be implemented. (copied from obenergy)

	* tools/obminimize.cpp: Don't call ValidateGradients before
	minimizing, takes long for proteins.
	
	* data/UFF.prm: Fix SMARTS patterns for phosphorus (Bob Hanson)

	* src/forcefields/forcefielduff.cpp,
	src/forcefields/forcefieldghemical.cpp: Move loop for better
	performance.

	* src/forcefields/forcefieldmmff94.*: Make Compute() functions inline,
	some optimization to VDW Compute().

	* src/formats/atomrecord.cpp: Added using namespace std.

2008-03-22  Noel O'Boyle  <baoilleach@gmail.com>
	
	* src/formats/xml/Makefile.am: CML format can now be built without
	shared_ptr, so I removed this dependency (c.f. CM 2008-03-14)

2008-03-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/gausscubeformat.cpp: Applied patch from Louis Ricard and
	make it work. Read function is done, write still needs to be done.

2008-03-21 Chris Morley

	* include/openbabel/builder.h, src/builder.cpp:
	Delay parsing of fragments.txt until first use, and then
	do only once, saving in a static variable. This matters for
	gen3D where operation on multiple molecules is common.
	I know OBBuilder is still under development and is not 'my'code;
	please revert if not suitable.

2008-03-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/atomrecord.cpp: New file to handle PDB-style atom
	records -- shared between PDB and PQR formats.

	* src/formats/pdbformat.cpp: Use it.

	* src/formats/pqrformat.cpp: Initial support for reading PQR style
	files (i.e., partial charge and VDW radius supplied with
	coordinates).

	* src/formats/Makefile.am, src/formats/Makefile.in,
	src/formats/CMakeLists.txt: Updates for above.

	* src/formats/cansmilesformat.cpp: Fix for bug exposed by Avogadro
	-- sometimes we only have one atom (and no canonical order data).

	* tools/obfragment.cpp: Update to generate new OBBuilder database.

2008-03-20  Carsten Niehaus  <cniehaus@kde.org>

	* src/*.cpp: Typo fixes

	* CMakeLists.txt: Require CMake 2.4.5.
	
2008-03-16  Noel O'Boyle  <baoilleach@gmail.com>
	
	* All .cpp and .h files: Set SVN property svn:eol to native

2008-03-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/CMakeLists.txt: Add ops and descriptors subdirectories.

	* src/ops.cpp, src/forcefield.cpp, src/ops/loader.cpp,
	src/ops/optransform.cpp, src/descriptors/cmpdfilter.cpp,
	src/descriptors/smartsdescriptors.cpp,
	src/descriptors/groupcontrib.cpp, src/format.cpp, src/alias.cpp,
	src/forcefields/forcefieldmmff94.cpp, src/formats/MCDLformat.cpp, 
	Change to UNIX line-endings for consistency. (Some files also had
	multiple line formats.)

	* include/openbabel/math/matrix3x3.h,
	include/openbabel/forcefield.h: Move to loop form. Compiler
	loop unrolling is effective, and loops can be vectorized for
	greater speed. 

2008-03-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/builder.h, src/builder.cpp: Added Swap function.

2008-03-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/builder.h, src/builder.cpp: More robust way to
	determine OBBitVec fragment masks. This is now handled internally and 
	actually checks if a and b (in Connect) don't belong to the same
	fragment. This also fixes the previously not working commit for: 
	c1cc(CC)ccc1

	* src/CMakeLists.txt: Remove groupcontrib.cpp, added some new files.
	Not sure if the ops/ dir is included.

	* data/CMakeLists.txt: Update data files to install.

	* CMakeLists.txt: Change version to 2.2.0b4.

	* include/openbabel/builder.h, src/builder.cpp: Moved some
	functionality from Build to Connect(). OBBuilder now constructs
	molecules with a single pass trough the database.

	* src/forcefield.cpp: Remove debug output.

2008-03-14  Chris Morley

	* src/formats/gausszmatformat.cpp: add replacement function for
	strcasestr, which is not in Visual Studio's library.

	* windows-vc2005/babelconfig.h: #define strcasestr _strcasestr

	* src/formats/mdlformat.cpp, src/formats/xml/cmlformat.cpp:
	Don't output property with attribute "PartialCharges", which isn't
	relevant in these formats. 
	
	* src/formats/xml/cmlformat.cpp: Make compilation of the code that dependends
	on OBReaction(and hence shared_ptr) conditional on HAVE_SHARED_POINTER.
	Means that most of cmlformat.cpp can be used even when HAVE_SHARED_POINTER
	is not defined, and that Noel's change on 2008-03-04 can be reversed
	(although I have not done it).
	
	* src/obconversion.cpp: prevent crash and add error message when multiple
	output files are used with no input file.
	
	* include/openbabel/obutil.h: actually do the reversion, see below
	
	* src/formats/crkformat.cpp, src/formats/inchiformat.cpp: small 
	changes in descriptions (to make GI look better).
	
	* windows-vc2005/Distribution/NSISScriptToCreateInstaller.nsi:
	Add several data files
	
	Update Windows single DLL build files

2008-03-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/mol.cpp (Separate): Make sure to throw out any bogus
	OBChiralData. This is much preferable to crashing.

	* src/builder.cpp: Support new fragment.txt format with comments,
	etc.

	* data/*.txt: Update comments and fix minor formatting changes.

	* tools/obgen.cpp: Update to add hydrogens, cleanup geometry,
	perform weighted rotor search, etc. Should produce decent 3D
	structures with MMFF94.

2008-03-11  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/msmsformat.cpp: New format to write input files for
	MSMS (Michael Sanner Molecular Surface) calculation program,
	contributed by Ugo Varetto and the Molekel project.

	* src/formats/moldenformat.cpp: Read input from Molden files,
	contributed by Ugo.

	* src/formats/Makefile.*: Add above.

2008-03-13  Chris Morley

	* include/openbabel/obutil.h: Revert the previous change.
	In Windows there is a min function in the default namespace
	(::min compiles ok). So it is essential that std::min is used.
	It's also better not to have using std; in header files. If
	there is a problem in Avagadro it would be better to find a
	solution there. Maybe a cause for its Windows version to crash?
	 
2008-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/obutil.h: replaced std::min() with min() and put
	using namespace std at the top of the file. The compiler only gave an
	error for this when compiling avogadro, not openbabel itself.
	(windows)

	* include/openbabel/builder.h: Added OBAPI.

2008-03-10  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/cifformat.cpp: export space group if known.
	* src/formats/xml/cdxmlformat.cpp: removed a printf debug instruction.

2008-03-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/smilesformat.cpp: Fixes from Craig James. Allow ring closure
	bonds in SMILES to be aromatic. Also check for ring closures in
	ParseComplex.

	* test/files/aromatics.smi: Add test for ring closure bug above.

2008-03-10  Noel O'Boyle <baoilleach@gmail.com>
	
	* test/cmlreadfile.cpp: Commented out the failing test. This is a
	minor bug on Linux.

2008-03-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/gausscubeformat.cpp: Read/write multiple cubes. Always
	write in bohr. More error checking in write might be needed.

2008-03-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/mol.h, src/mol.cpp: GetEnergy(int) and GetEnergies 
	now use OBConformerData to hold the energies.

	* include/openbabel/forcefield.h, src/forcefield.cpp: GetConformers
	and GetCoordinates attatches OBConformerData to the molecule. Energies
	and Forces are set.

	* src/forcefields/forcefieldmmff94.*: minimize the number of calls to
	atoi(GetType, ...) in Setup functions. Use OBBitVec class to replace
	vector<int> where possible.

2008-03-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp: The recent patch from Liu Zhiguo had a bug in
	OBMol::ConnectTheDots(). Inside a loop, NextBond was called without
	checking the return value directly. The return value was being checked
	outside the loop.
	
	while (valCount < bondCount[atom->GetIdx() - 1]) {
	  maxbond = atom->NextBond(l);
	  ...
	  if (!maxbond) // Added
	    break;      // Added
	  valCount++;
	}
	if (!maxbond)
	  break;

2008-03-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/parsmart.cpp: Add protection against double-free
	bugs. Assign pointers to NULL. Addresses bug reported from 
	Avogaro PR#1897745.

	* src/forcefields/forcefieldghemical.cpp: Fix problem with VDW
	gradients -- typo of "kb" instead of "ka."

	* src/forcefields/*.cpp: Remove many (but not all) compile
	warnings from GCC. 

	* src/kekulize.cpp, src/chains.cpp: Ditto.

	* src/ring.cpp: Before running FindSSSR(), delete old data. This
	improves potential race conditions in multi-threaded client code
	(e.g., Avogadro).

2008-03-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/gausscubeformat.cpp: Added write function.

2008-03-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/chains.cpp (DeleteByteCode): Add protection against double-free
	bugs in chains.cpp. Assign pointers to NULL.

2008-03-04  Daniel Leidert <daniel.leidert@wgdd.de>

	* doc/babel.1: Fixed unkown RE macro.

2008-03-04  Noel O'Boyle <baoilleach@gmail.com>
	
	* src/formats/xml/Makefile.am: Only compile cmlformat.cpp if
	HAVE_SHARED_POINTER is true

2008-03-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/math/vector3.h, include/openbabel/base.h,
	include/openbabel/residue.h: Fixes for compiling with GCC
	-pedantic flag, thanks to Daniel Leidert.

	* tests/* : New tests for UFF, Ghemical and MMFF94 unit
	tests. Compares energies and validates gradients. Still appear to
	be some small gradient errors (although these may be due to
	numerical instability.)

	* src/forcefields/forcefield*.cpp (ValidateGradients): Return
	false when gradient errors are > 5.0% anywhere along the line.

2008-03-03  Noel O'Boyle <baoilleach@gmail.com>
	
	* tests/Makefile.am, files/3d.head.2.cml, tests/cmlreadfile.cpp,
	test/wrapper.sh: Add tests for CML scripting support

2008-03-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/dlhandler_unix.cpp: Ensure files match .so exactly. Prevents
	errors when looking for .so.dSYM files.

	* src/formats/MCDLformat.cpp: Fix GCC compile error.

	* src/formats/Makefile.am, src/formats/Makefile.in: Build rsmi and
	MCDL formats.

	* src/config.h.in: Regenerate for HAVE_BOOST symbol.

	* src/forcefields/forcefielduff.*: Fix angular
	gradients. Previous implementation mis-read paper for force
	constant.

	* tools/obminimize.cpp: Validate gradients before starting
	minimize. Useful for debugging force fields.

2008-03-02  Noel O'Boyle <baoilleach@gmail.com>
	
	* configure.in: Only use BOOST for shared_pointer if the GCC4.x
	implementation is not available.

2008-03-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/perl: Add dependency checking for libopenbabel. This
	prevents people trying to run automated CPAN tests without the
	library.

2008-03-01  Noel O'Boyle <baoilleach@gmail.com>
	
	* acinclude.m4: Set "have_boost" to "yes" so I can test it in
	configure.in
	* configure.in: Set Automake variable HAVE_SHARED_POINTER if the user
	has either of Boost or tr1/memory (gcc4.x)
	If "have_boost" is "yes" then set both the Automake variable
	USE_BOOST_FLAGS and the C++ #define USE_BOOST
	* src/formats/Makefile.am: Set the compile flags for BOOST if necessary
	Only compile chemkinformat, rxnformat and chemdrawcdxformat if
	HAVE_SHARED_POINTER is true

2008-02-29  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/generic.h (OBVectorData): New class for storing vector3
	(e.g., dipole moment, transition dipole, etc.)

2008-02-29  Chris Morley

	* src/obconversion.cpp:mods to OBConversion destructor to prevent
	input or output stream being deleted twice when there is an
	associated XMLConversion object - with CML. Possibly closer to
	fixing bugs #1815533 and #1900480.
	
	Add OBMCDL for Windows OBF build.

2008-02-29  Noel O'Boyle <baoilleach@gmail.com>

	* acinclude.m4: Just say 'not found' if BOOST not found.
	
	* configure.in: Look for BOOST and look for tr1/memory.

2008-02-29  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-python.i: Bugfix for "[ 1904345 ] Angle, Pair,
	Torsion iterators dones not have deref() method". Turns out that I
	could have been using the __ref__() method all along. This doesn't
	seem to be in the SWIG documentation though.

2008-02-28  Marcus D. Hanwell  <marcus@cryos.org>

	* include/openbabel/grid.h, src/grid.cpp,
	include/openbabel/griddata.h, src/griddata.cpp: Fixed the
	interpolateDerivative function (hopefully). Added new functions to set
	and retrieve values from the grid using just grid indices. This should
	become the preferred way to access the grid values.

	* include/openbabel/grid.h, src/grid.cpp, src/griddata.cpp: Updated
	the grid classes to use an x, y, z index and added several new
	convenience functions using vector3 variables. Some more work is
	needed and a few extra functions to access/set grid values.

	* src/formats/gausscubeformat.cpp: Stop translating from x, y, z index
	to z, y, x as the grid classes now use the more common x, y, z index.

2008-02-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h, src/forcefield.cpp: Some
	improvements on the way gradients are handled. E_Bond, E_Angle, ...
	iterate over the calculations and Add the gradients to the correct
	atoms pointed to by the _gradientPtr. This pointer can then be used
	directly by line search.

	* src/forcefields/forcefieldghemical.*: Use it. GetGradient() function
	removed.
	
	* src/forcefields/forcefieldmmff94.*: Same.
	
	* src/forcefields/forcefielduff.*: Same, but UFF still uses old
	derivatives dunctions with all the vector3 objects.

2008-02-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefielduff.*: Remove redundant calls to
	Compute when calculating gradients. Remove un-needed angle/oop
	code. Problem lies elsewhere.

	* doc/Makefile.am, doc/Makefile.in: Add missing man pages and html
	documentation.

	* doc/roundtrip.1: Add missing man page. (More needed for new
	tools.)

	* test/roundtrip.cpp: Fix incorrect usage statement. Thanks to
	Daniel Leidert.

	* acinclude.m4: Add Boost detection code. Still needs addition to
	configure script.

2008-02-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/base.h, src/base.cpp: Add new GetAllData()
	function to return a vector of all OBGenericData of a given
	type. This has been long requested and is sorely
	needed. (For example, it's useful when you have multiple orbitals
	in a molecule.)

	* src/formats/gausscubeformat.cpp: Add the title of the cube as an
	attribute of the GridData.

	* tools/obprop.cpp: Update to new name of PSA descriptor.

	* configure.in, configure: Update with patch from Daniel Leidert
	for PR#1902640 and wx-config.

2008-02-25  Chris Morley

	* src/forcefield.cpp: added (double)cast to sqrt to prevent
	compiler error.
	
	* src/formats/xml/xml.cpp(XMLConversion::WriteStream): do not
	write when buffer empty. Workaround to prevent crash in CMLFormat
	which occurs when freeing libxml2 writer. I don't understand exactly
	what is happening here. I wish we had a C++ XML library!
	I hope cures bugs #1815533 and #1900480.

2008-02-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/msiformat.cpp: Finally fixed bond connections and
	single/double bonds. Still needs more testing.

	* src/formats/gausscubeformat.cpp: Try to skim to the end of the
	file after reading data.

2008-02-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldghemical.cpp: Small change for the new
	derivatives.

2008-02-24  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp: Output the number of possible rotamers when
	doing rotor search -- as a long unsigned int.
	Remove old derivatives in favor of BALL analogues.

	* include/openbabel/forcefield.h: Remove old derivatives in favor
	of BALL analogues.

	* src/forcefields/forcefieldmmff94.cpp: Ditto.
	
	* src/forcefielduff.cpp: More checks for real numbers, uncovered
	doing WeightedRotorSearch.

2008-02-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Added VectorAngleDerivative_BALL,
	VectorTorsionDerivative_BALL and VectorOOPDerivative_BALL.

	* src/forcefields/forcefieldmmff94.cpp: Use it. MMFF94 now has
	analytical gradients.

2008-02-23  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/rotamer.cpp (SetCurrentCoordinates): Allow -1 as a rotor
	setting -- implies do not change the dihedral angle.
	Some general code cleanups.

	* src/forcefield.cpp (WeightedRotorSearch): Fix some bugs -- check
	rotors without changing other dihedral angles and make sure to
	update the conformer structure after the search.

2008-02-22  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/atom.cpp (GetAngle): Return 0.0 for the angle if the vectors
	are too small. (The angle is ill-defined in these cases, so this
	is better than returning NaN.)

	* src/forcefield.cpp: Hunting down more divide-by-zero bugs.

	* src/forcefields/forcefieldghemical.cpp: Remove some rare
	divide-by-zero errors (e.g., when atoms are on top of each other).

	* src/forcefields/forcefielduff.cpp: Ditto.

2008-02-22 Chris Morley

	* src/mol.cpp(AssignSpinMultiplicity): Move the functionality
	recently removed from AddHydrogens() to here. Don't assign spin
	multiplicity to multi-atom molecules with no bonds.
	Molecules specified only by elemental formula from thermoformat,
	cmlformat and smilesformat seem to be handled ok.
	
	* src/formats/xml/cmlformat.cpp: handle <atomArray> occurring as
	a child of, formula> as well child of <molecule>.
	DoAtoms) Rewrite so that not confused when multiple sets of
	atom coordinates are present.
	
	* include/openbabel/forcefield.h: include float.h
	
	* windows-vc2005/babelconfig.h: add defines for IsNan and isfinite

	* src/descriptor.cpp: remove define for IsNan

	* test/files/FormulaTest.smi: correct the SMILES for carbene and
	add CH3D

2008-02-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp (WeightedRotorSearch): Check each individual
	rotor setting in isolation and use Boltzmann initial weightings.
	(*RotorSearch): Make sure to call Energy() evaluations without
	gradients.

	* src/rotamer.cpp (SetRotorToAngle): Remove unlikely (but
	possible) divide-by-zero error.

	* src/forcefields/forcefieldghemical.cpp: Fix divide-by-zero error
	in calculation of torsional term. Should be bullet-proof now.

	* src/formats/mdlformat.cpp: Fix rare crash when handling invalid
	alias records.

	* src/formats/msiformat.cpp: Remove debugging information and fix
	various bugs (e.g., dummy atoms).

2008-02-21  Marcus D. Hanwell  <marcus@cryos.org>

	* src/formats/gausscubeformat.cpp: Simplified the cube reading code,
	now more resilient to more loosely formatted cube data without the
	extra line ending at the end of each z data set.

2008-02-19  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp (LineSearch): Check gradients with isfinite()
	and for overly-large movements. Prevents any possible "explosions"
	or "disappearing atoms."

2008-02-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: When
	OBForceField::Setup was called and failed it returned false. But when 
	you did it again IsSetupNeeded() returned false and Setup() therefor
	returned true. This caused lots of crashes in avogadro's AutoOpt tool.
	OBForceField::_validSetup now checks to see if last Setup() failed, if
	so, a real Setup() is done (and will return false if failed).
	Get rid of compiler warnings: unused variable, changed function(bool
	gradients = true) into function(bool = true).
	Setup also calls UnsetSSSRPerceived() now.

	* include/openbabel/mol.h: Added OBMol::UnsetSSSRPerceived().
	Shouldn't this be called when we Add/Delete bonds.

	* src/forcefields/forcefieldmmff94.cpp: Some bug fixes related to atom
	typing of rings. Making and breaking rings in avogadro while MMFF94
	AutoOpt tool is running (in Avogadro) caused it to crash.

2008-02-17  Marcus D. Hanwell  <marcus@cryos.org>

	* src/formats/gausscubeformat.cpp: Rewrote the Gaussian cube format to
	use OpenBabel functions and data structures. Adding error checking and
	also reordered the grid data from the Gaussian order to the internal
	GridData order. Orbitals are now visible in Avogadro - success!

2008-02-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp: Removed check in AddHydrogens() to make sure hydrogens
	are added to molecules with no bonds. This check was probably put in
	to make sure you don't add hydrogens to a molecule comming from a QM
	program for which ConnectTheDots() was not called yet? 

2008-02-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/msiformat.cpp: Add new support for MSI/Accelrys
	Cerius II files. Still needs a bit of debugging, but works fine on
	single-molecule files.

	* src/formats/Makefile.*: Update for new format.

2008-02-13 Chris Morley
	
	* data/plugindefines.txt: comment out problematic entry
	
	* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi:
	update this installer for the multiple DLL build
	
	Update other Windows build files.

2008-02-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/griddata.cpp, include/openbabel/griddata.h: Fix for
	documentation (and code) for GetOriginVector -- return the minimum
	x, y, and z coordinates from the grid.

2008-02-12 Chris Morley

	* src/formats/MCDLFormat.cpp: NEW FILE Converted from his Java code
	by Sergey Trepalin. There is a Java applet viewer and editor for
	this linear format at http://sourceforge.net/projects/mcdl.
	Some of the utility functions have been temporarily shoe-horned
	into this file so there is only one MCDL related file. They will be
	separated when further code for 2D layout from the applet
	becomes available.
	
	* windows-vc2005/OpenBabelOBF.sln: updated
	
2008-02-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/grid.cpp: Added extra check to Interpolate() to make sure no
	_val[i] is used when i >= _xdim*_ydim*_zdim, this fixes some craches
	in the Avogadro surface engine. I suspect that larger molecules have
	larger errors in their _xmin, _xmax, _ymin, ... values (error
	propagation) which causes the first check to pass, but still request 
	an invalid _val[i]

2008-02-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/Makefile.am: Make sure to link src/alias.cpp with
	mdlformat.

	* src/Makefile.am: Build alias.cpp with main libopenbabel.

	* src/formats/smilesformat.cpp: Reject SMILES molecules with 0
	atoms. Fixes bug on test suite.

	* test/files/smartsresults.txt: Update for recent SMARTS and atom
	typing changes.

2008-02-08 Chris Morley

	* src/alias.cpp: NEW FILE with AliasData::Expand(). Currently
	just a crude parsing, rather than an alias look up.
	
	* include/openbabel/alias.h: Add AliasData::Expand()
	
	* src/formats/mdlformat.cpp: Call AliasData::Expand() so that
	more A lines have chemical meaning. Probably puts writeinchi
	test back ok.
	
	Update Windows builds.

2008-02-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldmmff94.*: New GetType(OBAtom *)
	function. This new function improves atom assignment times. This
	per atom method is also better suited for programs which allow
	interactive editing while running force field optimalization (e.g.
	Avogadro). This also allows to assign atom types to large
	molecules such as proteins.
	- Replaced old SetTypes() function with new one that makes use of the
	GetType(OBAtom*) function.
	- Added functions to calculate canonical parameter indices. (Not used
	yet)
	- Added "unsigned" where needed to get rid of compiler warnings.

	* data/mmffsup.par, data/mmffarom.par, data/mmffhdef.par,
	data/mmffsymb.par: Removed unneeded files.

	* data/Makefile.*: Removed unneeded files.

	* data/CMakeList.txt: Should MMFF94 and UFF parameter files be in
	here?

2008-02-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp: Bugfix for DeleteResidue()

2008-02-01 Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/examples/testpybel.py: Made test suite
	compatible with Python 2.3 (Pybel itself had no problems)

2008-01-31 Noel O'Boyle <baoilleach@gmail.com>

	* scripts/ruby/README: Updated as follows...
	(1) it's no longer necessary for the user to run ruby extconf.rb
	(2) added info on performing a local installation

2008-01-30 Joshua Ballanco <jballanc@gmail.com>

	* scripts/ruby/extconf.rb: Reworked the mkmf fix to be more
	generally applicable to *nix platforms.

2008-01-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	Fixes contributed by Liu Zhiguo via e-mail.
	* src/data.cpp (OBResidueData::AssignBonds): For pre-defined
	residues, do not check distances. (PDB files should be fairly
	clean.)
	(OBGlobalDataBase::Init): Make sure to check return value from
	OpenDatafile.

	* src/mol.cpp (operator +=): Make sure to preserve residue
	information when appending.
	(ConnectTheDots): Make sure to preserve existing bonds, e.g. from
	PDB files.

	* src/atom.cpp: (IsHBondAcceptor, IsHBondDonorH): Improvements for
	more accurate description of h-bonding. IsHBondDonorH now cleanly
	checks neighbors for IsHBondDonor rather than duplicating logic.

	* src/formats/mol2format.cpp: Don't attempt to re-perceive atom types.

2008-01-30  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-java.i: Updated to make identical (in terms of
	includes and header files) to python wrapper. Added ignore statements
	for operators as there are just too many warnings about these.

2008-01-29  Joshua Ballanco <jballanc@gmail.com>

	* scripts/ruby/extconf.rb: Fixed an error that had Ruby 1.8.6
	using gcc to compile and link the C++ extension file. Also updated
	the method of finding the correct include directories.

2008-01-24  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/setup.py: Changed search method to find openbabel.so
	(may need testing on other platforms)
	* scripts/openbabel-perl.i: Updated to make identical (in terms of
	includes and header files) to python wrapper.

2008-01-24  Chris Morley
	
	* src/formats/inchiformat.cpp(WriteMolecule): remove #ifdef _WIN32
	from InChIKey code.

2008-01-24  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/Makefile.am,Makefile.in: Incorporated Rich Apodaca's fix
	for Ruby OpenBabel error message "undefined symbol: Init_openbabel"
	* scripts/openbabel-ruby.i: Updated to include same header files as
	openbabel-python, but commented out problematic obfingerprint.h. Also
	upper-cased the first letter of the templates to avoid warning
	messages, and then needed to rename template VectorData to
	VectorGenericData to avoid a conflict with another object of the same
	name in OpenBabel.

2008-01-22  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/ops.cpp, src/pointgroup.cpp, src/kekulize.cpp, src/mol.cpp,
	src/obutil.cpp, src/ring.cpp, src/atom.cpp,
	src/forcefields/forcefielduff.cpp,
	src/forcefields/forcefieldmmff94.cpp,
	src/forcefields/forcefieldghemical.cpp,
	src/formats/cansmilesformat.cpp: Fix GCC warnings, adding explicit
	braces for if/else statements, explicit () around logic
	statements, etc.

	* include/openbabel/ring.h (GetRootAtom): Return unsigned int for
	comparison with atom indexes.

	* include/openbabel/plugin.h: Remove unused parameter for warning
	reduction.

2008-01-22  Chris Morley

	* src/formats/mdlformat.cpp(WriteMolecule): CHG line output
	corrected.

2008-01-22  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/yasaraformat.cpp: replaced const char* by string.

2008-01-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/atom.h, src/atom.cpp: Handle SetType(string)
	as const as well.

	* src/obconversion.cpp: When looking for .gz extensions, make sure
	substrings go to the end of the string. This prevents problems on
	extensions like ".gzmat."

	* src/formats/gausszmatformat.cpp: New format. Supports
	reading/writing to Gaussian Z-matrix files. PR#1863673 and #1696776.

2008-01-21  Jean Brefort  <jean.brefort@normalesup.org>

	* src/math/spacegroup.cpp: fixed all g++ warnings.

2008-01-20  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-perl,ruby,java.i: Merged in changes to
	openbabel-python.i.

2008-01-20  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/atom.h: replace char* by const char* where
	appropriate to get rid of the deprecated conversion from
	const char* to char* gcc message.
	* include/openbabel/chains.h: ditto.
	* include/openbabel/data.h: ditto.
	* include/openbabel/pointgroup.h: ditto.
	* src/atom.cpp: ditto.
	* src/chains.cpp: ditto.
	* src/data.cpp: ditto.
	* src/formats/PQSformat.cpp: ditto.
	* src/formats/chem3dformat.cpp: ditto.
	* src/formats/chemdrawcdx.cpp: ditto.
	* src/formats/crkformat.cpp: ditto.
	* src/formats/fastaformat.cpp: ditto.
	* src/formats/gromos96format.cpp: ditto.
	* src/formats/pdbformat.cpp: ditto. (don't let this format to
	modify etab).
	* src/formats/yasaraformat.cpp: ditto.
	* src/mol.cpp: ditto.
	* src/parsmart.cpp: ditto.
	* src/pointgroup.cpp: ditto.
	* src/tokenst.cpp: ditto.
	* test/roundtrip.cpp: ditto.

2008-01-20  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/cifformat.cpp: don't try to find the group when there
	is no symmetry related data in the data block.
	* src/generic.cpp: fixed a typo (bug).
	* src/math/spacegroup.cpp: return after throwing an error.

2008-01-19 Chris Morley

	* scripts/openbabel-python.i: include op.h
	* windows-vc2005/OBPython/openbabel.py: updated

	* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi:
	add installer script for  obf (multi DLL) build
	
	* windows-vc2005/OBPython/_openbabel.pyd,
	windows-vc2005/OBPython/OpenBabelDLL.dll: remove compiled files
	
	* src/plugin.cpp(ListAsVector):correct message when listing
	"plugins"
	
	* data/plugindefines.txt: remove some of the trivial examples
	
2008-01-19  Jean Brefort  <jean.brefort@normalesup.org>

	* src/math/spacegroup.cpp: accept white spaces in transforms
	descriptions in cif files. Fixes bug 1873908.

2008-01-17  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/pybel.py, scripts/python/examples/testpybel.py:
	Updated to use plugin descriptors. Changed to create a single instance
	of plugin descriptors and fingerprinters. Also, readfile now raises an
	IOError if the file does not exist.
	* scripts/python/examples/findcoverage.bat: Add .bat file to automate
	calculation of code coverage for pybel.

2008-01-16 Chris Morley

	* include/openbabel/obconversion.h(ReadObject),
	* include/openbabel/mol.h(CreateMolecule):
	These declarations were added by Jean, but do not seem to
	have definitions currently, which causes problems with SWIG.
	Comment them out for the time being.
	
	* include/openbabel/fingerprint.h: last commit was mistake;revert. 
	* scripts/openbabel-python.i: do not include groupcontrib.h
	* windows-vc2005/OpenBabelDLL/OpenBabelDLL.vcproj: updated
	for extra files etc.

2008-01-16  Noel O'Boyle <baoilleach@gmail.com>

	* include/openbabel/forcefield.h, plugin.h: Documentation fixes
	* src/bitvec.cpp: Documentation fixes

2008-01-16  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-python.i: Updated to allow compilation

2008-01-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/base.cpp: Fix API documentation for return(1), as mentioned
	by Andrew Dalke. PR#1827795.

	* src/formats/cacheformat.cpp: Fix incorrect chemical/x-alchemy
	MIME type. PR#1822511.

	* src/formats/mol2format.cpp: Fix trailing newline
	issue. PR#1868929.

	* src/formats/chemdrawcdx.cpp: Return false when attempting to
	read past the end of the file. This solves PR#1856016.

	* include/openbabel/generic.h: Fix template issue with
	OBPairTemplate, PR#1830110.

	* src/mol.cpp (OpenBabel): Add patch from Noel PR#1840908 for
	inertial matrix speedup.

	* data/phmodel.txt, src/phmodel.cpp: Fixes from Stephen Constable,
	related to PR#1838943.

	* src/typer.cpp: Ditto. (Re-enables CorrectAromaticNitrogen to
	handle tryptophan.)

	* configure.in: Bump for 2.2.0b2 snapshot.

2008-01-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/Makefile.*: Add tokenst.h

2008-01-11  Michael Banck  <mbanck@gmx.net>

	* src/Makefile.am (SUBDIRS): Added descriptors and ops.
	(libopenbabel_la_SOURCES): Removed filters.cpp, gen3d.cpp,
	smartsdescriptors.cpp and groupcontrib.cpp.
	(libopenbabel_la_LIBADD [BUILD_SHARED]): Added ops/libops.la and
	descriptors/libdescriptors.la.
	(libopenbabel_la_LIBADD [!BUILD_SHARED]): Likewise.
	* src/Makefile.in: Regenerated.
	* src/descriptors/Makefile.am: New file.
	* src/descriptors/Makefile.in: Generated.
	* src/ops/Makefile.am: New file, skipping op2d.cpp for now.
	* src/ops/Makefile.in: Generated.
	* configure.in (AC_OUTPUT): Added src/descriptors/Makefile and
	src/ops/Makefile.
	* configure: Regenerated.

2008-01-11  Michael Banck  <mbanck@gmx.net>

	* include/openbabel/tokenst.h: Add newline at end of file.

2008-01-10 Chris Morley

	* src/tokenst.cpp, data.cpp, include/openbabel/base.h, data.h:
	Move OpenDataFile from data.cpp to tokenst.cpp. Move declarations
	of tokenize and Trim to a new header file tokenst.h, so that
	these utility functions can be use in modules which do not
	include the main chemistry API. Other similar utilities should
	probably be treated in the same way.
	
	* src/descriptors/cmpdfilter.cpp: NEW FILE. plugin to combine
	descriptors in --filter and similiar options.
	
	* src/ops: NEW DIRECTORY. Move src/gen3d.cpp, op2d.cpp to there.
	
	* src/ops/loader.cpp: NEW FILE for plugin to make new
	plugins from text file.
	
	* src/obconversion(LoadFormatFiles):hook for OBDefine.
	
	* include/openbabel/plugin.h: add MakeNewInstance and GetPlugin.
	In MAKE_PLUGIN check for empty ID before registering.

	* src/plugin.cpp(ListAsVector), include/openbabel/op.h(OpOptions):
	no listing if ID starts with _  Allows dummy instances.

	* src/filters.cpp, smartsfilters.cpp, groupcontrib.cpp: Moved to
	src/descriptors
	
	* include/openbabel/bitvec.h: modify Windows build macros
	
	* src/descriptor.cpp:remove an unnecessary zero check and minor
	doc changes

2008-01-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/rotor.h: Added Yongjin Xu's rotorKeyList class as
	OBRotorKeys, added documentation and NumKeys().

	* src/forcefield.cpp, include/openbabel/forcefield.h: Use the new
	OBRotorKeys class in SystematicRotorSearch, angle constaints work and
	renamed BondConstraint to DistanceConstraint.

2008-01-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/rotor.cpp: remove _fix.Clear() from OBRotorList::Clear()

2008-01-04  Michael Banck  <mbanck@gmx.net>

	* test/cml.sh: Use /bin/bash to run, not /bin/sh as "source" is a
	bashism.

2008-01-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/xyzformat.cpp: Accept non-standard XYZ files with an
	atom number rather than an element symbol in the first column.

2007-12-20  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/pdbformat.cpp: fix crash [#1846728].
	* src/math/spacegroup.cpp: add missing header.

2007-12-19  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/forcefield.h (HasAnalyticalGradients): New
	method to define if full analytical gradients are implemented for
	a force field. Allows code to choose analytical vs. numeric based
	on implementation. Defaults to false (i.e., implement analytical
	later).
	
	* src/forcefields/forcefieldghemical.h,
	src/forcefields/forcefielduff.h: Define that analytical gradients
	are implemented.

2007-12-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: Cleaned up
	header file and documentation. All private variables now start with
	"_". Added support for Molecular Dynamics.

	* src/ops.cpp: fix compiler error.

2007-12-17 Chris Morley

	Try to resynchronize.
	
	* src/obconversion.cpp, /include/openbabel/obconversion.h:
	Change return type of AddChemObject from bool to int. 
	This allows the modes with and without a queue of 2 to be
	distinguished. It is backward compatible and in fact has been
	this way previously. Consequential changes in GetChemObject() in
	obmolecformat.cpp, rxnformat.cpp, 
	
	* include/openbabel/forcefield.h(UpdateConformers, UpdateCoordinates):
	return values.
	
	* src/dock.cpp(GridDockNextPose): add return value.

	* src/atom.cpp(GetResidue): return a value
	
	* src/transform.cpp: filter mol if DoOps returns false. 

	* include/openbabel/op.h(DoOps) return false if Do() does,
	to aid filtering. Minor documentaion.
	
	* include/openbabel/plugin.h: Minor documentation.
	
	* include/openbabel/reaction.h: Add support for an Agent molecule.

	* src/gen3d.cpp: Add start and stop ErrorWrap so OBBuilder diagnostic
	code to cerr is demoted to obInfo messages.
	
	* src/oberror.cpp(StopErrorWrap):Set _inWrapStreamBuf to NULL.
	so can handle multiple molecules.
	
	* src/builder.cpp: Set dimension of molecule to 3 (CML needs this).
	Replace tabs.
	
	* src/formats/getinchi.cpp: remove OBCOMMON macro. Not needed in a format.
	
	* src/kekulize.cpp: initialize expand_ successful to supress
	compiler warning.

	* src/formats/xml/cmlformat.cpp: Minor documentation
	
	* src/formats/chemkinformat.cpp(WriteReactionLine): if molecule has
	no title use its formula.
	
	* src/formats/xml/xml.cpp(~XMLConversion):check that document has
	been terminated.
	
	Update Windows OBF build files incl some new projects making OBF files.


2007-12-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldmmff94.cpp: Analytical gradients for all
	interactions except OOP.

2007-12-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldmmff94.[h,cpp]: Solved problem with VDW
	interactions. H-Bond donor/acceptor reactions were not handled
	correctly.

2007-12-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* srd/mol.cpp: Bugfix for FindTorsion. Now checkes to make sure the
	wing atoms are not the same atom. This occurs in 3-membered rings.

	* src/forcefields/forcefieldmmff94.cpp: Improved torsion and OOP
	energies.

2007-12-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: Setup now checks
	if the molecule actually needs to be set up by calling IsSetupNeeded()
	itself.

2007-12-10  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/base.h: add missing headers, see debian bug #455170.
	* include/openbabel/data.h: ditto.
	* include/openbabel/lineend.h: ditto.
	* include/openbabel/mol.h: ditto.
	* include/openbabel/obconversion.h: ditto.
	* include/openbabel/obmolecformat.h: ditto.
	* include/openbabel/plugin.h: ditto.
	* include/openbabel/xml.h: ditto.
	* src/bitvec.cpp: ditto.
	* src/dlhandler_unix.cpp: ditto.
	* src/format.cpp: ditto.
	* src/math/spacegroup.cpp: ditto.
	* src/matrix.cpp: ditto.
	* src/residue.cpp: ditto.
	* src/tokenst.cpp: ditto.
	* tools/babel.cpp: ditto.

2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/dock.h, src/dock.cpp: Added docking class.

	* src/forcefield.cpp: Implemented X, Y, Z atom constraints.



2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp, include/openbabel/forcefield.h: replaced double _energy
	with vector<double> _energies.

	* src/forcefield.cpp, include/openbabel/forcefield.h: update for
	restraint code.

2007-12-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/xyzformat.cpp: Fix bogus warning about titles when
	reading past the end of the file.

	* data/element.*: Fix atom colors to match Jmol standard. (Changes
	in Fe, Co, Ni, Cu only.)

2007-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>
	
	* src/forcefield.cpp, include/openbabel/forcefield.h: Added some log
	functions, documentation update and bond length constraints.

2007-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: OBForceField now
	defines Setup() itself. It calls the needed virtual setup functions
	which FF implementations can overwrite.
	Continue work on constraints implementation.

	* src/forcefields/*: Changes for new Setup system.
	
	* include/openbabel/atom.h: Removed old Ignore/Fixed functions.

2007-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: Updated support
	for constraints by added OBFFConstraints class.

2007-12-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/pointgroup.h, src/pointgroup.cpp: New class to
	wrap  S. Patchkovskii's brute-force 3D point group symmetry
	code. Still needs some updates from original C code, particularly
	to make it "less chatty."

	* tools/Makefile.am, tools/obsym.cpp: New tool to detect point
	group symmetry and eventually write newly "symmetrized" coordinates.

	* src/CMakeLists.txt, src/forcefields/Makefile.*: Update to remove
	MM2 forcefield from building.

2007-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: Added
	IsSetupNeeded to limit the number of calls to Setup, this improves
	performance for applications like avogadro (AutoOpt tool)

2007-12-02 Chris Morley

	* src/forcefield.cpp, include/openbabel/forcefield.h,
	forcefieldghemical.h, forcefieldmm2.h, forcefieldmmff94.h
	MakeNewInstance as pure virtual function to OBForceField
	for use in multithreaded environments.

2007-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: Added support
	to ignore and fix atoms. see doxygen documentation for more info.

2007-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp, include/openbabel/forcefield.h: Split 
	SystematicRotorSearch into ...Initialize and ...NextConformer. This 
	alows a progress bar to be displayed in avogadro.

	* src/forcefields/forcefieldghemical.cpp: Removed (commented out)
	special treatment of linear angles, wasn't workiung correctly, needs
	to be looked at...

2007-11-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/chains.cpp: Improve speed when clearing residue info in
	molecules with no residues.

	* include/openbabel/atom.h, src/atom.cpp: New method GetResidue()
	to optionally request no chain perception. Useful in
	builders/editors (e.g., Avogadro).

2007-11-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/Makefile.am, tools/Makefile.am: Fixes for building
	outside of the source tree.

	* test/iterators.cpp: Fix #include for OBRing. Now compiles cleanly.

2007-11-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/data.h, src/data.cpp: Added Allred-Rochow
	Electronegativities.

	* data/element.txt, data/element.h: idem.

	* src/forcefields/forcefieldmmff94.cpp: use it.

2007-11-28 Chris Morley

	* src/formats/smilesformat.cpp(ParseSimple): Add ForceImplH()
	to fix bug #1839589
	
	* src/mol.cpp(AssignSpinMultiplicities): Leave spinMultiplicity
	at zero (not hydrogen deficient) for atoms labelled as above.
	
	* include/openbabel/atom.h: newflag OB_ATOM_NOT_H_DEFICIENT
	with set and read functions the above.

2007-11-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: OBForceField::VectorTorsionDerivative() now
	returns 180 instead of 0. (was needed for MMFF94)

	* srd/forcefields/forcefieldghemical.cpp,
	src/forcefields/forcefielduff.cpp: Also changed 0 to 180 for torsions.
	Bug fix for OBForceFieldXXX::GetGradients(). (Compute() wasn't called)

	* src/forcefields/forcefieldmmff.*: More changes...

2007-11-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/formats/smilesformat.cpp: fixed compile error on gcc.

	* src/forcefields/forcefieldmmff94.*: Partial charges are now assigned
	correctly. 

2007-11-27 Chris Morley

	* src/formats/smilesformat.cpp: Replace ReadMolecule and add
	isNotSmiles(). Lines starting with non-SMILES characters are ignored.
	Input stream left at first non-SMILES char unless a whitespace.
	(WriteMolecule) Add options smilesonly and nonewline to ease
	rsmiformat. Not intended to be public.
	
	* src/formats/rsmiformat.cpp: New file for Reaction SMILES format

2007-11-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp (VectorOOPDerivative): Calculate forces, as
	per Tim's reference.

	* src/forcefields/forcefielduff.cpp: Use it.

	* tools/obminimize.cpp: Fix a bug to use conjugate gradients when
	-cg is specified. (Explosions seem to occur more often with CG for me.)

2007-11-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldmmff94.*, data/mmffsymb.par: Formal
	charges are now assigned correctly.

2007-11-25  Patrick Spendrin, Christian Ehrlicher
	
	* */CMakeLists.txt: some improvements to get it running under win32

2007-11-25 Chris Morley

	* src/dlhandler_win32.cpp, generic.cpp,
	
	* include/openbabel/atomclass.h, alias.h:
	Including atomclass.h and alias.h into dlhandler_win32.cpp breaks
	code segregation (OBConversion and user interfaces do not know
	about the chemistry.) Include in generic.cpp instead and change
	the build macros used by 'native' MSVC8 build from OBCOMMON to OBAPI
	I hope this fits ok with CMake.
	
2007-11-24  Patrick Spendrin, Christian Ehrlicher
	
	* include/openbabel/atomclass.h: adding support for sstream
	
	* src/config.h.cmake: cleanup
	
	* src/dlhandler_win32.cpp: improvements for msvc
	
	* */CMakeLists.txt: improving CMake based buildsystem esp. for win32
	and mingw32 - it builds now again, though there will come more improvements
	next

2007-11-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldmmff94.*, data/mmffsymb.par: Atom typing 
	works!!
	
	* src/forcefield.cpp, include/openbabel/forcefield.h,
	tools/obminimize.cpp: Added DetectExplosion() to aid in debugging the
	problem with planar molecules.

	* src/typer.cpp, data/ringtyp.txt, include/openbabel/mol.h: Fixed some
	bugs and added more ringtypes.

	* src/ring.cpp, include/openbabel/ring.h: Added GetRootAtom(), returns
	the index of the root atom (e.g. O in furan, ...)

2007-11-20  Chris Morley

	* src/formats/xml/cmlformat.cpp: Now Has own WriteChemObject
	so OBReaction object can bypass OBMoleculeFormat functionality
	and be passed directly to WriteMolecule.
	WriteMolecule passes OBReaction objects to CMLReactFormat.
	Restore handling of WriteAromaticBonds which somehow got deleted. 
	
	* src/formats/xml/cmlreactformat.cpp: Changes to handling of
	options MolsNotStandalone and ReactionsNotStandalone.
	
	* src/formats/xml/xml.cpp(GetDerived): transfer IsLast flag to
	extended object when writing.
	
	* src/formats/thermoformat.cpp: Replace changes made for cmake
	by _MSC_VER as macro indicating Visual C++ compiler
	
	Update Windows VS OBF build files.

2007-11-19  Chris Morley

	* src/formats/xml/cmlformat.cpp: extra string temp variable so
	that it will compile on gcc
	
	* src/formats/xml/cmlreactformat.cpp: minor changesfrom compiler
	warnings
	
2007-11-18  Chris Morley

	* include/openbabel/alias.h: New File with OBGenericData derived
	class to hold aliases of placeholder atoms.
	
	* src/formats/mdlformat.cpp: When reading an alias block put the
	data into the AliasData class above, without trying to interpret it.
	Write alias block is the atom has unexpanded AliasData.
	
	* src/format/xml/cmlformat.cpp: had forgotten Atom4Refs
	whem doing mods for atomclasses.
	
	* src/GUI/optswx.cpp:added a test for >0 to a parameter of isspace()
	
	* include/openbabel/plugin.h: Moved CharPtrLess to be a free
	standing struct rather than embedded in OBPlugin. Less to go wrong
	with SWIG.
	

2007-11-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/builder.cpp: Added some documentation. Now uses OpenDataFile().

	* src/typer.cpp, include/openbabel/typer.h, data/ringtyp.txt: Added
	OBRingTyper class. Brief doxygen documentation included on use.

	* src/ring.cpp, include/openbabel/ring.h: Added GetType() and
	SetType() (see OBRingTyper)

	* include/openbabel/mol.h: Added SetRingTypesPerceived() and
	HasRingTypesPerceived() (see OBRingTyper) 

2007-11-16  Chris Morley

	* include/openbabel/atomclass.h: New file with OBAtomClassData
	class, derived from OBGenericData and that attaches to OBMol.
	
	* src/formats/smilesformat.cpp: Added capability to reads and 
	optionally write atom class e.g [CH3:1].
	
	* src/format/cmlformat.cpp: Read and write atom classes (embedded
	in atom ids, with care that they remain unique, even when atom
	classes ar not.
	
	* windows-vc2005/OpenBabelDLL/OpenBabelDLL.vcproj: updated to
	remove RDKit references.

2007-11-16  Michael Banck  <mbanck@gmx.net>

	Make libinchi.la a convenience library.

	* src/formats/inchi/Makefile.am (lib_LTLIBRARIES): Renamed to ...
	* (noinst_LTLIBRARIES): ... this.
	* src/formats/inchi/Makefile.in: Regenerated.

2007-11-16  Michael Banck  <mbanck@gmx.net>

	* src/formats/xml/Makefile.am (INCLUDES): Added
	-I$(top_builddir)/include.
	* src/formats/xml/Makefile.in: Regenerated.

2007-11-15  Chris Morley

	Update Windows build files.
	
	* src/formats/pngformat.cpp(TargetClassDescription): modify so 
	that options for OBMol appears in GUI.
	
2007-11-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/griddata.cpp, src/grid.cpp: Change to new SetLimits method
	for assigning axes, origin -- everything required by OBFloatGrid.

	* src/formats/gausscubeformat.cpp: Use it.

	* include/openbabel/Makefile.am: Make sure to install new headers
	griddata.h, op.h.

2007-11-13  Chris Morley

	* src/formats/pngformat.cpp: Remove class name in declaration
	as patch #1830826 from LI Daobing. I haven't yet found how to
	get a warning on this in Visual C++.

2007-11-12  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/Makefile.am: Add "ops" code introduced by Chris, including
	gen3d coordinate generation.

	* src/formats/chemkinformat.cpp
	(ChemKinFormat::ParseReactionLine): Added some compilation fixes
	for GCC.

	* src/formats/Makefile.* : Enable compilation of png, rxn, and
	chemkin formats.

2007-11-11  Chris Morley

	Added gen3D.cpp, a wrapper for OBBuilder to make plugin option.
	
2007-11-11  Chris Morley

	* src/formats/chemkinformat.cpp: Reading rewritten so that it
	is like other formats - separate ReadChemObject and
	ReadMolecule. Allows -f and -l options and, potentially,
	filtering of reactions.
	Many parsing changes on reading, incl allowing species names 
	containing spaces with simple input.
	On writing extra option to omit zero rate reactions, formatting
	changes and correct loss of first species in list bug.
	
	* src/formats/xml/cmlreactformat.cpp: Separate out code as
	WriteRateData.
	Add molecules to list even if to be immediately output, so that
	they can benefit from being combined with other inputs.
	If ID of a molecule is a filename, remove the path and extension.
	
2007-11-11  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/inchi/*.c, include/inchi/*.h: Import InChI v1.02b
	distribution code.

2007-11-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

        * src/Makefile.*: Updated for new files.

        * include/openbabel/base.h: New	data type for grid data.

	* include/openbabel/grid.h, src/grid.cpp: Some modifications to
	support new OBGridData class. Still needs documentation	and other
	updates. (This code is showing some bitrot.)

	* include/openbabel/griddata.h, src/gridddata.cpp: New class to
	link a OBFloatGrid as an OBGenericData	(e.g., to a molecule).

	* src/formats/gausscubeformat.cpp: New format from Molekel project
	to read coordinates and cube/grid data from Gaussian cube files.
	
	* src/formats/gromos96format.cpp: Fix typo caused by residue
	numbers as strings.

2007-11-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/builder.cpp: rotation works! you can now create fragment based
	structures such as: CCC(c1ccc(C(c2c(c3ccccc3)cccc2))cc1)


2007-11-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/*.cpp, include/*.h: Change to UNIX line endings for
	consistency.

2007-11-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/builder.cpp, include/openbabel/builder.h: OBBuilder class
	for fragment based structure generation.

	* data/fragments.txt: fragment library for OBBuilder class.

	* tools/obgen.cpp: modified to use OBBuilder

2007-11-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefielduff.cpp: Fix VDW gradients.

2007-11-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp (WeightedRotorSearch): Improved conformer
	searching. Still needs geometry optimization for each
	rotamer. (That seems to uncover a bug in OBMol/OBForceField.)

	* tools/obconformer.cpp: Switch to WeightedRotorSearch followed by
	minimization.

	* data/UFF.prm: Improved typing.

	* src/forcefields/*: Add delayed initialization. Only parse the
	parameter file when the force field is called by Setup on a
	particular molecule.

	* src/forcefields/forcefielduff.cpp: Bug fixes.

2007-11-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* CMakeLists.txt */CMakeLists.txt: CMake build files contributed
	via Saro Engels and Christian Ehrlicher and the KDE-Win project.

2007-11-04  Chris Morley

	* src/forcefields/forcefieldghemical.cpp(ParseParamFile):
	replaced 4 instances of reserve by resize (on ipar etc).
	Was previously crashing for me.
	
	* include/openbabel/base.h, generic.h: Moved the declaration of
	the OBGenericData base class from generic.h to base.h. This
	potentially reduces dependencies. Most of the derived classes are
	still declared in generic.h. New OBGenericData classes would be
	better with their own header files.
	
	* include/openbabel/atom.h: consequent extra #include.
	
	* src/generic.cpp: OBVibrationData wasn't copying properly. 
	Simplify so uses implicit copy constructor and assignment, which 
	are more reliable.
	
	* src/mol.cpp: remove calculation of _totalSpin from 
	AssignSpinMultiplicity. Done on demand in GetTotalSpinMultiplicity.
	
	* src/descriptor.cpp: minor edit in comment
	
2007-11-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefielduff.*: Calculates full UFF energies,
	including out-of-plane bending. Still need to finish all analytical
	gradients.

	* data/UFF.prm: Fixed atom typing rules.

2007-11-02  Michael Banck  <mbanck@gmx.net>

	* src/formats/inchi/inchi.sym: New file.

	* src/formats/inchi/Makefile.am (libinchi_la_LDFLAGS): Use inchi.sym
	to restrict the exported symbols via libtool's -export-symbols option.

	* src/formats/inchi/Makefile.in: Regenerated.

2007-11-02  Kevin Shepherd <kshepherd1@users.sourceforge.net>

	* src/formats/cifformat.cpp: Further to 1821894 this patch
	implements vincefn's suggestion i.e. "whenever reading a data name
	(tag),replace all '.' by '_'" and rolls back the previous
	changes.
	
2007-11-01  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefielduff.*: First pass at a UFF
	implementation. It compiles, but that's about it for now.

	* data/UFF.prm: Initial parameters taken from RDKit under BSD
	license.

	* include/openbabel/forcefield.h, src/forcefields/*: Switch to
	ipar and dpar as vectors of int and double, respectively.

2007-10-31  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/residue.h, src/residue.cpp: Switch residue
	numbers to be strings internally. Added GetNumString() to return
	the number as a string (needed for backwards compatibility).

	* src/data.cpp, src/mol.cpp: Use new residue string support. Fixes
	problems raised by David Osguthorpe.

	* src/formats/pdbformat.cpp, src/formats/*: Ditto.

	* include/openbabel/rotamer.h, src/rotamer.cpp
	(SetCurrentCoordinates): New method to set the current coordinate
	set, rather than creating new conformers. More memory-efficient
	with large conformer searching routines.

	* configure, Makefile.in, */Makefile.in: Rebuild with current
	autoconf, libtool, etc.

2007-10-28  Kevin Shepherd <kshepherd1@users.sourceforge.net>

	* src/formats/cifformat.cpp: Fix for Request ID 1821894.  This
	change allows more CIF files to be understood, allowing the
	_atom_site.XXXX varient of the naming.
	
2007-10-27  Kevin Shepherd <kshepherd1@users.sourceforge.net>

	* src/formats/alchemyformat.cpp: Altered the ReadMolecule function
	to be more flexible in handling comments and whitespace.
	This fixes Request ID 1821003, and can be tested with Test File
	Request ID 1820997.
	
2007-10-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/pdbformat.cpp: Fix some issues with multiple-chain
	proteins. This is likely a minor fix until David Ogusthorpe
	contributes his changes.

2007-10-24  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/torlib.[h,txt]: New torsional library data, improving conformer
        searching.

	* tools/obconformer.cpp: New tool to do real conformer searching,
	using new random and Monte Carlo searching mechanisms in OBForceField.
	
	* tools/Makefile.*: Add above.

	* include/openbabel/forcefield.h, src/forcefield.cpp: Add geometry
	optimization steps to SystematicRotorSearch and new method
	RandomRotorSearch.

2007-10-22  Chris Morley

	Implement exact fastsearch option.
	* src/transform.cpp:Add test for same number of heavy atoms if the
	internal exactmatch option set.

	* src/format/fastsearchformat.cpp: Split out ObtainTarget() to
	make code less cumbersome. Add -ae option implementation.
	
2007-10-18  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/Makefile.am: The dl Python module is not present on (many?)
	64-bit systems, so it falls back to the DLFCN module which hopefully
	*is* present. I would appreciate if someone could rerun the toolchain
	and check in Makefile.in.

2007-10-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/forcefield.h: New LineSearch() method to
	update a step over the entire molecule's coordinates at once. Much
	faster, since it drastically minimizes the number of energy
	evaluations.

	* src/forcefield.cpp: Implement above, plus switch SteepestDescent
	and ConjugateGradients to use it.

	* include/openbabel/mol.h, src/mol.cpp: Add SetCoordinates() call
	to set the entire coordinate system at once.

2007-10-15  Chris Morley
	
	* src/babel.cpp, src/nbabel.cpp: The last commit gave incorrect
	error messages. Correct this, add Read or Write only to output
	from Hxxx and make both Hxxx and H xxx acceptable.

2007-10-15  Chris Morley
	
	* src/babel.cpp, src/nbabel.cpp: Abort and error message when
	SetInAndOutFormats fails. Fixes bug #1813493
	
2007-10-14  Chris Morley

	* src/fingerprints/finger3.cpp, src/formats/fingerprintformat.cpp
	Change format for -xs format again: functional groups tab 
	separated. Suggested by Chris Swain.

2007-10-11  Chris Morley

	* src/format/mdlformat.cpp: Remove warning about incorrect title
	line which is sometimes output when it should not be, bug#1752435
	
	(ParseAliasText) ignore alias blocks with just "?" Suggestion by
	Rajarshi Guha
	
	* src/fingerprints/finger3.cpp, src/formats/fingerprintformat.cpp:
	Slight change in output formatting for -xs and -xu options
	
	* src/formats/xml/cmlformat.cpp: still trying to deallocate
	strings supplied by libxml2. Should be using free (not delete)
	but still not working with my compiler so still commented out.

2007-10-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

        * src/forcefield.cpp, src/forcefields/forcefieldghemical.cpp:
        Defensive programming patch contributed by Ross
        Braithwaite. Prevents divide by zero in determining torsional
        angles in planar rings.

        * include/openbabel/atom.h, src/forcefield.cpp: Add "fixed atoms."

2007-10-08  Chris Morley

	* src/formats/xml/cmlformat.cpp: removed delete statement which
	probably is responsible for bug #1792938. See 2007-08-19
	
2007-10-08  Chris Morley

	* src/formats/mdformat.cpp: output v2000 formal charge as M CHG
	statement rather than in the atom block, which is in correct when
	M RAD or M ISO apppear. Suggestion by p.mortenson bug #1796960

2007-10-05  Chris Morley

	* include/openbabel/forcefield.h: correct back to OBFPRT
	and add default definaition as nothing.

	* include/openbabel/groupcontrib.h: add back to OBDESC
	and add default definition as nothing.
	
	* src/forcefields/forcefieldmmff94.cpp: add initial value for 
	energy and comment out several unused variables to reduce compiler
	messages.
	
	* src/formats/getinchi.cpp: Now reads unquoted InChIs split with
	XML elements like <br />
	
	* src/formats/inchiformat.cpp: Make InChIKey output replace 
	normal InChI rather than adding to it. Still Windows only until
	1.02beta InChI source files added.
	
	* src/formats/smilesformat.cpp(ParseRingBond): ensured that atoms
	are added to OBChiralData::Atom4Refs in the order of the ring closure
	digits on the chiral atom rather than the atom index order. Partial
	fix for bug #1805910
	Added SetChiralityPerceived after reading. Avoids doing it again 
	in FindChiralCenters() which seems not to work sometimes, e.g. for
	CN1CCC[C@H]1c2cccnc2 and CP(O)(=O)C[C@H](O)CN

2007-10-03  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/groupcontrib.h: removed undefined OBDESC.
	* include/openbabel/op.h: removed OBOp:: from inside class
	definition.

2007-10-03  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/forcefield.h: fixed typos.

2007-09-26  Chris Morley

	* src/formats/inchiformat.cpp: forgot to change InChIKey option
	in code  to -xK.
	
	* include/zconf.h: replaced. Needed for Windows builds.

	Added Windows build files for obf (multiple DLL) build

	* windows-vc2005/babelconfig.h: replace USE_OBF by USING_DYNAMIC_LIBS

2007-09-25  Chris Morley

	Added files:
	include/openbabel/op.h: new OBOp class, plugin options
	src/ops.cpp: trivial OBOp class for centering
	src/op2d.cpp: class to add 2D coordinates using RDKit
	src/RDKitConv.cpp: conversion OBMol to RWMol
	
	* include/openbabel/descriptor.h: changeprefix macro from OBERROR
	to OBAPI.
	
	* src/descriptor.cpp(Display), src/groupcontrib.cpp(Display),
	src/smartsdescriptors:
	added form -L descriptors ID to give verbose description at runtime
	
	* include/openbabel dlhandler.h, forcefield.h, fingerprint .h,
	groupcontrib.h, xml.h, src/forcefields/*.h, src/formats/getinchi.cpp,
	canon.h: change prefix macros
	
	* include/openbabel/plugin.h(GetTypeMap): improve error return when
	there are no instances, but still a mess, but should not occur.
	
	* src/GUI/OBGUI.cpp(MakePluginsMenu): modified to use ListAs Vector
	rather than ListAs String.
	
	* src/obconversion.cpp: get rid of ill-considered USE_OBF 
	and continue with USING_DYNAMIC_LIBS.
	
	* src/transform.cpp(DoTransformations): add two hooks for OBOp
	classes
	
	* windows-vc2005/babelconfig.h: remove USE_OBF and add OBDESC
	
	* src/formats/inchiformat.cpp: change InChIKey option to -xK.
	(-xk was already used.)


2007-09-02  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/chemdrawcdx.cpp: fixed bond order for triple and
	aromatic bonds.

2007-09-20  Chris Morley

	* include/openbabel/generic.h: add new class OBRotationData
	
	* src/formats/gaussformat.cpp: (GaussianOutputFormat::ReadMolecule)
	read in vibrational and rotational data to OBGenericData classes
	
	* src/formats/xml/cmlformat.cpp:(WriteMolecule) if mol title is a
	filename, remove path and extension before outputing to id attribute
	Add WriteRotationData and WriteVibrationData (mainly for MESMER)
	
2007-09-15  Chris Morley

	* src/mol.cpp(GetTotalSpinMultiplicity): now returns correct value
	(1 for normal molecule). Improve documentation. Fixes bug
	#1793980.
	
	* include/openbabel/atom.h, mol.h: improve documentation to emphasize
	OBAtom::GetSpinMultiplicity returns 0 for normal atoms.
	
	* tools/nbabel.cpp: alternative commandline, with explicit -O option
	for output file, less flexible option placing.
	
2007-09-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/mol.cpp (Separate): More defensive programming to prevent
	crashing with incomplete OBChiralData.

	* src/formats/cansmilesformat.cpp: Add support for new OBPairData
	"canonical order" -- space terminated string of canonical atom
	labels.

	* tools/obfragment.cpp: New version which outputs XYZ files with
	atoms in canonical order matching the SMILES.

2007-09-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp: Small improvements to LineSearch and
	ConjugateGradientsTakeNSteps for performance improvement. In
	particular, reset the CG direction periodically and only print
	output every 10 steps.

	* src/forcefields/forcefieldghemical.cpp: Smarter VDW calculation
	-- minimize the number of multiplies. Not much of an improvement,
	unfortunately.

2007-09-04  Chris Morley

	* include/inchi_api.h, windows-vc2005/libinchi.dll,
	windows-vc2005/libinchi.lib: updated to v1.02 beta
	
	* src/formats/inchiformat.cpp: added option to output InChIKey.
	Windows only until the appropriate files for UNIX are installed.

2007-09-03  Chris Morley

	* include/zlib.h, iconv.h, zconf.h: Added.
	Needed for Windows build. I hope they do not interfere 
	with unix builds
	
	* src/formats/xml/cmlreactformat.cpp: Added
	
	* src/formats/pngformat.cpp: remove include to insizes.h
	
	Update Windows project files
	* windows-vc2005/OBComLn/OBComLn.vcproj
	* windows-vc2005/openbabel.sln
	* windows-vc2005/OpenBabelDLL/OpenBabelDLL.vcproj

2007-09-03  Chris Morley

	* src/formats/rxnformat.cpp: removed spurious first line of file
	which gave misleading comiler error messages. Make references to
	tr1 etc consistent with other reaction formats
	
	* include/openbabel/reaction.h: make #include "tr1/memory"
	conditional.
	
	* src/formats/pngformat.cpp: Make independent of compiler and
	platform, esp size of int. Add WriteMolecule to embed into a
	PNG file. Would be better in a program that also wrote PNG files!
	
2007-09-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Merged in changes from 2.1.x branch.

2007-09-02  Chris Morley
	
	* src/formats/chemkinformat.cpp: removed warning and improved
	when writing with the simple option.

	* src/formats/freefracformat.cpp:no longer use TrimErrors which
	caused errors on Windows.

	* src/math/spacegroup.cpp: replace stdargs.h by more modern 
	cstdarg

	* src/mol.cpp(Separate): use code which does not crash when
	Atom4Refs from OBChiralData unaccountably has fewer than 4 
	elements.

2007-09-02  Jean Brefort  <jean.brefort@normalesup.org>

	* src/fingerprints/finger3.cpp: fixed compilation with g++.

2007-09-02  Jean Brefort  <jean.brefort@normalesup.org>

	* configure.in: applied patch from Klaus Heinz fixes #1786288.

2007-08-30  Chris Morley

	* data/SMARTS_InteLigand.txt: Replaced with slightly modified
	version. I think the existing file was not based on a version
	which had been modified to work within OB's SMARTS implementation.
	
	* include/openbabel/fingerprint.h and src/fingerprint.cpp: 
	added GetBit() and virtual DescribeBits()
	
	* src/fingerprints/finger3.cpp: added PatternFP::DescribeBits
	Added various Trim()s to remove CRs, which is why FP3 had not
	been working, (as Noel noticed).

	* src/formats/fingerprintformat.cpp: added options to output
	description of functional groups in a molecule (esp when using FP4)
	
	* src/math/spacegroup.cpp: included <stdarg.h>

2007-08-27  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/generic.h: make OBUnitCell use SpaceGroup.
	* include/openbabel/math/Makefile.am: add space groups.
	* include/openbabel/math/spacegroup.h: new SpaceGroup class.
	* include/openbabel/math/transform3d.h: new transform3d class (for
	use in space groups).
	* include/openbabel/math/vector3.h: add a new constructor and fix
	a const issue. 
	* src/formats/cifformat.cpp: use space groups.
	* src/generic.cpp: make OBUnitCell use SpaceGroup.
	* src/math/Makefile.am: add space groups.
	* src/math/spacegroup.cpp: new SpaceGroup class.
	* src/math/transform3d.cpp: new transform3d class.
	* src/math/vector3.cpp: fix a const issue.

2007-08-20  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/Makefile.am: removed obsolete cmlreactlformat stuff.
	* src/obconversion.cpp: fix dynamic libraries use on unix.

2007-08-19  Chris Morley

	Add chemical kinetics formats. These used std::tr1::shared_ptr
	and if this is not provided as such, the USE_BOOST macro needs to be
	defined and the Boost library installed.
	
	* include/openbabel/reaction.h: modified
	* src/formats/chemkinformat.cpp: added
	* src/formats/rxnformat.cpp: modified
	* src/formats/xml/cmlreactlformat.cpp: deleted
	
	* src/formats/xml/cmlformat.cpp(WriteMolecule):Handle when 
	OBChiralData::Atom4Ref has <4 items.
	(ReadMolecule): in <property> be more flexible in where the
	title attribute can be.
	Failed attempt to delete C strings from libxml2 to solve memory
	leak bug. Still unresolved.

	* src/formats/thermoformat.cpp: add option to terminate on END,
	rather than end of file. 
	For Windows use 2 digit exponents in output.

2007-08-18  Chris Morley

	* src/formats/pngformat.cpp: add format for extracting  chemical
	structure data from PNG files.
	
2007-08-18  Chris Morley

	* src/format/copyformat: Copy whole input stream if a 
	length is not found.
	
	* src/formats/getinchi.cpp: test for negative chars to avoid
	isspace() failing.
	
	* include/openbabel/plugin.h: small documentation changes
	
	* src/GUI/optswx.cpp: remove some debugging code
	
	* src/obconversion.cpp: re-enable Compressed input for Windows. 
	Add macro to deactivate compressed output which still has 
	problems.
	Use USE_OBF rather than USING_DYNAMIC_LIBS which was ambiguous.
	Zero wInpos and wInlen in itialization list - needed for mod
	to copy format.
	ReportNumberConverted(): allow text from TargetClassDescription
	to have only a single line.
	
	* windows-vc2005/babelconfig.h: enable compression but
	deactivate compression on write. 
	Rationalize the macros 	controlling the build in Visual Studio.
	Now define SINGLE_DLL for current OpenBabelDLL build.
	For future multiDLL builds USE_OBF with macros, like OBCONV 
	appropriate for the DLL being built.

2007-08-18  Jean Brefort  <jean.brefort@normalesup.org>

	* data/Makefile.am: add space groups descriptions.
	* data/space-groups.txt: ditto.
	* data/space-groups.xsl: ditto.

2007-08-13  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/obconversion.h:b removed extra
	OBConversion:: which made compilation fail.

2007-08-10  Chris Morley

	* src/obconversion.h,.cpp: Added ALL to Option_Type enum.
	Added CopyOptions() and IsLastFile() and 
	ReportNumberConverted() functions.
	
	* src/GUI/OBGUI.cpp, tools/babel: use ReportNumberConverted
	instead of explicit code.

	* include/openbabel/obmolecformat.h: Added RegisterOptionParam
	for "append".
	
	* src/formats/obmolecformat.cpp(ReadChemObjectImpl): clear
	stream flags to prevent stalling when eof set in previous file.
	Remove some debugging code.

	* src/GUI/optswx.cpp: untabify

2007-08-04  Chris Morley

	* src/formats/mdlformat.cpp: Add ReadCollectionBlock(),
	which currently just issues a warning that COLLECTION blocks
	are not implemented. The rest of the molecule in the example
	in bug #1753217 is now read ok.
	
2007-08-04  Chris Morley

	* include/OB_BGL/ :Added interface with Boost Graph Library
	written by Gerde Menche.
	
	* include/openbabel/mol.h: modified EndAtoms() and EndBonds()
	to return after the atomas and bonds in _vatom and _vbond
	rather than the overallocated end of the vectors. Needed for
	the above.

2007-08-03  Jean Brefort  <jean.brefort@normalesup.org>

	* include/openbabel/format.h: Format::FormatsMIMEMap() must
	return a reference, otherwise, a new copy is used each time
	and no mime type is usable.

2007-07-25  Chris Morley

	* src/formats/mdlformat.cpp(MDLFormat::ReadMolecule):
	Added more tests to prevent ill-formed lines in M RAD, CHG and ISO
	lines from causing a crash. Added informative error message.
	Deficiency pointed out by Andrew Dalke.
	
	*src/descriptor.cpp, src/include/openbabel/descriptor.h:
	Add wildcard * facility and simplify - remove GenericDataCompare.
	
2007-07-06  Chris Morley

	* src/descriptor.cpp, src/include/openbabel/descriptor.h:
	Add MatchPairData() so that Property names with spaces can be
	searched for by replacing them with underscores in the filter,
	append or delete strings, as suggested by Noel.
	(GenericDataCompare): fix test for two numbers
	Added GetValues() to implement --append
	
	*src/transform.cpp: Extra option: --append (to mol title).
	Does what Joey Bedell wanted.

2007-07-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/Makefile.am, src/Makefile.in: Bump library version for 2.1.1
	release.

2007-07-05  Chris Morley

	* src/formats/inchiformat(WriteMolecule): downgraded the InChI
	message "Tetrahedral stereo info not available" to obInfo, 
	since it arises from the workings of the the opaque OB chirality
	system. Also added the molecule number for identification.
	
	* src/GUI/OBGUI.cpp, tool/babel.cpp: added &std::cout to the
	call to OBConversion::Write() for the APIInterface, because the
	previous NULL value was causing it to be ignored. This meant
	that ---errorlevel wasn't working,  as again found by Noel.
	
2007-07-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/mdlformat.cpp (MDLFormat::ReadMolecule): Add
	additional error and warning messages, including a check if the
	atom/bond block doesn't work. Fixes crash reported by Joe Bedell,
	Sigma-Aldrich.

	* Makefile.am, Makefile.in: Skip INSTALL.Windows, deleted by
	Chris.

2007-07-04  Chris Morley

	* src/finger3.cpp: Trim firts line which decided format of
	patterns.txt. In Windows there was trailing \r which caused
	none of the patterns to be read, as found by Noel.
	
2007-07-04  Chris Morley

	* src/formats/smilesformat.cpp(CreateSmiString): call
	FindClosureBonds even when all atoms are chiral.
	(GetSmilesElement): only call GetChiralStereo when
	atom has is specified clockwise or anticlockwise, not just chiral.
	
2007-07-02  Noel O'Boyle <baoilleach@gmail.com>

	* include/oberrors.h: Fixed typo in Doxygen

2007-07-01  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure.in, configure, */Makefile.in: Updated with patch from
	Jean Brefort. Adds new --with-pkglibdir flag to facilitate
	packaging with versioned format directories.

2007-07-01  Chris Morley

	* src/obconversion.cpp(InstallStreamFilter): test for non-zero
	pInFormat to avoid crash with no input.
	
	* src/formats/gamessformat.cpp: Test for "$END" now works on $END$.
	Put size test first. Fixes bug #1738005 and probably #1745066.
	
	* INSTALL.Windows: deleted obsolete file
	
2007-06-30  Chris Morley

	* src/formats/smiles format.cpp(GetSmilesElement):do not always
	output atoms in 2D molecules in bracket form if the chirality
	is not specified (fix for bug #1738355)
	
	* src/GUI/OBGUI.cpp: small change to About text

2007-06-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/pdbformat.cpp: Fix for PR#1705895 -- check for
	string length before trying to read the 3rd character. Causes
	crash on Windows.

	* scripts/Makefile.*: Fix for change in Ruby build script.

	* src/formats/gaussformat.cpp (and others): Fix for
	PR#1737209. Return false for reading a molecule with no atoms. In
	these formats, empty molecules are invalid.

2007-06-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* tools/obenergy.cpp, tools/obminimize.cpp: Minor feature request
	1722878 to add hydrogens before running force field
	calculations for Chris Swain.

2007-06-24  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* NEWS: Update for upcoming 2.1.1 release.

	* src/formats/pdbformat.cpp (ReadMolecule): Add a new OBPairData
	for any record we don't currently parse. This way all data is
	preserved.

	* src/formats/mol2format.cpp: Fix PR#1739905. Add warning if
	elements cannot be interpreted as atom types correctly (e.g., this
	GaussView file). Instead, attempt to interpret as element names.

	* data/types.txt: Fix two HO typing errors, which masked this
	bug.

	* scripts/openbabel-ruby.i: Fix module declaration -- really
	OpenBabel.

	* tools/obminimize.cpp: Minor fix requested by Chris Swain --
	allow setting output format using -o flag.

	* tools/obfit.cpp: Add RMS output to standard error.

2007-06-23  Noel O'Boyle <baoilleach@gmail.com>
	
	* scripts/*.i (except Perl, which was already done): Added
	groupcontrib.h and updated wrapper code
	* scripts/python/Pybel stuff:
	Added calcdesc() method to Molecules for descriptor calculation 
	Added update() method to MoleculeData
	Convert to string before setting a value in MoleculeData
	Updated tests, and API docs

2007-06-15  Chris Morley
	
	* src/smartsdescriptors.cpp: Added SmartsDescriptor class to 
	allow filters based on SMARTStest (like Number of Hydrogen
	Bond Acceptors) to be defined in a single line.
	A few (SMARTS from JoelLib) are defined: HBA1 HBA2 HBD nF
	
	* src/filters.cpp: in SMARTS filter only look for single match.
	
	* src/formats/inchiformat.cpp: small change in Description()
	
2007-06-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure.in, configure, Makefile.*: Updates from the Cygwin
	ports project for better compatibility (e.g., shared format
	modules on Cygwin). Thanks to Yaakov of Cygwin ports and Noel.

2007-06-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/chemdrawcdx.cpp: Fix a Universal binary problem on
	Mac OS X. We cannot rely on an autoconf test since the compiler is
	run twice: for ppc and i386. Thanks to Mike Stump from Apple for
	help.

	* scripts/java/: Updated classes for vectors of rings and vectors
	of strings.

	* Makefile.am, Makefile.in: Update for Chris's removal of the
	windows directory below.

2007-06-05  Chris Morley

	* src/formats/smilesformat.cpp(PaseSmiles):ignore any char<0
	Caused crash in isspace() in Visual C++8. Fixes bug
	#1730132 for this compiler at least.

	* windows/: Delete. This should have gone before because we are
	no longer supporting VC++6.
	
	* src/GUI/OBGUI.cpp(OnGetInputFile): Delete  | wxHIDE_READONLY 
	so that compiles with v2.8.3 of wxWidgets.

2007-06-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/cansmilesformat.cpp (AddHydrogenToChiralCenters):
	Fix PR#1700301. Never attempt to create atoms while iterating
	through the molecule. Safer technique -- keep a list of atoms to
	add hydrogens, add in a separate step.
	(AtomIsChiral): Fix PR#1699418. When determining chiral
	information for canonical SMILES, make sure to check if the atom
	is 3D. Otherwise it will never have wedge/hash bond flags.

	* src/mol.cpp (DeleteHydrogens): Update to fix PR#1704551 with H-H
	bonds not deleted. 

	* src/formats/smilesformat.cpp: Add warning message for unmatched
	ring closures described below.

	* configure, configure.in: Bump to 2.1.1 version.

2007-06-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/smilesformat.cpp: Fix bug reported by Craig with
	un-matched ring closures. These should now always be rejected,
	since _rclose will not be empty.

	* test/files/invalid-smiles.txt: Add ring closure tests from
	Craig.

	* test/mol.cpp: Add test for H-H deletion bug reported by Donald,
	PR#1704551.
	
2007-06-01  Noel O'Boyle <baoilleach@gmail.com>

	Final changes for Windows release of OBPython 1.2

	* windows-vc2005/OBPython/setup.py: bumped version up to 1.2
	* scripts/python/pybelapi.py: updated API docs

2007-05-30  Chris Morley

	* include/openbabel/base.h(tokenize): Add \r to default
	delimiters in the two functions. Now Windows or old Mac files
	(esp data files) should be read properly. 
	Cures bug #1727333, I hope.
	
2007-05-30  Chris Morley

	* src/fingerprint.cpp(Tanimoto): return 0.0 if no bits set.
	Should cure bug #1728410.
	
2007-05-30  Chris Morley

	* include/openbabel/lineend.h: remove sync()call from destructor
	so that can delete in OBConversion's destructor after
	istreams have gone.
	
	* include/openbabel/obconversion.h, *src/obconversion.cpp
	Add InstallStreamFilter() and call from Read() and Convert().
	I hope this will cure the Windows Python bug, and is a neater
	method all round.
	 
2007-05-25  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/cdxmlformat.cpp: don't clear the molecule
	before writing. [#1725343]

2007-05-22  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* */Makefile.in: Regenerate UNIX build files.

	* src/plugin.cpp: Make sure to #include <iterator> to solve GCC
	compile problem. 

	* src/descriptor.cpp: Change _isnan to IsNan, as discussed on the
	list to solve GCC compile problem.

	* scripts/*: Updated to compile. May have removed functionality
	because of plugin changes.

	* tools/obminimize.cpp, tools/obgen.cpp, tools/obenergy.cpp:
	Switch to OBPlugin::List().

2007-05-17  Chris Morley

	* tools/obprop.cpp: mods to use new versions of logP etc.
	
	* include/openbabel/groupcontrib.h, src/goupcontrib.cpp:
	move declarations of OBGroupContib into header file and delete
	OBLogP etc which should not have been there but still compiled.
	
	* src/plugin.cpp(ListAsVector): Add support for only IDs.
	
	* include/openbabel/fingerprint.h:comment had become
	uncommented.
	
2007-05-16  Noel O'Boyle <baoilleach@gmail.com>

	* Added Chris's header changes to Makefile.am
	* Removed comments starting with //* as they confused SWIG as there
	was no matching */
	* python SWIG interface file: Included the new headers
	Note: the python bindings still don't compile.

2007-05-14  Chris Morley

	* src/obconversion.cpp(Read, Convert): Do not install a 
	FilteringInputStreambuf if stream already contains one. This
	solves my problem with multiple reads on the same input stream.
	 
2007-05-13  Chris Morley

	* src/obconversion.cpp(Read): Ensured that FilteringInputStreambuf
	is used. Previously it wasn't, which could cause errors
	except with unix reading unix files.
	 
2007-05-12  Noel O'Boyle <baoilleach@gmail.com>

	* SWIG interface files: Added template for vectors of strings
	* pybel.py: Added informats and outformats, dictionaries corresponding
	to the supported input and output formats

2007-05-11  Jean Brefort  <jean.brefort@normalesup.org>
	* include/openbabel/format.h: add missing new line (makes gcc happy).
	* include/openbabel/plugin.h: remove ClassName:: from method declaration.
	* src/formats/xml/cmlformat.cpp: ditto.

2007-05-10  Chris Morley

	* src/forcefields/forcefieldmmff94.cpp, .h: Mod for new plugin
	framework.
	Add return values to several functions, so that it would compile.

2007-05-10  Chris Morley

	Revision of plugin classes including OBFormat
	OBFormat, OBForcefield, OBFingerprint and the new
	OBDescriptor all derive from OBPlugin (not OBPluginiter)
	New files:
	include/openbabel/descriptor.h, include/openbabel/format.h
	include/openbabel/plugin.h, src/descriptor.cpp
	src/filters.cpp, src/format.cpp, src/plugin.cpp
	Removed file:
	include/openbabel/pluginiter.h
	Relocation of these and other files probably a good idea
	(incl new folder src/descriptors) but not done yet.
	class OBFormat moved out of obconversion.h, .cpp into
	its own files.

	* tools/babel.cpp: remove -F and add -L option

	* src/transform.cpp: reorganize to include new options
	--filter, --add, --delete

	* src/groupcontrib.cpp: remove OBLogP and similar classes;
	now descriptors which are instances of OBGroupContrib

	* src/formats/* : several forcefield and fingerprint files
	changed to fit new framework, obmolecformat.h to register
	new options.

	* src/formats/xml/cmlformat.cpp: if inchi is a property 
	write to <identifier> not <property> tag.

	* src/GUI/OBGUI.h, .cpp:display plugins in a menu item.

	* windows-vc2005: update Window build

2007-05-10  Noel O'Boyle <baoilleach@gmail.com>

	* pybel.py: Added support for unitcell, and deletion of OBPairData
	(need to update the tests and the API docs)

2007-05-08  Chris Morley

	* include/openbabel.h/base.h, src/base.cpp: corrected
	bug in DeleteData(OBGenericData*) which is the probable
	cause of bug #1715092. Added new function DeleteData(string)
	which makes it easier to use.
	Moved the declarations for Tokenize and Trim from mol.h to
	base.h so that they could be used more widely. Maybe there is
	an even better home.

2007-05-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/*.i: Added casting from OBGenericData to OBUnitCell.

2007-05-08  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/*.i: added a template for a vector of OBRing*
	which is required for OBMol.GetSSSR()

2007-05-08  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/*.i: added a method to cast OBGenericData to
	OBPairData.
	
	* scripts/python/pybel.*: added dictionary-like support for
	accessing molecule data, and updated the tests and the API
	documentation.

2007-04-30  Chris Morley 

	* NSIS installer script: Add some extra data files, replaced
	*.* which was causing extra files to be copied, and deleted
	HKCU/SoftwareOpenBabelGUI/ on uninstall.
	As used in OpenBabel2.1.0_Windows_Installer.exe	

2007-04-26  Noel O'Boyle <baoilleach@gmail.com>

	* NSIS installer script: Updated to install the MS VC++
	run-time installer

2007-04-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Merged 2.1.0 branch into trunk.

	* configure.in, configure: Bump to 2.2.0b1 version for trunk.
	(Not sure if we'll do 2.2 or 3.0, but we'll see.)

	* src/formats/inchi/strutil.c: Bug reported on the InChI mailing
	list.

	* src/formats/inchiformat.cpp: Bug caught during ChemSpotlight
	testing -- some files don't have chirality information (e.g., 3D
	files but with 0.0 coordinates throughout). Warn and give up.

2007-04-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* NEWS: Minor fixes for 2.1.0 final release.

2007-04-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* data/psa.txt: corrected smiles for 3-rings.

	* src/groupcontrib.cpp: call ConvertDativeBonds before assigning
	contributions, is needed for TPSA (e.g. [N](-*)(=*)=* ). Update to
	documentation.

	* include/openbabel/groupcontrib.h: documentation update.

2007-04-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/residue.h: Undo previous change. Rich Apodaca
	suggested some SWIG-fu instead.

	* scripts/ Update accordingly. Includes ruby changes, new README
	and examples.

2007-03-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/base.cpp: Additional "What's new" documentation for 2.1
	release.

	* include/openbabel/residue.h: Hide some residue names (e.g.,
	_1MG) from SWIG wrappers -- such constants are not valid symbols
	in some languages like Ruby.

	* scripts/ Update accordingly.

2007-03-29  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/: Updated interface wrappers, including new Java
	README. (Java is confirmed to work on Mac OS X.)

2007-03-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp: Make sure to always return from any
	exception. Otherwise we could crash running code.

	* src/formats/mdlformat.cpp: Avoid infinite loop in
	ParseAliasText.

	* src/formats/acrformat.cpp: Minor formatting change.

	* test/Makefile.am, test/Makefile.in, test/wrapper.sh: Add
	inchiwrite tests to suite.

	* test/inchiwrite.cpp, test/inchi.pl: Formatting to integrate into
	Perl "prove" test suite.

2007-03-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* tools/obprop.cpp (main): Fix PR#1688251 with while/for loop on
	CML files. Thanks to Tapani Kinnunen for the report.

	* src/formats/mol2format.cpp: Fix problem reported by Noel with
	"USER_CHARGES" appearing instead of Gasteiger.

	* src/data.cpp, src/groupcontrib.cpp: Fix doxygen warnings.

	* include/openbabel/groupcontrib.h: Documentation fixes.

	* NEWS: Minor fixes.

	* doc/*.1, doc/*.html: Documentation updates.

2007-03-24  Benoit Jacob <jacob@math.jussieu.fr>

	* include/openbabel/atom.h, src/atom.cpp: Change SetVector to
	const parameter.

2007-03-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* tools/obprop.cpp: Function string sequence(OBMol) was not returning
	any string.

2007-03-23  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/psa.txt, data/mr.txt, data/logp.txt: Small changes -- DOS
	to UNIX line endings. 

	* test/Makefile.am, test/Makefile.in: Make sure to add inchiwrite
	to compile list.

	* test/wrapper.sh: Add notes on passing arguments to "prove."

	* tools/obprop.cpp: Fix formatting problems - PR#1685879, reported
	by Tapani Kinnunen.

	* src/formats/mol2format.cpp: Add new -xl flag to output "ligand
	only" data (i.e., no residue info). Fixes PR#1683788.

	* src/formats/smilesformat.cpp: Fix PR#1680070 with output of
	chiral root (first) atoms. Really need to clean up BuildTree()
	since that if() statement is messy, but works for 2.1 release.

2007-03-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* data/psa.txt: Added ";heavy", fixes the logp_psa test.

2007-03-22  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp: When determining length, if two atoms are
	really close, add a small random separation (~0.1Ang). Fixed
	PR#1684479.

2007-03-22 Chris Morley

	* windows-vc2005: Simplified projects to OpenBabelDLL with driver
	programs for commandline, GUI, and Python interface.

	* include/openbabel/forcefield.h: So that the Python build
	in Windows will work, added a dummy function so that the 
	compiler will really make some functions of the templated class
	OBIter<OBForceField> which SWIG is expecting. The needs to be
	done properly, but needed to get it working for the 2.1 release. 
	
	* include/openbabel/obconversion.h and src/obconversion.cpp:
	added the patches supplied by Jerome Pansanel for providing a
	list of available formats.
	
2007-03-20 Chris Morley

	* src/formats/xml/cmlformat.cpp: Add code to write W and H in
	bondstereo. Ensure <bondStereo> is written in array form.
	
	Mods inDoAtoms to read the right set of atom coordinates.
	
	Add option to write bonds as aromatic.
	
2007-03-19  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp: Amend yesterday's change to address double
	free() bug, PR#1683541. Still don't like this, as it could leak
	the zip_istream we create.

	* src/parsmart.cpp: Fix PR#1683890 for SMARTS pattern 'x' with no
	number. Default is "at least one ring bond."

	* test/files/smartstest.txt, test/files/smartsresults.txt: Update
	for above. 'x' pattern and 'x0' pattern.

2007-03-19  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/mol.cpp: OBMol::DeleteAtom - Moved DeleteAtom to *after* the
	EndModify call.  At this point the atom is already removed from the _vatom
	vector.  OBMol::DeleteBond - Moved DeleteBond to *after* the EndModify
	call.  At this point the bond is already removed from the _vbond vector.

2007-03-18 Chris Morley

	* src/formats/mdlformat.cpp: Added support for atom aliases when
	reading. It's not much described in the main MDL specification,
	so this implementation is just adequate to handle the InChI
	samples, where for some reason, this antiquated feature is
	used in several molecules.
	
	* src/formats/inchiformat.cpp(ReadMolecule): Now reads implicit
	H isotopes.
	(WriteMolecule): rewrote option to not display routine warnings.
	
	* test/: Added inchiwrite.cpp, two NIST sample molecule sets and
	annotated results sets.
	
	* src/formats/getinchi.cpp: Added declaration of GetInChI().
	
	* src/canon.cpp (FixCisTransBonds): changed | to || in if statement
	
	* src/forcefield (GenerateCoordinates): initialize torang to 0,
	to avoid compiler warning. This variable doesn't seem to be
	doing much but please could somebody check this is ok.
	
2007-03-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/mol.cpp (Separate): Add support for copying, updating
	OBChiralData. Fixes PR#1680730.

	* src/obutil.cpp: Fix typo in yesterday's change.

	* test/logp_psa.cpp: Update to output predicted values, even if
	they match.

	* src/obconversion.cpp: Make sure to declare the new readbuf
	outside of the if() scope.

2007-03-17  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/molchrg.cpp: Add new OBPairData descriptor "PartialCharges"
	to express origin as Gasteiger charges.

	* src/formats/qchemformat.cpp, src/formats/mopacformat.cpp, 
	src/formats/gamessformat.cpp, src/formats/gaussformat.cpp: 
	Set PartialCharges descriptor to express origin as Mulliken
	charges.

	* src/formats/mol2format.cpp: Use above.

	* src/*: Strip out 0.0f and similar floating-point casts,
	extending yesterday's changes with forcefield.cpp. Defensive
	programming against similar floating-point issues.

2007-03-16  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/atom.h, include/openbabel/mol.h: Fix
	PR#1626789 with large PDB files. Fixes regression to 2006-09-25
	changes supporting >2^16 atoms or bonds.
	
	* src/mol.cpp(EndModify): Ensure idx is unsigned (to match atom indexes).

	* include/openbabel/chains.h, src/chains.cpp: Make sure atomids is
	int, not short. Atom IDs can go up to a full unsigned int.

	* src/formats/chemdrawcdx.cpp: Some code cleanups, including use
	of obErrorLog.

	* src/forcefield.cpp: Fix PR#1680717. Seems to be an issue with
	floating-point roundoff. When 0.0f and similar tags were removed,
	works great.

2007-03-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/groupcontrib.cpp, include/openbabel/groupcontrib.h: General
	class to handle group contribution algorithms (LogP, TPSA, MR, ...).
	Also contins OBLogP, OBPSA and OBMR. Should these simple classes be
	bundled in a OBDescriptors class?

	* src/logp.cpp, src/psa.cpp, include/openbabel/logp.h,
	include/openbabel/psa.h: moved to groupcontrib.cpp/h

	* data/mr.txt: data for molecular refractivity.

	* test/logp_psa.cpp: forgot to commit.

2007-03-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/inchiformat.cpp, src/formats/cmlformat.cpp: Fix compile
	problems with GCC and last changes. (Return value from
	OBChiralData should be assigned to a full object.)

	* src/obconversion.cpp, src/obconversion.h: Tackle some gzip
	problems, including PR  #1617838. We need to be sure we don't try
	to gzip twice. Create a zip_istream pointer, then free it as
	needed.

	* scripts/*: Updated for recent library changes.

2007-03-13 Chris Morley
	
	* src/formats/inchiformat.cpp: Add bond stereo handling to
	ReadMolecule(). Correct 0D stereo in reading and writing.
	Remove the waring message about stereochemistry. Apart from
	a few special cases, e.g. allenes, 'either' parity, I think
	the InChI writing and reading is now ok., but still more 
	testing needed...
	TestFormat messages improved.
	
	* src/formats/xml/cmlformat.cpp: Correct handling of 0D
	atomParity on reading and writing.
	
	* src/GUI/optswx.cpp: Added documentation

2007-03-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields/forcefieldghemical.cpp: Fix 1,4-scaling problem.

2007-03-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefieldmmff94.cpp: Switch pow() to use
	doubles to prevent compile problems on older Linux/GCC systems.
	Switch to using OpenDatafile.

	* src/logp.cpp, src/psa.cpp: Switch to use OpenDatafile() call.

	* src/fingerprints/finger3.cpp: Likewise.

	* src/forcefields/forcefieldmm2.cpp,
	src/forcefields/forcefieldghemical.cpp: Likewise.

	* src/formats/xml/Makefile.am, src/formats/xml/Makefile.in: Fix
	problems with compiling XML formats on Mac OS X.

	* include/openbabel/Makefile.am: Make sure to include psa.h and
	logp.h in distribution.

	* src/data.cpp: Move comments to provide better documentation for
	OpenDatafile. Switch OBGlobalDatabase::Init to OpenDatafile.

	* include/openbabel/data.h: Add envvar argument to OpenDatafile.

	* config.sub, config.guess, configure, Makefile.*: Update with
	automake-1.10 and autoconf-2.61.

2007-03-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* tool/obminimize.cpp: added '-sd', '-cg', '-c criteria' options

	* doc/obminimize.1: update for added options (man pages for obenergy
	and obminimize are also on wiki now) 

2007-03-12  Geoffrey Hutchison  <babel@geoffhutchison.net>	

	* src/formats/mopacformat.cpp: Added patch #1676963
	for MOPAC 2007 output format. Thanks to 'dn2010.'
	(Daniil Bratashov). Solves PR#1654907.

	* src/formats/qchemformat.cpp: Added support for keywords.

	* src/formats/acrformat.cpp: New format, contributed by Daniel
	Mansfield.

	* src/formats/Makefile.am, src/formats/Makefile.in: Add acrformat.

	* src/formats/gaussformat.cpp: Add feature to write bonds,
	contributed by Daniel Mansfield.

	* src/formats/fchkformat.cpp: Add initial support from Maxim
	Fedorovsky. (Maxim's contribution also supported vibrational data
	using Eigen and matrix operations.)

	* include/openbabel/generic.h, src/generic.cpp: Include
	OBVibrationData class (even if the matrix operations to use it
	aren't in Open Babel yet).

	* tools/obprop.cpp: Additional properties, including canonical
	SMILES and InChI. Fixes request PR#1620842.

	* THANKS: Work on updates for 2.1 release.

	* NEWS: Likewise.

2007-03-11 Chris Morley
	
	* src/data/atomtyp.h: Aggressive simplification of 
	IMPVAL for oxygen and new value for Si. Read and test with
	/test/files/FormulaTest.smi. Solves bugs 1635901 and
	1474930
	
	* include/openbabel/forcefield.h: Remove unused 
	#ifndef isnan

2007-03-11 Chris Morley

	* src/formats/inchiformat.cpp: Moved handling of InChI
	options to new subroutine and it added options to 
	ReadMolecule().
	In WriteMolecule() removed deletion of OBChiralData and
	re-zeroed z coords, so that OBMol is unchanged.
	
	* src/GUI/OBGUI.cpp, OBGUI.h: Made default ostream a 
	stringstream which is written to textbox at end. Solves
	bugs 1596906 and (probably) 1669973.
	Added facility for copying output to input.
	
	* src/GUI/optswx.cpp,stdwx.cpp:Leave header files in src/GUI

2007-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>
	
	* include/openbabel/psa.h, src/psa.cpp, src/Makefile.am,
	src/Makefile.in, data/psa.txt: Added OBPSA class.

	* tools/obprop.cpp: Added PSA property.

	* test/logp_psa.cpp: LogP and PSA test for 3 molecules.

2007-03-10 Chris Morley

	* src/formats/inchiformat.cpp(WriteMolecule): For 2D molecules
	use a modified CalculateChiralVolume() to add psueudo z
	coordinates, rather than using InChI's 2D bond stereo method.
	I think we are close to getting the InChI write stereochemistry
	right at last, but systematic checking needed.
	
	* include/openbabel/chiral.h, src/chiral.cpp
	(CalculateChiralVolume): add backwards-compatible extra 
	parameter to facilitate use of pseudo z coordinates.
	
	* src/formats/cansmilesformat.cpp(BuildCanonTree): two more
	instances of the bug corrected yesterday.

2007-03-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure, configure.in: Bump for 2.1.0b7 snapshot.

	* Doxyfile: Bump version for eventual 2.1.0 release.

	* src/*, src/formats/*: Add OBGenericData::SetOrigin calls to
	provide attribution to sources of data: file input, user input,
	perceived, etc.

	* tools/obfit.cpp: Likewise.

2007-03-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/logp.h, src/logp.cpp, src/Makefile.am,
	src/Makefile.in, data/LogP.txt:
	Added OBLogP class (see mailing list).

	* tools/obprop.cpp: Added LogP property.

2007-03-09 Chris Morley

	* src/formats/cansmilesformat.cpp(BuildCanonTree):The insert in 
	line 893 invalidates iterator ai. Add a line so that the subsequent
	test (outside the loop) does not crash my debug build but always
	is false - no push_back. Solves bug 1650790. I hope that Craig or
	somebody can check whether the cannonical SMILES output is still ok.

2007-03-09  Donald E. Curtis <dcurtis3@sourceforge.net>

	* include/obiter.h: added deconstructor functions.  Lack of these can
	cause problems when using the FOR_*_OF_* macros.

2007-03-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* forcefield.h/cpp: documentation update.

2007-03-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/smilesformat.cpp: Fix problem with "invented" stereo
	from 2D files -- make sure to check bond torsion ~0.0 and
	~180.0. Fixes PR#1663814.

	* doc/*.1: Initial cleanups of man pages, including new pages for
	obenergy, obminimize, and obrotamer.

	* Doxyfile-man: Update to point to new babel location.

	* src/chains.cpp: Fixing bug with chain perception related to
	PR#1626789, and 1577248. Setting visit flags skipped
	marking some atoms as members of residues.

	* test/residue.cpp: Add new tests for PR#1577248.

	* data/types.txt, data/types.h: Add Lp atom type for Sybyl based
	on PR#1672575.
	
2007-03-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/obutil.cpp: moved IsNan() to here. Hopefully this will eliminate
	the problem with non C99 compatible compilers.

	* src/forcefield.cpp: update documentation + small optimization
	changes.

	* include/openbabel/forcefield.h: update documentation (in progress).

	* tools/obenergy.cpp: Added man page.
	
	* tools/obminimize.cpp: Added man page.

2007-03-07 Chris Morley

	* src/for,ats/smilesformat.cpp(FixCisTransBonds): replace
	bitwise | by logical ||. 
	I guess if (v1 < 2 || v1 > 3 || v2 < 2 || v2 > 3) was meant.
	
	* include/openbabel/base.h(GetData(DataOrigin), base.cpp: 
	This was returning a reference to a local object. 
	Return a copy of it instead.
	
	* src/formats/inchiformat.cpp: Reformat Description().
	In WriteMolecule, modify bond stereo to work with new Up/Down
	usage.
	
	* src/formats/xml/cmlformat.cpp: For reading and writing,
	modify bond stereo to work with new Up/Down usage.
	Now writes bondStereo elements in array form.
	
2007-03-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* tools/obdoc.cpp: Update for wiki format to facilitate updates
	after 2.1 release. 

	* src/formats/pdbformat.cpp: Mark that chain/residue
	perception is not needed. Make sure that code anticipates atoms
	with no residue.

	* src/data.cpp (OBResidueData): Anticipate that some atoms will
	have no residue.

	* src/formats/mopacformat.cpp: Add keyword support, fix problem
	with writing molecules (i.e., molecule was cleared before
	cartesians written).
	
	* src/formats/smilesformat.cpp, src/formats/mol2format.cpp, 
	src/formats/xml/cmlformat.cpp, src/formats/carformat.cpp,
	src/formats/cifformat.cpp, src/formats/fastaformat.cpp,
	src/formats/gaussformat.cpp, src/formats/gamessformat.cpp,
	src/formats/alchemyformat.cpp, src/formats/cansmilesformat.cpp:
	Clean up descriptions and indentation.

2007-02-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefield.cpp, src/forcefield.h: Cut out some compiler
	warnings from	GCC. Remove is14(), already available through
	OBAtom::IsOneFour.

	* src/forcefields/forcefieldghemical.cpp: Make sure to return from
	all functions.

	* src/dlhandler_unix.cpp: Use global loading. May improve script
	language interface on Linux.

	* include/openbabel/base.h, src/base.cpp: Support for filtering
	OBGenericData based on the source.

	* include/openbabel/generic.h, src/generic.cpp: Likewise.

	* test/files/smartsresults.txt: Fix results based on Craig's
	SMARTS changes today.

2007-02-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Replaced isnan() by OBIsNan(). 

2007-02-28  Craig James <cjames@emolecules.com>

	* src/formats/smilesformat.cpp: Fixed PR#1663854 "Canonical SMILES
	gives incorrect cis/trans" in cansmilesformat.cpp, also fixed the
	same problem in smilesformat.cpp.

	* Disabled SMARTS parsing of cis/trans '/' and '\', these are
	temporarily treated as ordinary single bonds, due to severe bug
	in SMARTS matching.  See PR#1663730, this is a temporary workaround.

2007-02-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/mol2format.cpp: Fix PR#1666406 with mis-typed Sybyl
	atom types.

	* data/types.txt, data/types.h: Likewise.

2007-02-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/inchiformat.cpp: Fix compile problems on GCC.

	* src/mol.cpp: Fix PR#(PR#1665519) with AddHydrogens when no
	conformers are available.

	* Doxyfile: Remove babelconfig and config from header list.

	* src/patty.cpp: Mark as deprecated.

	* src/fingerprint.cpp, src/mol.cpp, src/typer.cpp
	src/parsmart.cpp, : Documentation updates.

	* include/obmolecformat.cpp, src/formats/obmolecformat.cpp,
	include/openbabel/xml.h, include/openbabel/typer.h,
	include/openbabel/parsmart.h, include/openbabel/rand.h, 
	include/openbabel/mol.h: Likewise.

2007-02-26 Chris Morley

	* src/formats/inchiformat.cpp(WriteMolecule): Mods to 0D and 2D
	stereochemistry; more to be done, work in progress.
	Added Option to use InChI options.
	
	* src/formats/mdlformat.cpp(ReadMolecule):Use the content of
	any "NAME"(case independent) property as OBMol title if there
	is not already one.
	
	* src/format/xml/cmlformat.cpp, xml.cpp(GetContent): Add Trim()
	after several cases of xmlTextReaderConstValue to remove any \n
	
	* src/obconversion.cpp(Convert): Add test for pInFormat to avoid
	crash with erroneous input.
	
	* src/mol.cpp(Separate): Copy dimension to each fragment.

2007-02-26  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/mol.cpp: OBMol::AddBond() / OBMol::DeleteBond() 
	Bond indexing starts at one.  Had to undo the change made by Tim and
	correct the fix on 2007-01-07 as a result of the bulk resizing.

2007-02-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/ring.cpp (FindRings): Don't return early if all atoms are
	visited. Some atoms may be in multiple rings and will be visited
	more than once on a graph traversal.

2007-02-25  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/mol.cpp: OBMol::DeleteBond()
	_vbond.erase(_vbond.begin() + bond->GetIdx());
	Since _vbond indices start at 0 and bond->Getdidx() indices start at
	1, the line is replaced by:
	_vbond.erase(_vbond.begin() + bond->GetIdx() - 1);

2007-02-25  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h: comment out Description() (comply
	with new pluginiter).

	* obmm, obenergy, obminimize, obgen: comment out the use of
	Description().

2007-02-25 Chris Morley

	* windows-vc2005/OpenBabelDLL: Updated OpenBabelDLL.vcproj.
	Temporarily added OpenBabelDLL.dll and OpenBabelDLL.lib
	(without forcefield)
	
	* include/openbabel/kinetics.h, lineend.h, pluginiter.h:
	documentation changes.
	
2007-02-25  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/ring.cpp: Added a check in FindRings to make sure the depth is
	not larger than the number of atoms we have. (see mailing list)

2007-02-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Added ConjugateGradientsInitialize() and
	ConjugateGradientsTakeNSteps(). ConjugateGradients() still exists and
	uses these two new function.
	Idem for SteepestDescent.

2007-02-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>
	
	* src/mol.cpp: changes OBMol::NewBond, fixes PR#1666785. AddBond() was
	resizing the _vbond vector and NewBond() used push_back to add items.
	This created a gap bewteen the bonds added by NewBond() and AddBond().
	The FOR_BONDS_OF_MOL iterator expects all bonds to be at the begin of
	the vector. Note: this also fixes the initial problem with the
	OBAngleData and OBTorsionData.

	* test/addhydrogens.cpp: added/deleted... (was used for debugging)

	* src/forcefield.cpp: changes "*logos << ..." to OBFFLog(...)

	* src/forcefields/forcefieldghemical.cpp: changes "*logos << ..." to 
	OBFFLog(...)

2007-02-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>
	
	* data/ghemical.prm: Final update. All molecules from the validation
	ste are given correct atom types and charges.

	* src/forcefields/forcefieldghemical.cpp: Calculated energies comply
	with those from ghemical except for 1,4-scaling. Ring atoms are not
	always scaled in ghemical, not sure why.

	* src/forcefield.cpp: Added OBFFLog, fixes PR#1664279. (tested, but
	needs to replace all "*logos << ..." lines)
	Moved IsInSameRing from OBForceFieldMMFF94 to OBForceField.
	Test molecule from PR#1665765 minimizes correctly, but added cutoff
	accuracy to make sure.

	* tools/obmm.cpp: Added commands for DelHydrogens, GenerateCoordinates,
	SystematicRotorSearch and NumConformers.

	* include/openbabel/forcefield.cpp: Added a definition for isnan.
	(should be replaced with a better method in the math class??)

2007-02-22  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/mol.cpp: Added SetParent call to NewBond function.  Should resolve
	segfault issues related to bug 1665519.

2007-02-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/mol.cpp (NewBond): Fix PR#1665649. Make sure to set the
	parent of a newly-created bond.

	* test/mol.cpp: Add test for above.

	* src/formats/Makefile.am, src/formats/Makefile.in: Fix linking
	problems on Linux discovered by Craig.

2007-02-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/*.i, scripts/*: Add access to OBForceField classes and methods.

	* tools/obprop.cpp: Remove "test" methods, introduced sometime
	since the last release.

	* tools/obmm.cpp: Make sure to set the OBForceField log to prevent
	crashes (e.g., PR#1664279).

	* Doxyfile: Bump version number to 2.1.0b6 for new snapshot.

	* configure.in, configure: Bump to 2.1.0b6 for new snapshot.

	* src/forcefield.cpp, tools/obrotamer.cpp: Update to use
	std::vector instead of arrays.

	* src/rotamer.h, src/rotamer.cpp: Update documentation to use
	std::vector. Fixes compile problems on Windows.
	AddRotamer(std::vector) New method for above.

	* src/base.cpp: Documentation updates.

	* src/canon.cpp, src/forcefield.cpp: Likewise.

	* include/openbabel/ring.h, generic.h, pluginiter.h, canon.h,
	forcefield.h, lineend.h: Likewise.

	* src/all.h, src/formats/all.h, src/Makefile.am, src/Makefile.in,
	src/formats/Makefile.am, src/formats/Makefile.in: Update to allow
	using precompiled headers again.

	* src/canon.cpp, src/formats/cansmilesformat.cpp: Fix crash caused
	by linking problem. CanonicalLabels() moved to the Open Babel namespace.

2007-02-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: UpdateCoordinates now 'knows' about conformers
	and selects the correct one before returning.

	* tools/obminimize.cpp: Implemented (was copy of obmm).

2007-02-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefield.cpp: Added vector analysis methods 
	VectorLengthDerivative(), VectorAngleDerivative(), 
	VectorTorsionDerivative()

	Removed SetEnergyCalculated and related methods for the moment.

	* src/forcefields/forcefieldghemical.cpp: Updated to use the vector
	analysis methods.
	
	* src/forcefields/forcefieldmmff94.cpp: Updated to use the vector
	analysis methods.

	* tools/obgen.cpp: Added -ff option.

	* tools/obenergy.cpp: Added. Calculate the energy of a molecule.
	
	* tools/obminimize.cpp: Added. Minimize the energy of a molecule.

2007-02-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/typer.cpp: Fix PR#1594657 -- long recursion for large
	multi-ring systems like fullerenes. This started by two calls to
	CheckAromaticity, including one allowing recursion depth of
	20. Discussion with Henry Rzepa suggested 14 as a reasonable
	cutoff.

	* src/forcefields/forcefieldmmff94.cpp: Fix compilation problem
	with call to NumericalDerivative.

2007-02-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/forcefield.h: Some doxygen comments updated.

	* src/forcefield.cpp: Added SystematicRotorSearch(), uses RotamerList
	class to rotate all torsions, select the best conformation (lowest
	energy) and minimize it (1000 steps).

	SteepestDescent(int steps, int method) and 
	ConjugateGradients(int steps, int method): 
	the "int method" argument is added, can be set to
	OBFF_ANALYTICAL_GRADIENTS (default) or OBFF_NUMERICAL_GRADIENTS.

	Added ValidateGradientError(vector3 &numgrad, vector3 &anagrad):
	calculate the difference in % between the analytical and numerical
	gradient.

	NumericalDerivative(OBAtom *atom, int terms) and
	GetGradient(OBAtom *a, int terms):
	the added argument terms can be set to OBFF_ENERGY (total gradient,
	default), OBFF_EBOND (gradient for bond stretching), ... (Mainly used
	for ValidateGradients

	* src/forcefields/forcefieldghemical.cpp: All analytical gradients are
	now correct (errors can still be minimized by limiting the number of
	devisions etc...) ValidateGradients also compares gradients for
	individual energy terms. 
	
	Electrostatic term implemented.

	* data/ghemical.prm: Added charge parameters.

	* tools/obgen.cpp: Changed to SystematicRotorSearch().
	
	* tools/obmm.cpp: Added help command.

2007-02-17  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/chemdrawcdx.cpp: don't center molecules.

2007-02-16  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/obmolecformat.cpp: make it compile again (gcc-4.1.2).

2007-02-15 Chris Morley

	Sorry that incomplete code keeps escaping. I'll put up Separate
	code now, although the performance for 0D stereochemistry (sigh)
	needs sorting out. Fulfills Feature Request 1581542
	* include/openbabel/obiter.h, src/formats/obiter.cpp: Extend
	OBMolAtomDFSIter operator* to return NULL to indicate end of a fragment.
	Add parameter to constructor allow the iteration to start at any atom.
	
	* include/openbabel/mol.h, src/formats/mol.cpp: Add API function
	OBMol::Separate() to return disconnected fragments in OBMol vector.
	
	* include/openbabel/obmolecformat.h, src/formats/obmolecformat.cpp:
	Code for applying Separate() in conversion process.
	Also, add ReadNameIndex() for indexing names in multiobject files.
	Requires further testing.
	
	* src/formats/transform.cpp: Added options --separate and 
	renamed -j as --join. (-j still works)

2007-02-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefieldmm2.cpp,
	src/forcefields/forcefieldmmff94.cpp: Remove exit() calls in favor
	of error messages and default return values. Fixes PR#1650132.

	* src/forcefields/forcefieldghemical.cpp: Add default
	electrostatic function (return 0.0) to fix compilation error.

	* tools/obmm.cpp: Add cg command for conjugate gradients.

2007-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* include/openbabel/obconversion.h: Removed OBConversion:: before
	CheckForUnintendedBatch(...); to fix compilation error.

	* src/forcefield.cpp: Added/Updated LineSearch, SteepestDescent,
	ConjugateGradients. Also added the same functions as Validate... to
	test the implementation for x^2 + 2 y^2.
	Added bool is14(OBAtom *a, OBAtom *b). Should move to atom.cpp??
	Started working on DistanceGeometry (needs more sophisticated matrix
	operations than OB currently supports).

	* src/forcefields/forcefieldghemical.cpp: Now uses
	OBFFXXXCalculationYYY to improve performance. All energy functions have
	analytical derivatives. Small corrections to the energy expressions to
	match energies produced by ghemical, added 14-scaling for non bonded 
	energy terms. Different bondtypes in ghemical.prm are no longer
	ignored. Added ValidateGradients().

	* src/forcefield/forcefieldmmff94.cpp: Continue work on MMFF94 to
	comply with the validation suite.
	Added ValidateGradients().
	
2007-02-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/obmolecformat.cpp: Comment out sections of
	ReadChemObjectImpl -- looks like code from Chris invoking
	OBMol::Separate().

2007-02-13 Chris Morley

	Clear OBMol objects by default at start of ReadMolecule.
	
	* include/openbabel/base.h: Add CastAndClear().
	
	* src/*format.cpp(ReadMolecule): Replace dynamic_cast by a call
	to CastAndClear().
	
	* include/openbabel/obconversion.h, src/obconversion.cpp
	(Read, ReadString, ReadFilemove): Remove clearFirst parameter,
	since it is no longer needed. 
	
2007-02-13 Chris Morley

	* include/openbabel/obconversion.h, src/obconversion.cpp:
	Corrected bug 1657817 - wrong name for batch conversion
	of one file - which was due to misinterpretation as 
	splitting operation. Solution requires that the base name
	for output files splitting is not empty - not a big constraint.
	Added extra warning messages and checks in 
	CheckForUnintendedBatch(). Made this function and 
	BatchFileName() and IncrementedFileName() protected.
	
2007-02-12  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/cansmilesformat.cpp
	(OBMol2Cansmi::AddHydrogenToChiralCenters): Fix PR#1658317 with
	chirality on last atom. Switched iterator to use obiter.h macros.

	* configure.in, configure, src/config.h.in: Add big-endian,
	little-endian check,	which defines WORDS_BIGENDIAN for
	chemdrawcdx.cpp (and other binary formats in the future).

	* src/formats/chemdrawcdx.cpp: Solve compilation problems with
	previous change. (endian.h and byteswap.h are GNU and Linux
	extensions.) Requires declaration of WORDS_BIGENDIAN in
	babelconfig.h (as above for Unix).

	* src/Makefile.am, include/openbabel/Makefile.am,
	src/obconversion.cpp: Remove references to newline.[h, cpp].

	* include/openbabel/lineend.h: Add std namespace declarations to
	solve compilation problems with GCC.

	* include/openbabel/ring.h, src/ring.cpp: Documentation updates,
	added new constructor to simplify OBRingSearch::SaveUniqueRing().

	* src/generic.cpp, include/openbabel/generic.h: Change reference
	of DataSource to DataOrigin, as suggested by Noel.

	* include/openbabel/bitvec.h: Fix bug (and documentation) with
	FirstBit().

	* include/openbabel/obutil.h: Fix GCC compile warning.

	* test/cansmi.cpp: New test program for Canonical SMILES format.

	* test/wrapper.sh, test/Makefile.am, test/Makefile.in: Use it.

	* data/types.txt, data/types.h: Fix PR#1650239 with incorrect
	Sybyl Mol2 atom types.

2007-02-11 Chris Morley

	Replaced filter for line endings with a version which works
	with fastsearch. Solves bug 1617324.
	* include/openbabel/newlinebuf.h and src/newlinebuf.cpp:
	replaced by include/openbabel/lineend.h
	
	* src/obconversion.cpp: code in Convert() and Read() replaced.
	
	Removed peek() in the Convert()loop. This was needed for 
	some other mod, which has probably not yet been committed.
	This is not causing any problems for me, but is rather
	central to the conversion process.
	
	Added some documentation on GetOutputIndex. 

2007-02-08  Noel O'Boyle <baoilleach@gmail.com>

	* scripts: Regenerated bindings for scripting languages
	
2007-02-07  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/chemdrawcdx.cpp: make it work on little-endian
	machines.

2007-02-02 Chris Morley

	* include/openbabel/mol.h: Remove definition of Separate()
	which was added prematurely.
	
2007-02-05  Noel O'Boyle <baoilleach@gmail.com>

	* scripts: Removed %apply of OUTPUT and regenerated scripts

2007-02-02 Chris Morley

	* windows-vc2005/Distribution: remove the Windows DLLs added
	yesterday.

2007-02-01 Chris Morley

	* windows-vc2005/Distribution: add some Windows DLLs for the 
	installer.

2007-01-31  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/canon.h, src/canon.cpp: Add canonical
	numbering code from Craig James. (Eventually needs integration
	into other methods -- these duplicate since they support
	fragments.)

	* src/formats/cansmilesformat.*: Add CANSMI format for Canonical
	SMILES output. Eventually needs better integration into current
	SMI format rather than duplication.

	* src/Makefile.* include/openbabel/Makefile.*: Add above files.

2007-01-27  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/cdxmlformat.cpp: add support for formal charges.

2007-01-26  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/cdxmlformat.cpp: fixed issues in writing
	multi-molecules files.

2007-01-26 Chris Morley

	* src/obconversion.cpp, include/openbabel/obconversion.h: Mitigate
	some of the uncertainties in writing multi-molecule files.
	pointed out by Jean Brefort, including bug 1644241.
	Added SetLast as an alternative name for SetOneObjectedOnly.
	Added documentation to GetOutputIndex().
	
2007-01-25  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/cdxmlformat.cpp: scale bond lentghs to 30 (using the
	first molecule) and enable write support.

2007-01-25  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/cdxmlformat.cpp: add some stereochemistry and initial
	write support (not enabled).

2007-01-24  Jean Brefort  <jean.brefort@normalesup.org>

	* src/formats/xml/Makefile.am: add cdxmlformat.
	* src/formats/xml/cdxmlformat.cpp: make it basically work.
	* src/formats/xml/xml.cpp: fix a memory leak.

2007-01-23  Donald E. Curtis <dcurtis3@sourceforge.net>

	* tools/obmm.cpp: Added check for cin.eof resolving bug 1639880.

2007-01-22  Donald E. Curtis <dcurtis3@sourceforge.net>

	* include/openbabel/bond.h: Added const versions of GetBeginAtom and
	GetEndAtom.

	* include/openbabel/atom.h: Added const version of GetVector.  Required
	changing _v to mutable.

	* src/atom.cpp: Added implementation of GetVector.

	* include/openbabel/math/vector3.h: Added const to function definition of
	AsArray function.

2007-01-17  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/Distribution: Added all of the remaining files to the
	installer script so that you can now make an installer directly after
	compiling the relevant projects (OBGUII and OBComLn). Have also
	checked in the example files included with the Windows distribution.

2007-01-16  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel/mol.h, src/*: Documentation updates.

	* include/openbabel/Makefile.am: Make sure pluginiter.h is included.

2007-01-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/snprintf.c: Update with declaration of GPL license in
	addition to Artistic. Checked with author:
	http://www.ijs.si/software/snprintf/

	* configure.in, configure, Makefiles: Bump version number to
	2.1.0b5.

	* src/forcefields/forcefieldmmff94.cpp: Added stub for
	electrostatic calculation. Solves linking problems on Mac OS X.

2007-01-14  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/Distribution: Edited the installer script to make it
	easier to set the version number. Also added explicit paths to some of
	the DLLs in the SVN repository.

	* COPYING: Removed the text after the terms and conditions. This is
	the text describing how to apply the license.

2007-01-13  Noel O'Boyle <baoilleach@gmail.com>
	
	* windows-vc2005/Distribution: Added files necessary for creating an
	installer using NSIS, an open source software for creating Windows
	installers. The current script needs to be edited to be able to pick
	up the files from the OpenBabelGUI build.

2007-01-12  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-python.i: quick fix to allow the openbabel module
	to be imported without errors. The OBFingerprintIter issue remains
	unresolved.

2007-01-09 Chris Morley <ob@gaseq.co.uk>

	* scipts/openbabel-python.i: changes to OBFingerprintIter. Not tested
	yet!
	
	* include/openbabel/pluginiter.h: comment out PluginIter::Description()
	and operator* which are causing problems with the Python build - 
	I suspect because they are not used in the C++ code.
	
	* include/openbabel/forcefield.h: src/forcefields/forcefieldghemical.cpp,
	 src/forcefields/forcefieldmm2.cpp: changes to several return values
	to avoid compiler errors. 

2007-01-08 Chris Morley <ob@gaseq.co.uk>

	* include/openbabel/pluginiter.h: correct documentation on 
	the use of FOR_EACH to iterate over all objects.

2007-01-07  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/mol.cpp: Moved all Destroy* calls to the end of Delete* functions so
	that indexes are updated and other meta information.

	* src/mol.cpp: NewBond was assigning indexes based on the size of the
	_vbond vector but since the vector is incremented in chunks of 100 this
	was producing incorrect index numbers.  Updated misc docs.  Also had a bug
	in DeleteBond using the bond variable for more than one purpose (added
	bondi for iterator usage).

2007-01-07 Tim Vandermeersch <tim.vandermeersch@gmail.com>
	
	* src/math/vector3.cpp: Added Point2PlaneAngle(vector3 a, vector3 b,
	vector3 c, vector3 d) (moved from OBForceField)
	
	* src/forcefield.cpp: Added logging features

	* src/forcefields/forcefieldmmff.cpp: All energy functions except
	E_Electrostatic() now use a OBFFXXXCalculationYYY class. Runs much
	faster.

	* src/formats/mopacformat.cpp: Added MOPAC Internal format (mopin)
	
	* data/exttype.txt: Updated for MOPAC Internal format (mopin)

2007-01-06 Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/OBPython/setup.py: Bumped up version number to 1.0.
	Added a postinstall script that sets BABEL_DATADIR. Included
	zlib1.dll.

	* Added windows-vc2005/OBPython/openbabel_postinstall.py: A post
	install script that sets the value of BABEL_DATADIR.

	* windows-vc2005/OBPython/README.txt: Updated instructions on how to
	run setup.py to create the distribution.

2007-01-06 Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-[python,java,perl,ruby].i: Added ability to handle
	the new pluginiter.h, and in particular, its use in
	OBFingerprint.Iter. Also, regenerated all of the dependent files.

	* scripts/openbabel-python.i: Removed python code added on 2006-12-20
	to set BABEL_DATADIR as it actually had no effect.

2007-01-06 Tim Vandermeersch <tim.vandermeersch@gmail.com>

	* src/forcefields: Ghemical now uses SMARTS for atomtype setting.
	
	* src/forcefields: Added initial MMFF94 implementation. (uses new
	OBFFCalculation class for better performance)

	* tools/obgen.cpp: Now uses OBForceField::GenerateCoordinates().

	* data/: Added SMARTS patterns to ghemical.prm for typing. Added
	ghemical.prm to Makefile.*
	Added parameters for MMFF94 (files for validating MMFF94 not included)
	Data needs forcefield subfolder??

	* test/obmmff94validate.cpp: Validate MFF94 using the validation
	suite.
	
2007-01-05 Chris Morley <ob@gaseq.co.uk>

	* include/openbabel.residue.h: Added EXTERN macro for global 
	variables for DLL builds. (Does nothing otherwise).
	
	* Updated OpenBabelDLL project file.
	
2007-01-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/*.cpp, include/openbabel/*.h: Compiler warning fixes from
	Jean Brefort.

	* include/openbabel/residue.h, include/openbabel/generic.h: Remove
	static declarations for OBGenericDataType and residue properties.

2007-01-05 Chris Morley <ob@gaseq.co.uk>

	* include/openbabel/fingerprint.h: Give OBFingerprint a virtual
	destructor. Noel found this was why SWIG was failing.
	
2007-01-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields/forcefieldghemical.cpp: Fix typo from file
	renaming. (Can't use Tripos since that's a copyright.)

	* Makefile.in: Regenerate all Makefiles to fix build problems.

2007-01-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/forcefields: New code from Tim for MM2 and Ghemical force fields.

	* include/Makefile.*: Updates for Chris's changes earlier today.

	* include/inchi/*.c: Moved actual inchi source files back to src/.

	* configure, */Makefile.in: Updates for inchi move and forcefield directory.

2007-01-03 Chris Morley <ob@gaseq.co.uk>

	* Update Windows project files. But Python SWIG interface isn't
	working on Windows.
	
	* Moved libxml and inchi header files to include.

2006-12-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Doxyfile: Change format slightly for better API documentation.

	* src/*, include/openbabel/*: Many API documentation updates.

	* include/openbabel/base.h, src/base.cpp (OBBase::Clear): New method in base
	class to improve OBConversion::Read() syntax.

2006-12-27 Chris Morley <ob@gaseq.co.uk>

	* src/newlinebuf.cpp: Revert to as in rev 1652.

2006-12-22 Chris Morley <ob@gaseq.co.uk>

	* include/openbabel/pluginiter.h, fingerprint.h: Modify so that most
	of code to implement plugin module behaviour is in pluginiter.h,
	making it easy to give this behaviour in future to other classes.
	Compatibility for OBFingerprint maintained except for iteration
	through fingerprint types which is now in the style of obiter,
	hopefully making it compatible with Python (binding not yet done).
	
	* formats/fastsearchformat.cpp: change implementation of F option
	to new iteration style.
	
	* src/fingerprint.cpp, include/openbabel/fingerprint.h: remove 
	the replaced static variable _pDefault and GetNxtFPrt().
	Add FastSearch::ReadIndexFile() alterantive to avoid 
	std::stream parameter which is no good for scripting.
	Add FastSearch::FindMatch() which is simialr to Find() but requires
	all bits of fingerprint to match.
	
	* src/obconversion.cpp: added NO_NEWLINEBUF to avaoid compiling
	newline buf which is currently incompatible with FastsearchFormat
	and OBConversion::SkipObjects().
	All types of line ending seem to work ok with VC++8 on Windows.

2006-12-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obiter.cpp (OBAtomAtomIter): Fix bug reported by Zhiguo Liu,
	with obvious typo.

	* src/formats/pdbformat.cpp: Fix atom typing bug reported by
	Zhiguo Liu. Fix problems with unknown elements (due to atom
	parsing) from PR#1577238.

2006-12-20  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/OBPython/setup.py: Install data files (e.g.
	patterns.txt needed for FP3) into site-packages/openbabel_data

	* scripts/openbabel-python.i: For Windows installs, set BABEL_DATADIR
	to the location into which the binary installer installs the data files

	* src/fingerprints/finger3.cpp: Replace instances of "/" by
	FILE_SEP_CHAR

2006-12-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/python/setup.py, scripts/perl/Makefile.PL: Updates from
	Dominik Mierzejewski to check for src/.libs directories. Prevents
	"chicken and egg" problem with what component is built first.

2006-12-16  Noel O'Boyle <baoilleach@gmail.com>

	* fingerprint.cpp/.h: Changed the FindFingerprint method to accept
	const string& instead of string&. This is necessary for access to this
	function from Python.
	
	* scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a method
	to Molecule for calculating a molecular fingerprint, handled by a new
	Fingerprint class.
	
2006-12-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure.in, configure, Doxyfile: Bump to 2.1.0b4 for upcoming snapshot.

	* src/*.cpp: Update class documentation (for many classes) to
	reflect <openbabel/header.h> syntax. Makes API documentation
	consistent with usage.

	* src/obconversion.cpp, src/obconversion.h: Enable on-the-fly line
	ending translation for input. Windows and Classic Mac files should
	now translate without problems. Right now, XML files are excluded
	through the new READXML flag.

	* src/formats/xml: Update for READXML flag and move of xml.h
	header.

	* include/openbabel/xml.h: Move header for public use.

	* src/formats/fastsearchformat.cpp: Add READBINARY flag.

	* include/openbabel/Makefile.am, Makefile.in: Fix "make dist"
	target to remove generated babelconfig.h header for snapshots and
	releases.

	* scripts/Makefile.am, scripts/Makefile.in: Make sure to clean
	java targets.

	* data/mm2.prm, data/Makefile.am, data/Makefile.in: MM2 parameters.

2006-12-15 Chris Morley <ob@gaseq.co.uk>

	* tools/babel.cpp, src/obconversion.cpp, src/formats/obmoleculeformat.h:
	Move -k option help info into OBConversion::Description, where it can
	be used by other front-ends. (The info in help() is specific to the
	command-line interface.) Register it as having no parameters.
	
2006-12-14  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/formats/gaussformat.cpp: Will export "model/basis,method" if keyword
	translation is enable however is not tested accurate.
	
	* src/formats/ghemicalformat.cpp: Re-wrote and tested the GAMESS keyword
	export.
	
	* src/formats/gamessformat.cpp: Modified keyword import operations.
	Should now import the model,basis,method for keywords it knows about.
	This method is all statically implemented.  We need a new way to do this
	translation such as OBKeyword class.
	
	* tools/babel.cpp: Added help information for the '-k' parameter which
	attempts to translation keywords along with molecule information.

2006-12-13  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-[python,ruby,java,perl].i: Updated to include all
	iterators in obiter.h. Note: there is a problem getting
	OBMolPairIter to work even if std_pair.i is included and a template
	<int, int> created (compile of openbabel_python.cpp fails in this case
	so these additions have not been included). 

2006-12-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* tools/babel.cpp: Moved src/main.cpp here -- more consistent with
	new directory structure.

	* configure, configure.in, src/Makefile.*, tools/Makefile.*: Ditto.

	* scripts/: Regenerated files based on Noel's changes today.

	* test/files/smartsresults.txt: Updated after Craig's bug-fixes.

	* test/cmltest/: Update scripts to handle new location of babel
	binary.

2006-12-13  Craig A. James <cjames@emolecules.com>

	* src/parsmarts.cpp, src/formats/smilesformat.cpp: Fixed bug in
	SMILES parser/writer and SMARTS parser that reversed Cis/Trans
	chirality when the "/" or "\" followed an open-parenthesis "("
	character.  Commented out an unused function from parsmarts.cpp.
	Fixed a bug where a semicolon ";" was printed for an aromatic bond
	instead of a colon ":" for external bonds.
	
2006-12-13  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-[python,ruby,java,perl].i: Tidied up the
	references to classes in obiter.h (e.g. there's no such thing
	as OBResidueBondIter). Added some comments. Added wrappers for Python
	to allow iteration over atoms in a molecule, etc.
	This involved renaming the original OB method, and replacing
	it by a Python class implementing the iterator protocol.

2006-12-12  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-[python,ruby,java,perl].i: Added a line to
	create a vector of unisigned ints, required to use the Fingerprint
	class. Also, added lines to prevent warnings due to shadowed classes
	in obiter.h.

2006-12-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* include/openbabel: New directory for public headers. Ensures
	internal and external code use the same 
	#include <openbabel/header.h> syntax.

	Also, all related UNIX-based build changes.

2006-12-04  Vincent Favre-Nicolin <Vincent.Favre-Nicolin@ujf-grenoble.fr>

	* src/format/ciffformat.cpp: Added new OBFormat-derived class to
	handle Crystallographic Information Files. Initial implementation
	handles reading & writing atomic coordinates, reading unit cell
	and spacegroup name but no interpretation of symmetry is done.

2006-12-04  Benoit Jacob <jacob@math.jussieu.fr>

	* src/math/vector3.cpp: optimize createOrthoVector(), update doc.

2006-12-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/generic.h, src/generic.cpp (OBRingData): Add new methods for
	iterating over rings. (OBAngleData): Modifications from Tim
	Vandermeersch to facilitate iteration over angles in an OBMol.

	* src/mol.h, src/mol.cpp (FindAngles()): New method to parallel
	FindTorsions() for filling an OBAngleData record in an OBMol,
	contributed by Tim.

	* src/obiter.h, src/obiter.cpp: New classes and macros, including
	FOR_RINGS_OF_MOL, FOR_ANGLES_OF_MOL, FOR_TORSIONS_OF_MOL
	FOR_PAIRS_OF_MOL, contributed by Tim.

	* src/forcefield.h, src/forcefield.cpp, src/Makefile.am,
	src/Makefile.in: New classes for mol. mechanics force fields
	contributed by Tim Vandermeersch.

2006-12-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/Makefile.am, test/Makefile.in: Remove outdated vector3 and
	matrix tests.

	* scripts/: Added fingerprint.h header for direct access to
	OBFingerprint classes.

	* src/grid.h, src/grid.cpp (OBGrid): New base class, derived from
	OBBase to allow conversion to handle grids. Also simplifies
	OBFloatGrid and OBProxGrid code.

	* src/*: Documentation updates.

	* src/formats/xml/cdxmlformat.cpp: New file for ChemDraw CDXML format.

	* src/formats/inchiformat.cpp (InChIFormat::ReadMolecule): Fix
	compile error with GCC. OBMol::SetTitle() can't handle implicit
	string operations.

2006-12-07 Chris Morley <ob@gaseq.co.uk>

	* src/formats/inchiformat.cpp: Read capability added using the NIST
	code but stereochemistry not yet implemented.
	
	* src/formats/getinchi.cpp: parser to extract InChIs (possibly
	split) from other text. Examples in the file.
	
2006-12-06 Chris Morley <ob@gaseq.co.uk>

	* src/formats/mdlformat.cpp: SDFormat and MOLFormat now derived from
	base class MDLFormat. SD files now always output with $$$$
	(cures bug 1604992), mol files do not output properties.

2006-12-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/math.cpp: Improve speed by switching from endl (causes
	flush) to "\n". Make sure to output number of tests 1..testCount.

	* test/wrapper.sh: Switch to call new math test program.

2006-12-04  Benoit Jacob <jacob@math.jussieu.fr>

	* test/math.cpp: match the Test::Harness output format. Fix a bug
	in testEigenvalue.

	* src/obutil.h, src/math/vector3.cpp, src/mol.cpp: revert to using
	std::min instead of fmin.

2006-12-03  Benoit Jacob <jacob@math.jussieu.fr>

	* src/math/vector3.h, src/math/matrix3x3.h,
	  src/math/vector3.cpp, src/math/matrix3x3.cpp:
	 --- IMPORTANT: disable floating-point checks and exception-throwing
	     by default. Now that is compiled only if OB_OLD_MATH_CHECKS is
	     defined.
	 --- Fix compilation error on Windows reported by Noel O'Boyle.
	     (another compilation error on Windows remains to be fixed).
	 --- Fix some more methods. Now all the floating-point code
	     should be quite sane.
	 --- Optimize/simplify several more methods.
	 --- add matrix3x3::operator*=( const double &), make operator /=
	     use it.
	 --- remove #define PI, use the standard M_PI instead.
	 --- replace #define SQUARE() by a static inline function.
	 --- remove hyper-dangerous #define x,y,z

	* test/math.cpp: extend tests, merge (an improved version of)
	matrixtest.cpp. Now math.cpp covers all what vector3.cpp and
	matrixtest.cpp did cover, plus a lot more. Geoff: maybe it's time
	to remove the tests vector3 and matrixtest?

        * test/vector3.cpp: fix bugs, if that still matters.

	* src/obutil.h: add note clarifying that to check if x is zero, one
	should use IsNegligible( x, 1.0) instead of IsApprox( x, 0.0 ).

	* src/rotor.cpp, tools/obxyz.cpp: use M_PI instead of PI.

2006-12-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/*: Cleanups and fixes, including for compilation
	problems with Perl. (Derives from some macro expansion for THR.)

2006-12-01  Benoit Jacob <jacob@math.jussieu.fr>

	* src/grid.h, src/grid.cpp: In class OBFloatGrid:
	cleanup and simplifications, minor optimizations, add a FIXME
	comment in operator<< about endianness issues, replace a dangerous
	memset by a for loop. (This memset relied on the fact that the
	floating-point value 0.0 is represented by the bits 0....0, which
	happens to be true, but is not something we want to depend on.
	Plus, compilers are/should be clever enough to make the for loop
	just as fast.)

2006-11-29  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/openbabel-python.i: Added some SWIG magic that allows the
	creation of a C doubles array. Also added a Python convenience
	function that converts a list to a C doubles array. This will allow
	users to access functions such as OBMol::Rotate.

2006-11-29  Benoit Jacob <jacob@math.jussieu.fr>

	* math/vector3.cpp: fix a bug that I had introduced a few days ago
	in createOrthoVector. Thanks go to the new unittests.

	* math/matrix3x3.h, math/matrix3x3.cpp: fix some defines in the
	same way as in vector3.h, add both constant and non-constant
	operator()(int,int) to access the matrix elements easily.
	Fix isUnit(), isOrthogonal(), isDiagonal().

	* test/math.cpp, test/Makefile.am, test/Makefile.in:
	New tests for the math/ subdirectory. Covers the constructors, access
	methods, various operators, operations on rows and columns and
	(partly, will be completed) the distances/angles/orthogonality stuff.

	* src/obutil.h: add new function IsNegligible(), checks whether a is
	much smaller than b with given precision.

2006-11-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* tools/obrotate.cpp: Use a simpler implementation with
	OBMol::SetTorsion(). (Need to rewrite command-line parsing to
	allow setting torsions of all matches, but no time now.)

	* tools/obrotamer.cpp, src/Makefile.am, src/Makefile.in: New tool
	to generate random rotamers using OBRotamerList and
	company. Additional example of using rotamer code.

	* src/rand.h, src/obutil.h, src/Makefile.am, src/Makefile.in:
	Split out OBRandom to mirror rand.cpp.

	* src/rotamer.cpp, src/rotamer.h, src/rotor.h, src/base.cpp:
	Documentation updates. 

	* src/rotor.cpp (OBRotorRules): Make sure Init() is called before
	any action, i.e.., GetRotorIncrements(). Fixes a bug uncovered
	with obrotamer.cpp

2006-11-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/*.cpp: Update to switch from OBNodeBase and OBEdgeBase
	iterators to OBAtom and OBBond respectively. Follows on 2006-11-20
	change contributed by Gerd Menche. Switch many iterators to
	preincrement for minor optimization.

	* tools/*.cpp: Ditto.

	* scripts/*: Regenerate for continuing API changes (e.g., vector3,
	etc.)

2006-11-27  Benoit Jacob <jacob@math.jussieu.fr>

	* src/math/vector3.h, src/math/vector3.cpp: Remove some inline
	keywords from yesterday's patch, further optimize
	vector3::createOrthoVector().

2006-11-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obutil.h, src/obutil.cpp: Optimizations and improvements
	from Benoit Jacob, including documentation clarifications.

	* src/math/vector3.h, src/math/vector3.cpp: Optimizations and
	improvements, including documentation clarifications. Inline some
	small methods, mark 'const' where possible, remove 'friend'
	declarations, etc. contributed by Benoit Jacob.

	* src/math/matrix3x3.h, src/math/matrix3x3.h: Use it.

	* Doxyfile: Update for 2.1.0b3 snapshot and current Doxygen
	version (1.5.1).

	* src/rotamer.h, src/rotamer.cpp, src/rotor.h, src/rotor.cpp:
	First step at documentation updates on rotamer/conformer
	generation routines.

	* src/fingerprint.cpp, src/tokenst.cpp, src/generic.h: Eliminate
	minor Doxygen warnings.

	* src/data.h, src/data.cpp (OBTypeTable::Translate): Add new
	method for returning the translated string as a value --
	simplifies scripting language access.

	* src/mol.h: Documentation updates.

2006-11-25  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005/OBPython/logo.bmp: Replaced logo with one that Geoff
	sent me.

	* scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a
	.close() method to the Outputfile class of Pybel. This uses the
	CloseOutFile() method added by Chris Morley in r1606. This is
	necessary to ensure that all tests pass on Windows.

2006-11-24 Chris Morley <ob@gaseq.co.uk>

	* src/obconversion.cpp(Write),(Read): Check for stream pointers
	being NULL.

	* src/obconversion.h, src/obconversion.cpp: Added CloseOutFile()
	at the suggestion of Noel O'Boyle.
	
2006-11-24  Noel O'Boyle <baoilleach@gmail.com>

	* windows-vc2005: added libxml2.dll (taken from Chris' Windows OB GUI
	distribution)
	* windows-vc2005/OBPython/logo.bmp, setup.py: new files added that
	allow the creation of a Windows OB scripting installer
	* windows-vc2005/OBPython/Readme.txt: Updated with instructions on
	running setup.py

2006-11-23 Chris Morley <ob@gaseq.co.uk>

	* windows-vc2005: Added OBPython project to allow OB to be used
	form Python on Windows.
	
	* src/parsmart.h(SmartsLexReplace), src/ring.h(CompareRingSize):
	Added OBAPI to declarations of these exported global functions.
	
2006-11-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/atom.h, src/base.h, src/bond.h, src/residue.h, src/mol.h,
	src/ring.h, src/mol.cpp, src/base.cpp, src/obiter.h: Remove
	OBNodeBase, OBEdgeBase, and OBGraphBase classes, contributed by
	Gerd Menche.

	* tools/obprop.cpp: Ditto. Example of changing iterators to new format.

	* scripts/*: Updated based on above changes.

	* src/formats/xml/cmlformat.cpp: Change size_t to
	string::size_type to be sure of 64-bit correctness.

2006-11-17 Chris Morley <ob@gaseq.co.uk>

	windows-vc2005: Added projects for OpenBabelDLL, OBComLn, and OBGUII
	
2006-11-18  Michael Banck <mbanck@gmx.net>

	* test/textbuffer.cpp: Do not include "zipstream.h" if HAVE_LIBZ is 
	not defined.  Do not check for a gzip'd input stream if HAVE_LIBZ is
	not defined.

2006-11-18  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/testpybel.py: Needed to relax one of the tests of
	molecular weight, as it was failing for the OB2.1b2 snapshot (there
	must have been some changes to the atomic masses). Also,
	corrected tolerance tests to use the absolute value of the difference
	rather than the actual value.
	
2006-11-18  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/setup.py, pyopenbabel.py, testpyopenbabel.py,
	pyopenbabelapi.html: Changed all references to pyopenbabel to pybel
	(new name). Also, corrected minor typo in docstring in pybel.py.

2006-11-17 Chris Morley <ob@gaseq.co.uk>

	* src/formats/xml/cmlformat.cpp: mods to input and output properties
	with the title attribute on <property>, as requested by Carsten Niehaus. 
	
2006-11-17 Chris Morley <ob@gaseq.co.uk>

	* src/formats/turbomoleformat.cpp: Added input and output options to
	read and write in Angstroms (default is bohr).
	Modified WriteMolecule() so that the use of strlwr doesn't corrupt
	etab. (Was apparent only in GUI where etab persists between molecules.)
	
	* src/obconversion.cpp: changed some results of string finds to
	std::string::size_type. 

2006-11-15  Noel O'Boyle <baoilleach@gmail.com>

	* scripts/python/pyopenbabel.py: Updated to be consistent, fast, pass
	all unit tests, and to have API documentation in docstrings.

	* scripts/python/testpyopenbabel.py: Added complete coverage unit tests
	for pyopenbabel.py.

	* scripts/python/test/*: Removed previous attempts at testing

	* scripts/python/pyopenbabel.txt: Removed previous attempts at
	providing documentation (we now have a wiki, and API documentation)

	* scripts/python/head.sdf: Added small test file, used by
	testpyopenbabel.py.

	* scripts/python/pyopenbabelapi.html: Added API documentation for
	pyopenbabel.py, automatically generated using "pydoc -w"

2006-11-09  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/formats/gamessformat.cpp: Gamess output parsing now only gathers
	run information from the input deck rather than gather all and defaults
	from gamess.  we may need to reconsider this in the future or add an
	option for it.

2006-11-08  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/formats/gamessformat.cpp: Bug fixes after further testing.

	* src/formats/gamessformat.cpp: For now keywords are in uppercase.  This
	needs to be decided on by the dev community and will be discussed with
	the gamess developers for gamess-specific keywords.

	* src/formats/ghemicalformat.cpp: Read GAMESS info from the "gamess"
	namespace

	* src/generic.h: Added GetData(const char *s) to OBSetData
	so that you can retrieve data from a const char rather than
	having to instanciate a string.

	* src/formats/gamessformat.cpp: More improvements on reading generic
	computational meta data.  (added runtyp / dfttype / basis).  Also modified
	the location of gamess extra information.  GAMESS now stores it's
	information in an OBSetData with attribute "gamess" which is part of the
	molecule.

2006-11-07 Chris Morley <ob@gaseq.co.uk>

	* src/formats/xml/cmlformat.cpp(WriteMolecule): Output new
	namespace URL rather than the old one.
	
	* src/obutil.cpp" Remove static from Solvelinear() and 
	SolveQuadratic() so that would compile on VC8.
	
	* windows-vc2005/babelconfig.h: Extra macro definitions.
	
	* windows-vc2005/libinchi.dll,  windows-vc2005/libinchi.lib:
	1.01 versions from NIST

2006-11-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/main.cpp, src/obutil.cpp, src/fingerprints/finger3.cpp,
	src/format/fastsearchformat.cpp: Patch from Martin Vogt to address
	PR#1590609. Crashes due to incorrect handling of string parsing on
	64-bit platforms.

2006-11-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure.in, configure, Makefile.in: Add back support for
	optional compile of wxWidget GUI in src/GUI.

	* scripts/*: Split openbabel.i into individual copies for each
	language.

	* scripts/java/*: Initial attempt at a java interface from SWIG. Untested.

2006-10-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/molreport.cpp: New psuedo-format to generate atom
	and bond information as suggested by Rich Apodaca. Addresses
	PR#1587499.

2006-10-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/openbabel.i, scripts/*: Updated with changes from Martin 
	Vogt to fix break (likely dating back to header split of atom.h,
	bond.h, residue.h). 

2006-10-20 Chris Morley <ob@gaseq.co.uk>

	* src/formats.xml/xml.cpp (ReadChemObject): added extra error
	message and convert the rest to use obErrorLog.
	
	* src/formats/mdlformat.cpp: modify description to work around
	bug in wxWidgets radiobuttons.
	
2006-10-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.h, src/obconversion.cpp: Make sure to free
	streams created using ReadString, ReadFile, or WriteFile()
	methods. Fixes PR#1578916.

2006-10-17  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/chemdrawcdx.cpp: Fixed corruption of 2D coordinates
	caused by attempted conversion from CDX scale to Angstroms. Fixes
	PR#1576703.

	* configure.in, configure, Makefile.*: Bump to version 2.1.0b2 for
	next snapshot (now using autoconf-2.60).

	* data/*, src/fingerprints/finger3.cpp: Rename pattern file to
	SMARTS_InteLigand.txt.

	* src/obiter.h: Fix GCC warning reported by Carsten.

	* src/formats/*format.cpp: Update chemical MIME types,
	specification URLS and extensions from the chemical MIME project:
	http://sf.net/projects/chemical-mime 

	* scripts/openbabel.i: Add output string for
	OBTypeTable::Translate().

	* scripts/*: Regenerate.

	* test/textbuffer.cpp, test/vector3.cpp: New tests for newline
	translation and vector3 manipulations.

2006-09-30 Chris Morley <ob@gaseq.co.uk>

	* src/formats/fastsearchformat.cpp(ReadChemObject):
	Output message with the properties of the index if no
	SMILES structure provided.
	
	* src/fingerprint.h: Added FastSearch::GetIndexHeader()
	Reformat tabs.
	
2006-09-30 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/chemdrawcdx.cpp (Flags): added NOTWRITABLE
	
	* src/formats/fastsearchformat.cpp: Made timing of indexing
	work properly.
	
	* src/oberror.cpp(ThrowError) : return immediately if _logging is
	false; do not add to list of messages.
	
	* src/generic.cpp(GetLatticeType, GetSpaceGroupNumber) : ensured
	all paths returned value to avoid compiler warning (no real effect)

2006-09-27  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/generic.h: Updated OBSetData to initialize to correct
	OBGenericDataType enumeration.
	* src/formats/ghemicalformat.cpp: GPR format now exports GAMESS
	information correctly if it exists as part of the molecule.

2006-09-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/ruby: Add new ruby interface -- probably needs to be
	moved to allow compilation into main libopenbabel.

	* scripts/*: Updated for above changes.

2006-09-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/base.h, src/atom.h, src/bond.h: Update internal atom
	indexing to use an unsigned int, rather than short. Fixes
	PR#1556819, caused by large molecules (i.e. >2^16 atoms or bonds).

	* src/newlinebuf.h, src/newlinebuf.cpp: Fix bugs uncovered during
	ChemSpotlight testing. Now appears to smoothly handle old Mac OS
	9, DOS, and Unix line endings with no problems.

	* src/generic.h, src/generic.cpp: Incorporate patches from Carsten
	for lattice type and space groups.

	* src/formats/chemdrawcdx.[h, cpp]: New format code for ChemDraw
	CDX binary code, contributed by Fredrik Wallner.

	* src/formats/Makefile.am, src/formats/Makefile.in: Update for
	above.

	* tools/obgen.cpp, tools/Makefile.am: New "obgen" tool for
	creating simple 3D coordinates for SMILES and other 0D
	formats. Contributed by Tim Vandermeersch.

2006-09-06  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/generic.h: Added new OBGenericData subclass: OBSetData

2006-08-30  Donald E. Curtis <dcurtis3@sourceforge.net>

	* src/mol.cpp: Added OBMol::CreateResidue() function.

2006-08-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/inchi/: Update InChI library with final release of
	1.0.1. Need to update configure script to detect libinchi version
	to only build newer revisions when needed.

2006-08-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/smilesformat.cpp (ParseComplex): Ensure complex
	expressions end in a ']' character. Added patch from Nick England
	for handling chiral output using OBChiralData. Should fix
	PR#1508741.

	* test/files/invalid-smarts.txt: Add additional complex expression
	for tests.

	* src/generic.cpp (OBUnitCell): Update lattice detection to use
	IsApprox instead of IsNear.

	* src/mol.cpp (PerceiveBondOrders): Ditto.

2006-08-04 Chris Morley <ob@gaseq.co.uk>
	
	* src/kinetics.h(OBRateData): Change constructor to fit in with
	the recent change in OBGenericData constructor.
	
2006-08-03 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/smilesformat.cpp (ParseSimple)(ParseComplex)
	Removed extension labelled "is this safe" and added support for
	* and [*] as wildcard elements. arom = false was also needed.
	
	* src/kekulize.cpp(getorden): Treat Te (atNo=52) the same as Se.
	Allows c1cc[te]c1 to be interpreted as better rubbish.

2006-08-02 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/smilesformat.cpp (ParseSimple)(ParseComplex)
	Accept, with a warning, the illegal aromatic elements
	b [si] [ge] [sb] [bi] [te] [sn]
	
2006-07-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/cmlformat.cpp (BeginElement): Make sure to call
	BeginModify() on a <molecule> tag, since EndModify() is already
	called. Fixes PR#1512054 and probably PR#1523956.

2006-07-21 Chris Morley <ob@gaseq.co.uk>

	* src/obconversion.cpp(AddChemObject): remove compiler warning by
	returning Count!=0 rather than Count.
	
	* src.obutil.cpp(IsApprox): replaced fmin, which is not known to
	MS compiler, with std::min.

2006-07-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/internalcoord.h: New header to encapsulate OBInternalCoord.

	* src/Makefile.am, src/Makefile.in, src/mol.h: Updates for above.

	* src/obutil.h: Remove old-style casts, and minor documentation
	updates. 

	* src/data.h, src/generic.cpp, src/generic.h, src/math/vector3.h
	src/obiter.h: Update to use initialization lists more
	consistently.

	* src/formats/inchiformat.cpp: Use obiter classes to remove
	shadowed temporary variables.

	* src/typer.cpp: Fix bug with aromatic typer claiming errors on
	blank lines. 

	* src/data.cpp: Fix bug with reading data files from versioned
	directories. 

	* data/phmodel.txt, data/phmodel.h: Fix bug with seed charge on
	hydroxamic acid reported by Noel.

2006-07-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/math/vector3.h, src/math/vector3.cpp: (IsApprox) Add new
	method to compare vectors based on approximate floating-point
	comparisons, rather than potentially dangerous == and !=
	operators.

	* src/chiral.cpp: Use vector3::IsApprox instead of ==.

	* src/residue.cpp, src/bond.cpp, src/atom.cpp, src/bond.h: Add
	back needed headers for compilation, removed with yesterday's
	change dividing up mol.h

2006-07-17  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/atom.h, src/bond.h: New headers to encapsulate OBAtom and
	OBBond interfaces, respectively.

	* src/bond.cpp: Switch #include of mol.h to new header.

	* src/atom.cpp: Ditto. (SetHybAndGeom): Fix missing break
	statement, uncovered using AntiC static analysis program.

	* src/Makefile.am, src/Makefile.in: Make sure to include above in
	distributions. 

	* src/residue.h, src/residue.cpp: Move OBResidue class declaration
	from mol.h. 

	* src/mol.h: Remove OBAtom, OBBond, and OBResidue, as above.

	* src/obutil.h, src/obutil.cpp: Add IsApprox() and CanBeSquared()
	contributed by Benoit Jacob.

	* src/math/vector3.h, src/math/vector3.cpp: Add new implementation
	of vector3::normalize and createOrthoVector, contributed by Benoit.

2006-07-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp, src/main.cpp: Remove unneeded semicolons,
	which prevent compilation with GCC at high warning levels.

	* src/mol.h: Remove extra OBMol:: specification -- prevents
	compilation with GCC and confuses Doxygen.

	* src/gaussformat.cpp: Add -xk and -xf write options to output
	supplied keywords to Gaussian input. Allows batch output of files
	with the same options.

	* src/gamessformat.cpp: Ditto. Add contributions from Donald
	Curtis for reading GAMESS input files.	

2006-06-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/chains.cpp: In TracePeptideChain and TraceNucleicChain, test
	for atom visit before recursing. Otherwise, leads to an infinite
	loop and crash. Fixes PR#1515198, reported by Noel.

2006-06-29  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure, configure.in: Fix logic in last change.

	* Doxyfile: Update to grab obmolecformat.h now in src/format/.

	* src/*.cpp, src/*.h, src/formats/*.cpp:
	Cleanup #includes for iostream, fstream -- only use iostream when
	needed (i.e. for cout, cerr, cin, clog declarations).

	* src/all.h, src/formats/all.h: Trim precompiled header templates
	to most common headers.
	
	* src/patty.cpp: Remove unused "COMPILE_PATTY_MAIN" #ifdef.

	* src/chiral.cpp: Remove unused floating-point methods.

	* src/rand.cpp: Remove unused #ifdef DEBUG code.

	* src/parsmart.cpp, src/formats/crkformat.cpp: Update calls to
	printf with calls to obErrorLog.

	* src/obutil.cpp (InternalToCartesian): Check index requests to
	avoid requesting past the vector end.
	(#ifdef): Remove ifdef, leave code for roots.

	* src/formats/ghemicalformat.cpp: Remove dummy atoms, which can
	cause problems. Mark all aromatic bonds as bondtype 'C'.

	* test/files/attype.00.smi: Add unspecified chiral alkane for @?
	SMARTS testing.
	
	* test/files/formalchargeresults.txt, test/files/ringresults.txt,
	test/files/formularesults.txt, test/files/smartsresults.txt:
	Update for changes to attype.00.smi using generate.sh.

	* test/Makefile.am: Cleanup.

2006-06-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure, configure.in, src/all.h, src/formats/all.h,
	Makefile.in: Add experimental support for precompiled headers with
	GCC, using the --enable-precompiled-headers flag to the configure
	script. Haven't performed much timing/optimization -- appears to
	help about 10-12%.

	* src/base.h, src/mol.h, src/obconversion.h, src/generic.h:
	Warning eliminations and documentation improvements from Carsten.

	* src/obiter.cpp: Further improvements to documentation on DFS and
	BFS iterators.

	* src/chains.cpp: Updated call to fprintf(... stderr) to use
	modern OBMessageHandler.

	* scripts/*: Regenerate for latest header changes.

	* Doxyfile, doc/api-style.css: Updated for doxygen-1.4.7 and new
	style changes.

2006-06-28 Chris Morley <ob@gaseq.co.uk>

	* src/obiter.cpp: Some of the examples wouldn't compile - need 
	&*a rather than a in parameter calls. Added comment in all the
	examples. I ran into this personally with FOR_NBORS_OF_ATOM(b, &*a)
	but haven't tested the similarly modified OBResidue example.
	
	* src/formats/mdlformat.cpp(GetTimeDate): Change second parameter
	which was corrupting output of mol file line 2.  
	
2006-06-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obiter.cpp: Add improved documentation on DFS and BFS atom
	iterators. Fix bug with disconnected fragments uncovered with unit
	testing.

	* test/iterators.cpp, test/wrapper.sh, test/Makefile.am,
	test/Makefile.in: New test for atom and bond iterators.

2006-06-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/base.h src/generic.cpp, src/generic.h, src/mol.h,
	src/bond.cpp: Documentation changes, including several from Carsten.

	* src/*.cpp: Remove un-needed header #includes turned up by a
	script adapted from KDE suggested by Carsten.

2006-06-23  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obiter.h, src/obiter.cpp: Add depth-first and breadth-first
	search iterators for atoms through an OBMol. Fixes feature request
	PR#1273213.

	* src/bitvec.h: Minor cleanup of #include paths.

2006-06-22  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/generic.h, src/generic.cpp (OBUnitCell): Add lattice type
	definition, requested by Carsten Niehaus and add GetCellVolume()
	method contributed by Carsten.

	* src/newlinebuf.h, src/newlinebuf.cpp: New "filtering streambuf"
	class to filter line-endings, e.g. \r\n or \r -> \n expected by
	much of the code. Fixes PR#1510008 and goes towards feature
	request PR#1499615. Currently unused until testing is complete.

	* src/Makefile.am, src/Makefile.in: Add newlinebuf.

2006-06-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/mol.h, src/atom.cpp (CountRingBonds): New method to return
	the number of explicit ring connections to an atom.

	* src/parsmart.h, src/parsmart.cpp: Add support for Daylight 'x'
	primitive for total # of ring connections using above method.

	* test/files/smartstest.txt, test/files/smartsresults.txt:
	Test 'x' patterns above.

	* scripts/*: Regenerate to add new OBAtom::CountRingBonds()
	method.

	* src/formats/xyzformat.cpp (WriteMolecule): Only output "Energy" in
	title if it's nonzero. General cleanup.

2006-06-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/smilesformat.cpp: Allow use of H atoms for a root
	atom when used in a cis/trans "/" or "\" specification. Make sure
	to output [H] atoms when in a cis/trans specification. Fixes
	PR#1508783. Fix part of PR#1508741 -- chiral atoms should be fine
	as root nodes (which preserves the ordering).

	* src/parsmart.cpp: Add support for @? matching unspecified chiral
	centers. Fixes PR#1364638. Add support for [H] explicit hydrogen
	atoms, fixing PR#1463791.

2006-06-19  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/files/invalid-smarts.txt: Add invalid ring closure bond
	specifications suggested by Craig in PR#1503849.

	* src/parsmart.cpp: Fix PR#1503849 for invalid SMARTS ring
	closures -- check both beginning and end bond specifications for
	the closure. Uses new function EquivalentBondExpr to test if
	two bond specifications are equivalent.
	Fix part of PR#1506408 for SMARTS matching @ and @@ atom
	specifications.

	* src/formats/smilesformat.cpp: Fix cis/trans problem with
	PR#1506408 -- IsUp/IsDown parsing support in SMILES was
	inconsistent with mol.h and parsmart.cpp. "/" is Up "\" is Down.

	* test/files/smartsresults.txt: Regenerate using above changes.

	* src/kekulize.cpp: Fix PR#1504089 by adding a special case to
	prevent double bonds between aromatic S-S systems, which is
	unneeded to show aromaticity.

	* test/wrapper.sh: Add smilesmatch to list to prevent regression
	on PR#1506408.

	* test/ringtest.cpp, test/smartstest.cpp: Correct minor errors in
	finding filenames and result generation.

	* test/files/nci.smi: Add new test SMILES file.

	* test/smilesmatch.cpp: Use it.

2006-06-15 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/smilesformat.cpp(ParseSmiles): when using 
	extension and bond is doubled, add 
	UnsetImplicitValencePerceived() so that implicit hydrogens are
	recounted.
	
	* src/formats/smilesformat.cpp(GetSmilesElement): ensure explicit
	hydrogens are always written with bracketed atoms (esp when
	charged; [OH3+] was being output incorrectly).
	
	* test/files/FormulaTest.smi: Added. Contains several small
	molecules to test SMILES input, implicit hydrogen detection
	and elemental formula generation. 

2006-06-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/base.h, src/base.cpp: Add "const" qualifiers to
	OBGenericData methods.

	* src/mol.h: Add documentation, including patch contributed by
	Carsten Niehaus.

	* scripts/*/*.cpp: Regenerated using SWIG for above changes.

	* test/invalidsmiles.cpp, test/files/invalid-smiles.txt: New
	test. Check to see that invalid SMILES are properly rejected.

	* test/smilesmatch.cpp: New test. Check to see if SMILES strings
	match themselves using SMARTS.

	* test/Makefile.am, test/Makefile.in, test/wrapper.sh: Add
	invalidsmiles and smilesmatch to test list.

2006-06-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/parsmart.cpp: Completely reject dot-disconnected SMARTS
	e.g. "C.C" which currently are unimplemented and can cause
	crashes, e.g. PR#1505711.

	* src/obutil.cpp (SafeOpen): Make filename arguments "const".

	* test/*.cpp: Update to use new SafeOpen prototypes and remove
	old-style casts to (char*) to remove const.
	
	* test/invalidsmarts.cpp: New test to check that invalid SMARTS
	patterns are properly rejected. Also tries buffer smashing with
	random binary data.

	* test/files/invalid-smarts.txt: Initial set of invalid SMARTS
	which hopefully will tests certain parts of the SMARTS
	parser. Crude start, but more devious patterns to come.

	* test/files/random*: Random binary data for invalid format
	testing and "fuzz" testing.

	* test/formalcharge.cpp: New test to check formal charge
	assignment. Currently does not test, simply generates results for
	debugging.

	* test/files/formalchargeresults.txt: Results from above.
	
	* data/bin2hex.pl: Condense multiple spaces to one. Provides a
	small amount of compression for data headers (about 3K out of
	435K).

	* data/*.h: Rebuild using above.

2006-06-12  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp (BatchFileName): Make sure to properly
	strip off ".gz" extension if zlib compression is enabled. Fixes
	PR#1503596.

	* src/parsmart.cpp: Support for [D], [v], [X] patterns
	(i.e. default values of 1), fixing part of PR#1474716. Support for
	[as] as an aromatic As atom, per SMILES aromaticity for arsenic.
	Support for [se] for aromatic Se atom, per SMILES aromaticity --
	fixes PR#1503851.

	* test/files/smartstest.txt: Add tests for [D], [v], [X], [c],
	[p], [as], [s], and [se] SMARTS patterns as above.

	* test/files/smartsresults.txt: Regenerate after above fixes.

	* test/wrapper.sh: Make sure to pass along command-line arguments
	to "prove" command. Allows "./wrapper.sh -v" for verbose output.

	* src/formats/mdlformat.cpp: Make default molecular dimension to
	be 2D, but check for 3D coordinates too. Many non-standard files
	out there with no real dimension line (e.g. PR#1409133).

	* src/formats/xyzformat.cpp: Smarter handling of
	"energy" tag in title -- if present, remove it from title. If
	mol.GetEnergy() is near zero, don't print it.

	* scripts/openbabel.i: Update from Noel to use
	vector<OBGenericData*> instead of vector<OBGenericData>.

	* scripts/*.cpp: Regenerate using SWIG 1.3.29.

2006-06-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/data.cpp: (Init): Fix problem with parsing data --
	introduced with changes on 05-24. Add null to right char*
	buffer. Fixes PR#1502795.

2006-06-07  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/oberror.h, src/oberror.cpp (GetMessageSummary): Added
	methods to track counts of messages at each level, implementing
	PR#1449517.

	* src/main.cpp: Use it.

	* Makefile.am, Makefile.in: Make sure to eliminate .svn
	directories when running "make dist"

	* test/Makefile.am, test/Makefile.in: Make sure to build "smarts"
	not "smartstest" on platforms without Perl.

	* src/tokenst.cpp: Modified to check buffer and delimiters for
	NULL strings, use default string ctor.

	* src/generic.h (Clone): Change from a pure virtual function to a
	virtual which returns NULL as a default. Allows building script
	wrappers with vector<OBGenericData>.

	* scripts/*: Regenerate to solve compilation problems, addressed
	by generic.h changes above.

2006-06-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/hinformat.cpp (WriteMolecule): Make sure to escape
	molecule titles in double quotes. Fixes PR#1501694.

	* src/formats/xml/cmlformat.cpp (EndElement): Back out yesterday's
	change after discussion with Chris -- would cause problems with
	compound documents with embedded <cml></cml> blocks.

	* test/roundtrip.cpp: Add check for failed OBConversion::Read()
	calls suggested by Chris.

	* src/base.h: Documentation updates for OBGenericData methods to
	address Noel's PR#1484029.

	* scripts/openbabel.i: Added template support for
	vector<OBGeneric> to address iterating through generic data for
	PR#1484029.

	* scripts/*: Regenerate as above.

2006-06-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/rxnformat.cpp (WriteMolecule): Cast size_t to
	unsigned for sprintf statement. Eliminates warning with GCC.

	* src/formats/mpdformat.cpp: Eliminate unsigned/signed warning.

	* src/formats/*format.cpp (more files): Remove calls to sprintf,
	sscanf, strcpy.

	* src/formats/xml/cmlformat.cpp (EndElement): Make sure </cml> tag
	returns false (end of processing).

	* src/residue.cpp: Make sure to call base class in copy
	ctor. Eliminates GCC warning.

	* test/cmltest/test.sh: Skip test if cml cannot be loaded.

	* test/roundtrip.cpp: Fix faulty error problems with
	multi-molecule CML files. Before trying a read at the end of the
	file, make sure to clear molecular information.

2006-06-04 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/xml/xml.cpp(ReadXML): Made so that returns false at
	the end of the file. Solves problem with roundtrip.
	
	* src/formats/mdlformat.cpp(ReadMolecule): Added Trim to new code
	to read multiline properties, because was sometimes confused by
	trailing CRs in Windows.
	
2006-06-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure.in, configure, src/config.h.in: Update to include
	snprintf prototype in all files -- increased use with changing
	sprintf calls to snprintf to minimize buffer overflows.

	* src/math/*: Remove calls to exit(!) on faulty input -- return
	errors and default values.

	* src/formats/*format.cpp (more files): Remove calls to sprintf,
	sscanf, strcpy.

	* test/*.sh: Protect against existing environment variables when
	re-defining. For test calls, we need to ensure only our binaries
	load.

2006-06-02  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/data.cpp (OBElementTable::ParseLine): Change sscanf call to
	use fixed length (256 chars) for name string, rather than
	preprocessor #define BUFF_SIZE.

	* src/formats/xml/xml.cpp, src/formats/xml/xml.h, 
	src/formats/*format.cpp: Remove calls to sprintf, sscanf, strcpy.

	* scripts/*: Regenerate to add Craig's UnsetHash() and
	UnsetWedge() calls.

2006-05-30  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/xml/xml.cpp (ReadXML): Fix PR#1486678 for
	multi-molecule files. The libxml2 library is very unhappy reading
	a file past EOF, so make sure to check the state of the istream
	before reading.

	* test/cmltest/*: Renamed roundtrip.sh script, which
	was a confusing name, to cycleformats.sh.

	* src/formats/pdbformat.cpp: Run PerceiveBondOrders regardless of
	size (most PDB multiple-bonds should be picked up by residue
	information). Fixes PR#1493626.

2006-05-30 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/smilesformat.cpp (ParseSimple): Tidied up code
	to handle extension lc as conjugated double bonds and radical.
	Defer potential double bonds to end of ParseSmiles() when molecule
	complete to ensure not applied to aromatic atoms. PR#1493148
	still ok and extension works again.
	
2006-05-26  Craig James <cjames@emolecules.com>

	* src/mol.h Added UnsetHash() and UnsetWedge() macros.
	
2006-05-26  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp (AddChemObject): Output a warning when a
        format is WRITEONEONLY and more molecules are coming. Fixes
        PR#1473192.

	* src/formats/mdlformat.cpp (ReadMolecule): Make sure to grab all
        lines of potentially multi-line properties. Fixes PR#1489209.
	
	* src/formats/smilesformat.cpp (ParseSimple): Change behavior when
	encountering a bond between two potential radical or aromatic
	atoms. Previously marked bond as double, now mark as 5 -
	potentially aromatic bond. Appears to fix PR#1493148.

	* src/kekulize.cpp (NewPerceiveKekuleBonds): Make sure that
	bestorden is reset when traversing cycle. Previous code would only
	check one atom for adding extra electrons. Appears to fix
	part of PR#1445453.
	(expandcycle): Ensure a bond is in a ring before expanding. Fixes
	part of PR#1445453 for 1-phenyl-1H-pyrrole.

	* test/aromatest.cpp: Make sure to test that all ring bonds are
	aromatic to confirm that above bugs do not come back.

	* test/files/aromatics.smi: Add additional test cases for above
	bugs.

	* test/ringtest.cpp, test/smartstest.cpp: Update so that
	generating results is aware of test directory.

	* test/generate.sh: Shortcut to properly generate test results
	under "make check" conditions.

	* test/files/smartsresults.txt: Update after all of todays changes.

2006-05-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/main.cpp, tools/*.cpp, test/*.cpp: Added USING_DLL
	declarations for WIN32 compiles. Thanks to Noel and Donald Curtis
	for pointing out Cygwin problems.

	* src/Makefile.am, src/Makefile.in: Add missing -no-undefined for
	Cygwin compilation.

	* src/formats/Makefile.am, src/formats/Makefile.in: Add missing
	obmolecformat.cpp for Cygwin compilation.

2006-05-24  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/dlhandler_unix.cpp (findFiles): Fix PR#1493706 problem with
	misplaced NULL terminator.

	* README: Updated to mention 2.1 development.

	* Doxyfile: Make sure to exclude src/GUI/

        * src/patty.cpp, src/typer.cpp, src/rotor.cpp, src/chains.cpp,
        src/parsmart.cpp, src/data.cpp, src/atom.cpp: Updates to fix calls
        to strcpy, replacing some static char* with std::string.

2006-05-23  Craig James <cjames@emolecules.com>

	* src/formats/smilesformat.cpp: Fixed a potential buffer
	overflow when parsing SMILES.

2006-05-21 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/xml/xml.cpp (ReadXML): Output the error 
	message from libxml2 when parser fails. Was previously seen
	in unix builds (for some reason), but not in Windows.
	
2006-05-19 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/xml/xml.cpp, xml.h (ReadStream): Simplify so that
	input chunks up to '>' are taken, rather than trying to get up
	to endtag. Remove gettomatch(). I hope this solves bug #1486678
	and allows roundtrip test to run properly (but not tried). 
	 
2006-05-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/inchi/ : Update with InChI 1.01 pre-release.

	* src/formats/inchi_api.h: Ditto.

2006-05-16 Chris Morley <ob@gaseq.co.uk>

	* src/mol.cpp: Remove BeginModify and EndModify from AddAtom(),
	 NewAtom() and AddBond(). Doesn't seem sensible to call 
	 EndModify() (which calls Kekulize()) before all the molecule
	 is there. The change should speed up conversion of large molecules.
	 This only change for this revison for easy reversion if
	 this is too drastic a change.
	 
2006-05-12  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/patty.cpp, src/kekulize.cpp, src/fingerprint.cpp,
	src/rotor.cpp, src/chains.cpp, src/parsmart.cpp, src/chiral.cpp,
	src/bitvec.cpp, src/main.cpp, src/grid.cpp, src/mol.cpp,
	src/bondtyper.cpp: Update to remove #ifdef for SSTREAM
	(stringstream is ISO C++ and widely accepted). Remove other
	spurious #ifdef's where possible.

2006-05-11  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/cml.sh, test/cmltest/roundtrip.sh, test/cmltest/test.sh:
	Provide more fine-grained test errors and messages.

	* test/roundtrip.cpp: Finding extra molecules in a file should
	exit with an error.

	* src/mol.cpp (GetMolWt, GetExactMass): Simplify and improve
	performance by handling explicit hydrogens like any other explicit
	atom. Functions identically to previous version on regression
	test. Improves performance on isolated protons or bridging hydrogens.

2006-05-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/formula.cpp, test/files/formularesults.txt:
	New test for OBMol::GetFormula(), OBMol::GetMolWt(), and
	OBMol::GetExactMass().

	* src/mol.cpp (GetMolWt, GetExactMass): Fix PR#1485580. Missing
	parentheses in calculating # of implicit + explicit
	hydrogens. Thanks to Noel for suggestion.

	* src/dlhandler_unix.cpp (findFiles): If environment variable
	BABEL_LIBDIR is set, ignore compiled-in default. (User setting
	should always take precedence)

2006-05-09  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/files/: New subdirectory to contain test data files.

	* test/Makefile.am: Update TESTDATADIR accordingly.

	* test/*: Ditto.

2006-05-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure.in, configure, src/config.h.in: Update to include
	#define's for OBERROR, OBFPTR, and OBCOMMON as below.

	* scripts/*: Regenerate using SWIG.

	* test/wrapper.sh: Update to include export for BABEL_DATADIR.

	* test/*: Add many new unit test frameworks (atom, mol, bond,
	conversion, format, etc.)

2006-05-08 Chris Morley <ob@gaseq.co.uk>

	* src/formats/xml/cmlformat.cpp(WriteMolecule): since the id
	must start with letter, add "id" if it doesn't and write a <name>
	element.
	
	* src/generic.h: add virtual GetValue function for OBGenericData
	and also definitions in OBComment and OBPairData. Hopefully will
	solve bug 1483112.
	
	* src/oberror.h: Add default define for OBERROR as nothing
	 
2006-05-07 Chris Morley <ob@gaseq.co.uk>

	* oberror.h: Change classes from OBAPI to new OBERROR
	so that can be compiled separately.
	
	* src/mol.h, src/bitvec.cpp, oberror.cpp, obconversion.cpp:
	change to OBERROR extern OBMessageHandler obErrorLog;
	
	* src/obconversion.h: add #include "oberror.h";
	
	* src/obconversion.cpp: now that oberror can be accessed everywhere
	change all cerr messages to use obErrorLog.
	
	* src/fingerprint.h: replace OBAPI by OBFPTR to allow fingerprint
	code to be separately compiled.
	
	* src/formats/xml.h: add OBCOMMON so that XML classes can be
	separately compiled. Add implementation of SkipObjects for
	XMLBaseFormat and XMLConversion::SkipXML.
	
	* src/formats/obmolecformat.cpp: Add ReadNameIndex to speed access
	in files with many molecules. I wasn't going to commit this until
	it was tested a bit more, but I must have misunderstood what
	Tortoise SVN was doing.
	
	* src/GUI/OBGUI.cpp: don't crash if there are no formats.  

2006-05-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

        * src/formats/smilesformat.cpp (SmiToMol): Since SMILES sets
        formal charges, turn off automatic updates. Some general cleanups
	(removing commented-out code.)

2006-05-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/chains.h, src/chains.cpp: Initial work on	documenting,
	indentation, and general cleanup of chains.cpp.
	(ConstrainBackbone): Check for valence of backbone atoms 
	should actually be for HvyValence() since all hydrogens are ignored.
	Fixes PR#1442779.

2006-04-27  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Doxyfile: Add map of included files in headers to
	documentation. Need to work on removing un-necessary #includes in
	headers.

	* src/math/*: Minimize #include headers.

	* src/generic.h: Include obutil.h for triple class -- was included
	indirectly by way of vector3.h.

	* test/smartstest.cpp: Changed the way tests are counted -- per
	molecule instead of per pattern AND per molecule (cuts drastically
	down on the test overhead). Remove endl and sync with stio to
	improve buffering.

	* test/smartstest.txt, test/smartsresults.txt: Add additional
	SMARTS pattern tests and results.

2006-04-24 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/xml/cmlformat.cpp: Accept coordinate2 and
	coordinate3 elements for CML1.
	Laxer acceptance of atomRef?? which is sometimes misused - but added
	warning. Converted cerr calls to obError.
	Added option to read 2D rather than 3D coordinates.
	Output formula only when no bonds AND no coordinates.
	Ensured atoms from formula marked as having no H.
	GetMolID() gets name or number for error messages.
	
	* src/GUI/OBGUI.cpp: uncommented standard stream redirection.
	Do we need some conditional compilation?
	
	* src/formats.smilesformat.cpp, src/mol.cpp: Recent change in
	ImplictHydrogenCount broke GetMolWt,GetExactMass,GetSpacedformula
	and explicit H form of output in SMILES. But it is better that
	ImplictHydrogenCount means what it says. Added in appropriate form
	of GetExplicitHydrogens to these routines.
	
	* src/formats/xml/xml/cpp(gettomatch): rewrite to allow stream to
	be discarded up to next match.
	
2006-04-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp: Fix broken gzip-decoding of input
	(PR#1473243) introduced by 2006-04-11 change. Fix bug when writing
	multi-molecule files using WriteFile() (PR#1474265).

	* src/atom.cpp, src/residue.cpp: Remove inadvertant debug messages.

2006-04-20 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats.xml/xml.h, src/formats/obmolecformat.h, 
	windows-2005/babelconfig.h: added OBCOMMON macro to aid DLL build.
	(Usually empty).
	
	* src/obconversion.cpp(AddChemObject): prevent formats with 
	WRITEONEONLY from writing more than once.

2006-04-19 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/molecformat.h: added #ifdef _WIN32 around 
	experimental code which cause problems in unix build.

2006-04-16 Chris Morley <ob@gaseq.co.uk>

	* src/transform.cpp, src/main.cpp, src/GUI/OBGUI.cpp: To avoid
	messing up help output revert to original wording of OBMol::
	ClassDescription, and pick out the last word for the conversion
	info message.
	
	* src/GUI/OBGUI.cpp, src/GUI/OBGUI.h: initialize HelpFile in
	current folder at program start.
	
	* src/formats/smilesformat.cpp(CreateSmiString): ensure unbonded [H]
	e.g. from formula, is output.
	
	* src/formats/thermoformat.cpp, src/formats/xml/cmlformat.cpp: 
	ensure formula are read in correctly by adding ForceNoH() and 
	calling Assign SpinMultiplicity	in the right place.

2006-04-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/Makefile.am, test/Makefile.in: Only run CML tests if XML
	formats were compiled. (i.e., if libxml not available, can't test
	CML)
	
	* test/ringtest.sh, test/smartstest.sh, test/cmltest/test.sh:
	Minor shell script portability fixes.

2006-04-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/perl/META.yml, scripts/python/setup.py: Packaging
	changes for the scripting wrappers.
	
	* src/formats/mdlformat.cpp: Remove inadvertent debug statement
	left from yesterday.

2006-04-12  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/mdlformat.cpp (ReadMolecule): Add support for atom
	stereo in v2000 format and OBChiralData. Partly addresses
	PR#1463796.

	* src/formats/smilesformat.cpp (GetChiralStereo): If we have a 2D
	molecule and stereochemistry is unspecified, don't assume we have
	a particular stereochemistry. Partly address PR#1463796.
	Also fix a problem with writing chiral "H" designations with explicit
	hydrogens, introduced with yesterday's fix to
	OBAtom::ImplicitHydrogenCount.

2006-04-11  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.h, src/obconversion.cpp: Added a test to be
	sure that we do not check gzip encoding multiple times (much less
	try to gzip repeatedly). Fix PR#1465586 where ReadString() or
	ReadFile() followed by Read() will fail because input streams are
	closed prematurely.

	* src/atom.cpp (ImplicitHydrogenCount): Fix a bug where formulas
	were calculated incorrectly -- explicit hydrogens should count
	against an implicit hydrogen count too. Fixes part of PR#1463787.
	(i.e., SMARTS 'h' token was matching total number of hydrogens)

	* src/mol.cpp (AddBond): Fix a bug exposed by PDB parsing, where
	code attempts to add a bond from one atom to itself.

	* src/formats/mol2format.cpp: Fix residue parsing to remove
	calls to create a residue when in fact, the molecule has no residues.

	* src/formats/pdbformat.cpp: Fix CONECT record parsing to read
	malformed records (e.g., created by very old Open Babel versions)
	via splitting by spaces. Fixes PR#1468802.

	* src/parsmart.cpp: Reformat indentation for clearer code
	reading. Fix bug with syntax of 'H' token -- should refer to the
	*total* number of hydrogens. PR#1463787.

	* test/smartsresults.txt: Regenerate after above bug-fixes.

	* src/formats/crkformat.cpp (ReadCRK): Change to correctly read
	multi-molecule files, where the </Structure2D> tag would appear,
	but parsing would continue, uncovered using roundtrip testing.

2006-04-08  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* scripts/openbabel.i, scripts/*: Update to add Cygwin DLL headers.

	* THANKS: Update with contributors to 2.0.1 release.

2006-04-06  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/dlhandler_unix.cpp: Upgrade to use the opendir/readdir
	replacement for the non-portable scandir contributed by Mikael
	Johansson.

	* src/formats/Makefile.am, src/formats/Makefile.in: Fix error in
	logic with building inchi, introduced yesterday. D'oh!

	* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
	Add --no-undefined flag to produce proper compilation on Windows
	(i.e., Cygwin).

2006-04-05  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* NEWS: Update for 2.0.1 release notes.

	* configure, configure.in, acinclude.m4: Add new configure options
	for silent libtool use & compiler flags.

	* scripts/Makefile.am, scripts/Makefile.in: Provide better
	"distclean" target to remove python build targets and backup
	files.

	* src/mol.h: Update IsRotor() and NumRotors() documentation to
	explain the current minimal definition of a rotatable
	bond. Addresses PR#1463505.

	* src/oberror.cpp: By default, retain a maximum of the 100 most
	recent entries in the error log in memory. All errors will be
	filtered and sent to output, but only retain some (not all). Fixes
	PR#1439893.

	* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
	Only install the inchi_api.h header.

	* src/formats/xml/Makefile.am, src/formats/xml/Makefile.in: Turn
	off optimization -- appears to fix crashes on FC4 and FC5,
	PR#1447233.

	* src/formats/xml/xml.h: Add std:: namespace declarations, solving
	compilation problems on some GCC compiler versions.

	* src/formats/Makefile.am, */Makefile.in: Changes to only build
	libinchi when the library is not available on the system. Fixes
	PR#146451.

2006-03-28  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* test/aromatest.cpp: New test to check aromaticity. When supplied
	with a test file, it checks to be sure all non-hydrogen atoms are
	aromatic.

	* scripts/*: Update scripting wrappers with SWIG 1.3.29.

	* src/Makefile.am, src/Makefile.in : Add @LIBDL@ as
	suggested by Michael Shigorin (PR#1458706). Make sure
	babelconfig.h isn't included in dist tarball, as suggested by
	Michael Banck.

2006-03-27  Michael Banck  <mbanck@gmx.net>

	* src/fingerprint.h: Fix compilation error with gcc-4.1.
	  Patch by <vlaaad@users.sourceforge.net>.
	* src/formats/copyformat.cpp: Likewise.
	* src/formats/crkformat.cpp: Likewise.
	* src/formats/xml/cmlreactlformat.cpp: Likewise.
	* src/formats/xml/xml.h: Likewise.
	* src/formats/xml/xmlformat.cpp: Likewise.

	* src/formats/fastaformat.cpp: Include babelconfig.h.

	* src/rand.cpp: Include <time.h> and <sys/time.h>.

2006-03-18 Chris Morley <ob@gaseq.co.uk>
	
	* src/obconversion.cpp, obconversion.h,
	src/formats/molecformat.cpp, src/formats/rxnformat.cpp:
	The ability to stop conversion on a write error has somehow
	been removed. Restored this by changing the return of 
	AddChemObject()	to a bool indicating any failure of 
	WriteChemObject(). I don't expect that many people are
	programming at this depth for this change to matter.
	
	* src/mol.cpp(AddHydrogens): Do not add hydrogens
	when to a molecule which has no bonds and more than one atom. We
	do need a review to clarify these functions, but they are generally
	working ok. 
	
	* src/data.cpp, data.h: Added a global function OpenDatafile which
	looks in the normal places for data files. It also starts in the
	current directory. If this is acceptable, it could be used to collect
	the code for this functionality in one place. 
	
	* src/formats/xml/xml.h: added std:: to a string
	
	* src/GUI/OBGUI.cpp:Added warning when output extensions mixed.
	
	* src/GUI/optswx.cpp: Be less restrictive with punctuation in options.
	
	* src/formats/inchiformat.cpp: Now calculates InChI for C and CH.
	
	* src/formats/thermoformat.cpp: minor parsing corrections

2006-03-16 Chris Morley <ob@gaseq.co.uk>

	* data/atomtyp.txt: IMPVAL for halogen ions
	
	* /src/formats/smilesformat.cpp(ParseComplex): Move hcount test
	back again so that [C] is read as C not CH4
	(GetSmilesElement): Restrict addition of implicit H by
	resurrecting normalValence variable. Output [C], not [CH0].

2006-03-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/xml/xml.h: Fix std:: namespace decl for type_info.

	* src/Makefile.am: Temporarily disable compilation of src/GUI
	until compile errors are all fixed.

	* scripts/* : More changes to allow building, linking, and running
	(again!) with current CVS tree.

	* src/generic.h (OBTorsion): Add default code for SetData(OBBond*)
	-- not sure what this *should* do. Allows compilation of script
	wrappers.

	* src/obutil.h, src/math/matrix3x3.h, src/math/vector3.h: Add
	#ifndef SWIG portions to prevent SWIG from choking on some
	non-class function declarations.

	* */Makefile.in: Regenerate (get rid of bogus --gnu flags).

2006-03-14 Chris Morley <ob@gaseq.co.uk>

	* src/GUI/OBGUI.cpp(Expand): Mods to avoid errors when filenames
	are empty, have trailing paces, semicolons, etc.
	
	* src/formats/obmolecformat.cpp, obmolecformat.h: Deferred 
	molecule routines (-C -j options) rewritten to ensure no memory leaks
	under normal or error conditions. (Previously rather carelessly
	written, I'm afraid.)
	
	* src/formats/smilesformat.cpp: Corrected [CH0] extension on
	input and made work on output.
	 
	* src/formats/thermoformat.cpp: Added SetDimension(0). Initialise
	MidT. Added tdd extension.
	
	* src/mol.h: Comments on OBMol copy ctor and assignment saying
	that OBGenericData is copied and on operator+= that it is not.

	* src/base.h, kinetics.h: Mods consequent on OBGenericData changes 

2006-03-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

        * configure.in, configure, src/Makefile.am, src/config.h.in: Add
	initial support for DLL builds on Cygwin. Seems to compile a
        libopenbabel.dll, but still linking problems for
        babel.exe.
	Also add support for detecting wx widget library to build src/GUI.

	* */Makefile.in: Regenerated using automake.

	* src/GUI/OBGUI.cpp: First pass at removing compilation warnings
	with GCC -- make sure all functions are passed correctly.

	* src/GUI/stdwx.h: Use a new babel.xpm if needed (e.g., Mac, UNIX).
	
	* src/formats/xml/cmlreactlformat.cpp: Add back missing
	reaction.h.

        * src/fingerprint.h, src/formats/xml/xml.h: Change static
	declarations to avoid spurious memory leak warnings with
	valgrind.

	* src/base.h: Add #ifdef to remove non-implemented iterators for
	SWIG.
	
        * scripts/*: Build updates for Perl and Python wrappers.
	
	* test/roundtrip.cpp: Update to remove spurious warnings with CML
	(and other) format translation.

	* test/smartsresults.txt: Update to reflect recent SMARTS updates.

2006-03-13 Chris Morley <ob@gaseq.co.uk>

	* src/mol.cpp(GetSpacedFormula): I like the approach added by
	Craig to be independent of implicit/explicit H without
	changing the OBMol. But needs some mods.
	Remove call to	ExplicitHydrogenCount(); they are already
	included in ImplicitHydrogenCount(). Add test to correctly
	handle molecules with no bonds,	hydrogen isotopes. Works with
	SMILES C C[2H] C[H] (=carbene) [H][H] [2H][H] 
	Added support for D and T.
	
	* src/mol.cpp(GetMolWt and GetExactMass): Mods similar to above
	so that implicit or explicit H is handled.
	
	* src/atom.cpp, atom.h(ExplicitHydrogenCount): Add extra parameter
	to not count D and T. (Backward compatible) 
	
	* src/mol.cpp(AssignSpinMultiplicity): Exclude D and T so that
	SMILES CC[2H] is interpreted as C2H5D. Previously was CH3CH:
	
	* src.formats/smilesformat.cpp(OBMol2Smi::GetSmilesElement):
	Reduce implicit H count by number of explicit H isotopes, which
	already were output explicitly. CC[2H]=> add Hs => [CH3][CH2][2H]
	(ParseComplex): [CH0] means explicitly there are no hydrogens.
	
	* src/mol.h, atom.cpp: Added flag on OBAtom to indicate there 
	are no hydrogens. Added get and set methods.
	
	
	* src/atom.cpp(ImplicitHydrogenCount), src/mol.cpp(AddHydrogens):
	Add support for SpinMultiplicity>=4. As in molecule CH - the source
	of ions	in a flame ionization detector.
	
	* src/mol.cpp(AssignSpinMultiplicity): Use positively set no Hs to
	allow SMILES [CH0] = C atom.
	 
	* src/rotamer.cpp(PackCoodinates,UnpackCoordinates): Make cf double
	rather than float to avoid compiler warnings.
	
	* src/transform.cpp: Added --addformula option.
	
	* src/mol.cpp:(operator=): OBGenericData objects now copied with 
	OBMol.
	
	* src/generic.cpp, generic.h: Clone function given parameter
	referring to new molecule, so that OBAtom pointers can be rebased.
	Added documentation that using atom and bond pointer in
	OBGenericData objects is a bad idea.
	
	* src/rotamer.cpp, rotamer.h): Moved code for copying 
	OBRotatmeterData into Clone(). Significant rewriting required;
	not tested yet.
	
	* src/formats/obmolecformat.cpp(MakeCombinedMolecule): simplify code
	because of GetFormula changes (don't need to make copy to compare
	formulae) and OBMol copying changes.
	
	* src/GUI: Small bug when selected format begins with t now corrected.
		
2006-03-10 Chris Morley <ob@gaseq.co.uk>
	
	* src/formats/smilesformat.cpp: make a default format so that
	the default object is OBMol even when MOLformat (the other default
	format) is not present.
	
	* src/formats/smilesformat.cpp(ParseRingBond): prevented crash
	and give error message when parse failure (e.g. a line starting
	with a number) - common and of long standing.
	
	* src/formats/obmolecformat.cpp(ReadChemObjImpl): another delete
	for OBMol object when ReadMolecule returns false;    
	
2006-03-09 Chris Morley <ob@gaseq.co.uk>

	* src/reaction.h, src/format.rxnformat.cpp: revert to previous
	versions, rxnformat.cpp from OB2.0.0. The boost dependent versions
	were committed in error -  work in progress on new some new
	reaction formats.
	
	* several formats, mainly output formats, converted to derive from
	OBMoleculeFormat and their WriteChemObject functions deleted. I
	don't think these were responsible for memory leaks, but it the
	less code to maintain the better.
	
	* src/formats/obmolecformat.cpp(WriteChemObjectImpl): OBMol
	object not being deleted in the event of an error. Moved delete
	statement so that it is.
	
	* src/transform.cpp(DoTransformations): ensure OBMol deleted
	in the event of an error.
	
	* src/GUI/OBGUI.cpp: #include selformats.h: make lc 
	
2006-03-09 Chris Morley <ob@gaseq.co.uk>

	* src/bitvec.cpp, bond.cpp, bondtyper.cpp, chains.cpp,chiral.cpp,
	generic.cpp,grid.cpp,kekulize.cpp,matrix.cpp,
	mol.cpp,molchg.cpp,obiter.cpp,patty.cpp,phmodel.cpp,
	rand.cpp,ring.cpp,rotamer.cpp,	rotor.cpp,tokenst.cpp,transform.cpp
	/src/formats/ most cpp files
	/src/formats/xml/pubchem.cpp
	/src/fingerprints/finger2.cpp, finger3.cpp 
	/src/math/matrix.cpp, vector.cpp
	Add #include "babelconfig.h" at top of files. This eases my use
	of pre-compiled headers and I thought (wrongly) that it would
	assist memory in leak detection. Many cpp files already have this
	header directly rather than relying on it through mol.h.
	Not a very useful exercise, but I hope harmless.
	
	* src/obconversion.cpp(FullConvert): Added extra test to remove an
	extraneous error message under some circumatances. The bug was
	introduced in when facility to use the same file for input and
	output was added.
	Reversed the memory leak related change of 2006-03-02 (see devel
	forum discussion).
	
	* src/formats/xml/xml.cpp(ReadXML):Add continue shortcut for nodes
	that are not elements. (SetUpWriter): remove extra writer creation.
	
	* src/dhandler_win32.cpp(findFiles): Rewritten, now handles * and *.*
	Was getting confused by . and .. directories.
	
	* src/mol.h Remove unnecessary #include "reaction.h"
	
	Added /src/GUI for OpenbabelGUI source files. Put here because
	it is now potentially cross-platform.
	
2006-03-02 Craig James <cjames@emolecules.com>

	* src/bitvec.cpp, src/bitvec.h: Added new operator<(bv1, bv2) that
	returns true if the bits in bv1 are a subset of the bits in bv2.

	* src/dlhandler_unix.cpp (findFiles): Fixed a memory leak.  The
	code to free the memory was there but had been commented out.

	* src/mol.h, src/mol.cpp: Added functions UnsetUp(), UnsetDown().
	Modified SetUp() and SetDown() to also invoke UnsetUp() and
	UnsetDown(), respectively, so that both up and down flags aren't
	set simultaneously.  Changed UnsetAromatic() to use UnsetFlag().

	* src/mol.cpp (GetSpacedFormula, GetFormula): Molecular Formula
	was counting only explicit hydrogens, e.g. might report C20H2.
	Changed to report the total (implicit plus explicit) hydrogen
	count so that Molecular Formula is correct.

	* src/obconversion.cpp (OptionParamArray): Fixed memory leak.

	* src/formats/mdlformat.cpp (ReadMolecule): Fixed reference to
	uninitialized memory that caused random behavior.  Reformatted
	file to correct indenting problems.

	* src/math/vector3.cpp (Comments only): Added comments to
	CalcTorsionAngle() explaining how it works.
	
2006-03-01  Geoffrey Hutchison  <babel@geoffhutchison.net>

 	* src/obconversion.cpp (ReadFile): Fix bug PR#1435777 for crash
	when calling when only the input format was set -- code mistakenly
	referenced pOutFormat.

	* src/parsmart.h: Add #ifndef SWIG to prevent wrapping internal
	struct's used to form the Pattern type.

	* src/formats/mdlformat.cpp: Use old-style Trim() syntax to
	prevent backwards-incompatibility. Remove final " 0" for REGNO from
	v3000 COUNTS line. Fixes PR#1439475, as susggested by Ernst-Georg.

	* test/smartsresults.txt: Update to match previous atom type changes.

2006-02-22  Geoffrey Hutchison  <babel@geoffhutchison.net>

        * src/data.cpp (AssignBonds): Make sure that OBResidueData calls
	Init() before starting and some minor cleanups to atom type
	assignment, exposed by comparing PDB->Mol2 files from Babel and
	Sybyl. Thanks to Kevin Parkes for the example file.

	* src/formats/mol2format.cpp (WriteMolecule): Add back atom names
	from residues, add a residue number to each residue name (e.g.,
	THR1 vs. THR). Should better match mol2 files from Sybyl.

	* data/atomtyp.txt; Add an implicit valence rule for phosphates to
	fix PR#1403974.

2006-02-22 Chris Morley <ob@gaseq.co.uk>

	* src/formats/mdlformat.cpp: Mod to read files with no M END.
	Bug found by Hassan Mamdani.

2006-02-20 Chris Morley <ob@gaseq.co.uk>

	* src/obconversion.cpp(Description): Make dependent on HAVE_LIBZ.
	
	* src/parsmart.cpp: Rename STRICT to OB_PARSMART_STRICT because of
	conflict in VC8. Not used anyway.
	
	* src.typer.cpp(OBAromaticTyper::ParseLine): Ignore blank lines
	to avoid error messages.
	
	* src/formats/mdlformat.cpp: Add Trim() after a getline() to remove
	erroneous CRs when Windows binary mode used. Add m option to 
	Description.
	
	* src/xml/cmlformat.cpp(WriteFormula): Pass copy of OBMol so that
	can add implicit hydrogen when molecule is an atom.
	As suggested by Tappani Kinnunen:
	Added test for NULL pointer in reading Nasa_OldThermo;
	deleted erroneous xmlTextWriterStartElementNS(); but
	have not yet added empty dictRef attribute to property
	(needs more consideration).
	
	* src/format/xml/xml.cpp(ReadXML):Skip over non-elements.

2006-02-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/parsmart.cpp (ParseComplexAtomPrimitive): Fix PR#1364604 for
	no default value for "X" primative (should default to one
	connection if no number is specified).

	* ChangeLog.1.x: New file, contains changes for 1.x releases.

	* Doxyfile: Update to allow 2.1 documentation generation.

	* configure, configure.in, Makefile.*: Update to test for Perl and
	"prove" used for new test harness.

	* test/*: New test "harness" using Perl, if available to provide
	summary output. Yields much better summary information and sets
	BABEL_LIBDIR as needed to prevent user problems with the 2.0.0 release.

2006-02-19  Geoffrey Hutchison  <babel@geoffhutchison.net>

        * src/formats/pdbformat.cpp: Fix PR#1368851 for PDB export with
        large coordinates. Optionally shifts coordinates if needed.

        * src/mol.h: Fix PR#1373650 -- return NULL if no coordinate array
        is available. Prevents segfault.

        * src/atom.cpp (GetResidue): Make sure to return NULL if chains
        perception fails.

        * src/chains.cpp: If only one residue is found, and it's UNK, it's
        probably not a residue, so nuke it. 

        * src/formats/mol2format.cpp: Combined with two above fixes,
        ensure atom labels are printed correctly for mol2 files. All three
        fix PR#1371789.

        * src/obconversion.cpp: Update documentation to point out
        workaround for PR#1368969 with static members of OBConversion --
        declare dummy variable to make sure LoadFormatFiles() has been called.

	* tools/obxyz.cpp: New program to allow cartesian transformations
	(translations, rotations).

2006-02-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* residue.h, residue.cpp: Move residue property definitions into
	new header to support biomolecule formats.

	* src/formats/fastaformat.cpp: New format, contributed by Sangwoo
	Shim. Resolves format request PR#902406.

	* src/formats/mdlformat.cpp: Fix possible memory leak
	with comment data and ensure comment is stored properly.
	
	* src/math/matrix3x3.cpp, src/math/matrix3x3.h,
	src/math/vector3.cpp: Fix documentation errors.

	* src/obconversion.h, src/obconversion.cpp: Add option to
	WriteString to omit any trailing whitespace. Resolves PR#1396953.

2006-01-25  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/zipstreamimpl.h (overflow): Patch calls to setp as
	suggested by Rathann Mierzejewski.

	* scripts/perl/* : Added more unit tests, fixed bug with
	case-sensitive filesystems, and problems with dynamic loading on
	Linux. 

	* scripts/python/*: Updated to fix problem with dynamic loading on
	Linux.

	* aclocal.m4, configure, configure.in, ltmain.sh, */Makefile.in
	*/Makefile.am: Update to libtool-1.5.22 and ensure libxml2 is only
	used if v2.6.5 or later.

	* src/kinetics.h: Move from src/formats/xml/ for general utility.

	* src/formats/xml/xcmlformat.cpp: Remove deprecated file.

2005-12-22 Chris Morley <ob@gaseq.co.uk>

	* src/main.cpp (main): removed unsigned from pos to correct bug
	found by Mikael Johansson.

	* src/formats/turbomole.cpp: Updates by Mikael Johansson.
 
2005-12-19 Chris Morley <ob@gaseq.co.uk>

	* src/molecformat.h, molecformat.cpp: Put most of code into static
	functions which can be called from elsewhere.
	Changed implementation of the -j option so that combining is done by
	+= of OBMol so that useable with any format.
	
	* src/formats/xml/xml.h(XMLMoleculeFormat): Reduced code duplication
	by calling static OBMoleculeFormat functions.
	
	* src/mol.cpp(operator+=): Combined molecule has a dimension equal
	to the smallest of its constituents.
	
	* src/chiral.h: added missing std:: and #include <vector>

2005-12-18 Chris Morley <ob@gaseq.co.uk>

	* src/obconversion.h, obconversion.cpp (IsFirstInput())mod.
	(OneObjectOnly) Added inverse call.
	(Convert) Call WriteChemObject only at end with C option
	(FullConvert) Can now have input and output files the same
	#define ZEROATOMSOK

	* src/generic.h, src/mol.h, tokenst.cpp(Trim): Now returns a reference 
	to the string	to make it easier to use, esp in function parameters.
	
	* src/generic.h: OBGenericData and derived classes: OBCommentData,
	OBExternalBond,	OBPairData,OBVirtualBond,OBRingData,OBUnitCell,
	OBConformerData,OBSymmetryData,OBTorsionData,OBAngleData,OBChiralData,
	OBSerialNums added virtual Clone() method to	allow copying given a 
	polymorphic	OBGenericData pointer.
	
	* src/rotameter.h:	ditto OBRotameterData
	
	* src/residue.cpp: Commented out OBGenericData methods in OBResidue
	and deletion of objects in destructor - now in base class.
	
	* src/mol.h: OBResidue now derived from OBBase; comment out its 
	OBGenericData methods and _vdata. ditto OBAtom, OBBond, OBMol,
	
	* src/mol.h, mol.cpp: I kept needing a more easily parsed
	GetFormula(). Added GetSpacedFormula()and changed the	implementation
	(but not interface) of GetFormula().
	Initialized and copied _dimension in constructors.
	
	* src/parsmart.cpp: changed error message handling.
	
	* src/transform.cpp: Added --title and --property options. Improved
	handling or error conditions while doing options.
	
	* src/main.cpp: Ensure that long options can take more than one
	following text parameter. (Used for --property).
	Make clog message describe the type of object converted, e.g.
	"2 reactions converted" (when reaction.h is updated) Small
	consequent change in help().
	
	* src/formats/APIInterface.cpp, main.cpp: All long options are now
	GENOPTIONS
		  
	* src/obmolecformat.h: Split out implementation into a new
	src/formats/obmolecformat.cpp. Added code for -C option to defer
	output of molecules so that	molecular properties, defined in several
	files can be combined. Move obmolecformat.h to src/formats/ 
	
	* src/formats.mdlformat.cpp: Corrected bug #1370212 with code along
	the lines suggested.
	Attempt to reconcile bug #1368849 and earlier suggestions:
	As before $$$$ is written between molecules but is now written at the
	end only if any properties have been written (sdf) but not if they haven't
	(mol). Add option -xm to not output any properties.
	
	* src/formats/fastsearchformat.cpp: Added -u option for updating index.  
	* src/formats/: add thermoformat.cpp and titleformat.cpp.
	
	* src/formats/xml/xml.h: remove SetFormatting; add missing std::	
	* src/formats/xml/xml.cpp: add option to have no xml formating	

	* src/formats/xml/xcmlformat.cpp: add option to output properties.
	Read and write properties, read and write Nasa thermo data.
	GetSpacedFormula() simplifies cml output!
	Renamed to src/formats/xml/cmlformat.cpp
	
	* src/formats/smilesformat.cpp: reads * as radical centre, as NIST is doing. 
	
	* src/formats/titleformat.cpp added. 	
	
	* src/formats/xml/kinetics.h added, containing OBRateData and 
	OBNasaThermoData classes derived from OBGenericData. 	

2005-11-25  Chris Morley  <c.morley@gaseq.co.uk>

	* src/formats/mdlformat.cpp, rxnformat.cpp: Yesterdays change
	broke rxnformat. Add option to supress $$$$.
	
	* windows/obabel/OBabel.dsp: This config sees fingerprints ok.
	
	* windows/OBRunTime.dsw: rename to OpenBabel.dsw
	
2005-11-24  Chris Morley  <c.morley@gaseq.co.uk>

	* windows-vc2005: upadtae files but struggling with wrong tags
	on some files. Renamed as OpenBabel.sln
	
	* src/INSTALL.WINDOWS: removed. (First draft 2004 by PMR)
	
	* src/README: removed. (about 2003 oblib)

2005-11-23  Chris Morley  <c.morley@gaseq.co.uk>
	
		* src/fingerprint.h, fingerprint.cpp: rearrange so that FptIndex
	has member functions.
	 
	* src/formats/fastsearchformat.cpp: Add -xu option to update
	index.

	* src/parsmart.cpp(SMARTSError): Error messages were being
	writen by fprintf(stderr... and stdout. This made no difference
	on console output but was not being picked up by the Windows GUI.
	Changed to obErrorLog style.
	
	* src/chains.cpp(GenerateByteCodes): Changed error messages to
	obErrorLog style.
	
	* zipstreamimpl.h(flush):Added test for NULL ostream, which had
	been causing crashes (in Windows).
	
	* kekulize.cpp: L152 bestorden was not being initialized (my new
	debugger tells me) and the code was testing it. Moved the line 
	bestorden=99 to before the while loop. Not extensively tested but
	seems to give the same as before for a few molecules. 
	
	* src/obconversion.cpp(Write): Added conditional compilation to
	remove zipstream call in Windows. Started crashing with 
	---errorlevel. A kludge until we sort out	the Windows compression
	problems. Two other similar calls in obconversion are still there...
	
	* src/obconversion.cpp(FullConvert): Added SetInStream and changed
	the names of pInStream and pOutStream which were stupidly
	given names which are also member variables! It's a bit late to
	be altering core code like this but splitting, aggregation,
	batch and normal all seem ok on Windows.
	
	* src/finger3.cpp: Change name of FP3 file.
	
	* data/SMARTS_InteLigand_051110.txt: replaced by 
	SMARTS_InteLigand.txt
	
	*src/formats/mdlformat.cpp: Writes $$$$ for every molecule to
	resolve bug #1362781
		 
	* INSTALL.windows: rewritten

	windows-vc2005: Add DLL projects and update.
	
2005-11-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/mdlformat.cpp: Correctly handle unspecified chiral
	centers (CFG=3), fixes PR#1324929.

2005-11-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Makefile.am, Makefile.in: Make sure INSTALL.Windows is included
	in dist.

	* doc/babel.1: Update with recent format additions.

	* src/formats/amberformat.cpp, src/formats/balstformat.cpp,
	src/formats/smilesformat.cpp, src/formats/turbomoleformat.cpp:
	Update specification URLs.

2005-11-16  Chris Morley  <c.morley@gaseq.co.uk>
	
	* src/obconversion.cpp(Convert): m_IsLast set more definitely
	as part of solution to bug #1357957.
	(FullConvert) Extra gzip code to solve bug #1357705.
	[Windows builds are now reading gzip ok but not always writing it
	properly.]

	src/formats/fastsearchformat.cpp: Extra lines withconditional
	SetMoreFilesToCome to solve bug #1357957. [There may possibly be
	a gzip incompatibility here as well].
	
	* src/fingerprint.h, src/fingerprint.cpp, 
	src/fingerprints/finger2.cpp, src/fingerprints/finger3.cpp:
	Make bitsperint a private variable and provide a Get(). Not
	worth doing - the bug was a missing USING_DYNAMIC_LIBS in 
	the settings for OBExtraFormats project.
	
	Windows build files.  

2005-11-15  Chris Morley  <c.morley@gaseq.co.uk>
	
	* src/obconversion.cpp: remove #include <dflcn.h>

	* windows/OBGUIDlg.cpp (OnInitDialog): add dummy OBConversion
	object to load format files.

2005-11-15  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Makefile.am, Makefile.in: Remove non-functional b32.mak file
	from distribution.

	* NEWS, THANKS: Further updates for 2.0 release.

	* data/types.h, data/types.txt: Added PCM atom types.

	* doc/Makefile.am, doc/Makefile.in: Removed defunct Migration.html
	(from OELib).

	* doc/FAQ.html, doc/OBTwoMigration.html, scripts/python/Examples.html:
	Updated documentation (from the new website).

	* src/formats/pcmodelformat.cpp: Initial support for PCModel
	files. Possibly does not include all atom types, but does read all
	the initial files I threw at it.

	* src/formats/Makefile.am, src/formats/Makefile.in: Compile it.

	* src/formats/freefracformat.cpp: Add support for reading files
	with atomic symbol in 4th column, rather than first (i.e.,
	PCModel-style "free form fractional").

2005-11-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/atomtyp.h: Updated with Chris's recent changes.

	* data/Makefile.am, data/Makefile.in: Add Christian's data file.

	* scripts/perl/Makefile.PL, scripts/python/setup.py: Bump version
	number for 1.0 release.

	* src/obconversion.cpp: Patch from Jean Brefort to ensure dynamic
	loading of modules occurs correctly on UNIX.

	* src/fingerprints/finger3.cpp: Update to also check versioned
	directories. Fixes bug reported by Chris Swain.

	* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
	Fix capitalization errors pointed out by Jean Brefort.

	* src/formats/xyzformat.cpp, src/formats/freefractformat.cpp: Add
	specification URLs to point to Open Babel website. New format
	database will give information on what OB reads/writes.

	* src/formats/gaussformat.cpp: Fix error uncovered in roundtrip
	test with graphite & 2D translation vectors. TV are reported as
	atomic number -2.

	* test/Makefile.am, test/Makefile.in: Clean-up of Makefile.am.

	* tools/obdoc.cpp: Fix HTML -- there was a trailing </h2> tag.

2005-11-12  Chris Morley  <c.morley@gaseq.co.uk>

	* src/finger3.cpp: reads two formats of patterns file. Added FP4
	with patterns in...

	* data/SMARTS_InteLigand_051110.txt: from Christian Laggner with
	extra LGPL line.

	* data/patterns.txt: Added extra firstline to identify format.

	* data/atomtyp.txt: Added additional IMPVAL lines for
	atoms of F Cl Br I P S to allow implicit hydrogens(e.g.in SMILES)
	and improve the reversibility of add/remove hydrogens. Needs to be
	put into equiv .h file.
	 
	* src/formats/xml/xcmlformat.cpp: Now writes correct namespace uri
	for CML1. Test for no bonds (for outputting a formula instead)
	now made before removing hydrogens.

	* src/formats/xml/xcmlformat.cpp, xml.h: Mods to allow nested
	molecules.

	* src/formats/xml/xml.cpp: XML programming notes added.

	* src/formats/xml/xmlformat.cpp, xml.cpp, xml.h: files can now
	contain objects of different types, e.g. molecules in cml and pubchem
	
	* test-set/others/: added some cml files    

	* src/obconversion.cpp: minor changes to comments
	
	Update Windows build files

2005-11-10  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/bgfformat.cpp (ReadMolecule): Fix problem with atom
	type translation uncovered during roundtrip testing -- atom type
	was "cleaned" before assignment.

	* src/formats/Makefile.am, src/formats/Makefile.in: Make sure
	libinchi is correctly linked to inchiformat module.

	* src/formats/PQSformat.cpp, src/formats/fastsearchformat.cpp,
	src/formats/fingerprintformat.cpp, src/formats/inchiformat.cpp,
	src/formats/rxnformat.cpp: Found a few remaining calls to
	cerr. Updated to use OBMessageHandler framework, fixing PR#1281758.

2005-11-09  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Doxyfile: Update version number for 2.0 release.

	* NEWS, THANKS: Updates for 2.0 release.
	
	* data/patterns.txt: Updated with new version from Chris Morley
	with corrected SMARTS patterns.

	* doc/Makefile.am: Remove man.1 pages from target list for now -- new
	versions are much better than doxygen generated versions.

	* doc/api-header.html, doc/api-footer.html: Updated for new
	website template.

	* doc/*.1: Updated man pages by hand.

	* configure, configure.in, src/config.h.in, */Makefile.in: Updated
	to always build InChI now that the IUPAC code is distributed under
	the GNU LGPL.

	* src/formats/Makefile.am, src/formats/Makefile.in,
	src/formats/inchi/*: Ditto.

	* scripts/perl/Makefile.PL: Make sure to include libz in
	compilation.

	* src/bitvec.cpp, src/bondtyper.cpp, src/chains.cpp,
	src/chiral.cpp, src/fingerprint.cpp, src/generic.cpp,
	src/obconversion.cpp, src/patty.cpp, src/resdiue.cpp,
	src/rotor.cpp: src/formats/mdlformat.cpp,
	src/formats/mol2format.cpp, src/formats/smilesformat.cpp:
	Updated to use OBMessageHandler framework for errors rather than
	old ThrowError or cerr directly. Solves PR#1281758.

	* src/parsmart.cpp: Actually implement up & down bond
	primitives. Solves PR#1219329.

	* src/formats/PQSformat.cpp: Remove calls to exit() which should
	never be used in production code.

	* src/formats/balstformat.cpp: Add specification URL.

	* tools/Makefile.am, tools/obdoc.cpp: Add hint for "obdoc" tool
	which creates the file format documentation.

	* tools/obchiral.cpp, tools/obprop.cpp: Add Doxygen man page.

2005-11-01  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/formats/hinformat.cpp: Make sure to mark all aromatic bonds
	as "a" in output. Fixes bug reported by Rajarshi Guha.

2005-10-21  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/atomtyp.txt, data/atomtyp.h, data/types.txt, data/types.h:
	Updated Dreiding atom types, contributed by Menno Deij.

2005-10-20  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Makefile.am, Makefile.in: Make sure both windows and
	windows-vc2005 directories are included.

	* src/data.cpp (OBTypeTableTranslate): Fix possible crashes when
	translating atom types and one or both columns are out of range.

	* src/freefractformat.cpp: Add TrimErrors routine to trim trailing
	standard error notations in numbers. Now properly reads 1.234(56)
	as input.

	* test/ringresults.txt, test/smartsresults.txt: Updated to reflect
	atom typing changes.

2005-10-19  Chris Morley  <c.morley@gaseq.co.uk>

	* src/formats/xcmlformat.cpp: Added reading and writing
	of <crystal> xFract etc.

	* src/formats/freefracformat.cpp: added kludge for
	getline() in Windows(binary mode) possibly returning 0x0d 
	from a blank line.
	Removed two unreferenced variables

	* doc/OBTwoMigration.html: Replace example of Reaction SMILES
	(sadly not yet done) by CMLReact. Couple of typos.

2005-10-18  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* Doxyfile: Updated for new doxygen release (1.4.5).

	* NEWS: Updated with initial release notes for 2.0.

	* configure, configure.in: Fix problems with libz detection.

	* doc/OBTwoMigration.html: Add a draft migration guide, touching
	on four key code updates.

	* doc/*.1: Updated manpages.

	* scripts/*: New versions (1.0.0b5) using SWIG 1.3.27.

	* src/atom.cpp, src/mol.cpp, src/molchrg.cpp: Documentation
	updates (switching to new iterators).

	* src/chains.h, src/chains.cpp: Updates from last OELib GPL
	version, which were not previously incorporated.

2005-10-17  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* COPYING: Updated FSF address.

	* src/formats/Makefile.*: Add new copyformat code.

	* src/atom.cpp, src/base.cpp, src/ring.cpp, src/patty.cpp,
	src/mol.h, src/molchrg.cpp, src/oberror.h, src/oberror.cpp,
	src/obiter.cpp: Documentation updates.

	* src/obconversion.h, src/obmolecformat.h : Revert change of
	std::type_info -- GCC requires the namespace declaration.

2005-10-17  Chris Morley  <c.morley@gaseq.co.uk>
	
	* src/formats/xml/xcmlformat.cpp: Added CML1 writing.
	Corrected bug in writing "x","y" instead of "x2","y3" etc.
	Corrected bug in x and z 3D coords in array mode.  

2005-10-17  Chris Morley  <c.morley@gaseq.co.uk>

	* src/obconversion.h:Replaced std::type_info by type_info
	in preparation for mods to ensure STL/VC6 compatibility.
	I hope it will still compile in unix.

	* src/obconversion.cpp,obconversion.h: Added GetInLen(), wInlen,
	rInlen to provide the length of the object being written.
	This simple operation is irritatingly complex because of object
	queue.

	* src/copyformat.cpp: simple new format which allows chemical
	filtering from a multi-object file with no possibility of losing
	content by OB's conversion, e.g. sdf or xml files.

	* src/formats/exampleformat.cpp: Now a heavily commented
	format template. Maybe should be put in another folder.

	* src/formats/inchiformt.cpp(WriteMolecule): correct bug sometimes
	causing crash when no 0Dstereo info.

	* windows-vc2005: Added project files for Visual C++ 2005

2005-10-14  Geoffrey Hutchison  <ghutchis@Alumina.local>

	* Source-code documentation updates. Ensure all classes and struct
	definitions have at least a brief description.

2005-10-14  Chris Morley  <c.morley@gaseq.co.uk>
	
	Update Windows build files and documentation. Remove unused files.

2005-10-13  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* acinclude.m4: Fix bug in CHECK_ZLIB macro to correctly disable
	zlib support if --without-zlib option is selected.

	* src/data.h, src/typer.h, src/bondtyper.h, src/phmodel.h,
	src/rotor.h: Add a GetSize() method to all OBGlobalDatabase
	classes. Ensures a data table is not empty after calling Init().
	
	* configure.in, configure, src/config.h.in: Update for a 2005-10-15
	snapshot. Require libxml2 >= 2.6.0 (which adds the xmlwriter API).

	* doc/api-header.html, doc/api-style.css: Update with new Doxygen
	version (which adds "tabs" to organize sections).

	* src/Makefile.am, src/Makefile.in: Update to zipstreamimpl.h
	instead of zipstream.cpp.

	* src/zipstream.h: Switch basic_zip_ostream and
	basic_unzip_istream to using public base classes, which works
	around a bug in some versions of GCC.

	* src/formats/xml/Makefile.am, src/formats/xml/Makefile.in: Switch
	from defining LDFLAGS to correct AM_LDFLAGS (which allows the user
	to customize LDFLAGS as desired).

2005-10-11  Chris Morley  <c.morley@gaseq.co.uk>

	* src/obconversion.cpp(FormatFromExt): correct mistake 
	in last mod.
	src/obconversion.h Add explicit copy constructor for 
	OBConversion (just so	pAuxConv is set to NULL).

	* src/generic.cpp, src/chiral.cpp: added return statements 
	etc to avoid compiler warnings.

	* src/data.h: Added OBAPI to class OBResidueData (for DLL builds)

	* src/mol.h, src/formats/pdbformat.h, src/data.cpp: Moved 
	global variable	OBResidueData resdat to data.cpp and
	treat it like other global variables. (This makes DLL builds
	easier.) If its use is specific	to pdb format, perhaps it
	should be a a static variable in PDBFormat?
	
	* windows/babelconfig.h: removed HAVE_LIBZ because in DLL
	builds unzipping code was preventing input of any file. OK
	in OBGUIs where is now defined in Settings.
	
	Updated Windows build files. 

2005-10-09  Chris Morley  <c.morley@gaseq.co.uk>
	
	* src/obconversion.cpp(FormatFromExt): test failure of 
	string::find,	etc by return of string::npos

	* src/obconversion.cpp(SetStartAndEnd):
	If EndNumber < StartNumber output only one object 
	
	* src/mdlformat.cpp(SkipObjects): inverted test for "$$$"
	which was causing -f and -l errors reported by Chris Swain.
	
	* src/formats/inchiformat.cpp: Added 'test' format for
	doing round trip, testing before and after with InChI
	
	* src/zipstreamimpl.h: Name changed from zipstream.cpp 
	
	* src/zipsteam.h: consequent name change of #include
	
2005-10-07  Chris Morley  <c.morley@gaseq.co.uk>

	Update Windows build files.

	* src/chiral.cpp(CalcSignedVolume): change name of second
	loop variable from i to j (VC6 deficiency)

	* src/data.cpp(OBElementTable::ParseLine); make symbol[5]
	[3] wasn't enough. (Better debugger!)

	* src/fingerprint.cpp: remove #if HAVE_CONFIG
		
2005-10-05  Chris Morley  <c.morley@gaseq.co.uk>
	
	* src/zipstream.cpp(add_footer): changed 2nd var n to m to
	accomodate VC6 compiler. (But still not writing properly in VC6)

	* src/obconversion.cpp: moved compression code from Convert()
	to Convert((std::istream* is, std::ostream* os) and restored
	pOutStream after conversion. Also in write();

	*  src/obconversion.cpp (FullConvert): moved call to 
	OneObjectOnly() inside loop in splitting section to cure bug
	#1313201.
	
	* src/formats/fastsearchformat.cpp: Changed Convert() to
	Convert(NULL,NULL) (two places) so that compression code will
	be called.	 

	* src/formats/smilesformat.cpp (SmiToMol): removed call to 
	AddHydrogens().


2005-10-04  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* tools/obgrep.cpp: Fix PR#1286797. Count of matching molecules
	was stored as a char??. Corrected code to store as unsigned int
	and output correctly. Thanks to Chris Swain for the bug report.

	* src/zipstream.h, src/zipstream.cpp: Update to (hopefully) fix
	syntax problems with VC++ experienced by Chris Morley.

	* src/atom.cpp (GetType): Make sure to save and restore
	OBTypeTable patterns -- otherwise higher-level code will see
	unexpected type translations.

	* src/data.h src/data.cpp (OBTypeTable): Set const on parameters
	where needed, add error checking for GetToType and GetFromType()
	methods.

	* src/formats/*.cpp: Add code to move to ifs.eof() after reading
	to ensure the multiple-molecule parsing doesn't attempt to add an
	invalid empty molecule.

	* src/formats/smilesformat.cpp: Add defensive code around chiral
	search code -- ensure all pointers are valid before dereferencing.

	* test/roundtrip.cpp: Ensure the filestream is not at EOF before
	attempting to read another molecule (and complain that a format
	has translated an incorrect number of molecules).

	* tools/README: Remove comments about deprecated obtanimoto program.

2005-10-03  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* configure, configure.in: Fix BUILD_SHARED condition to only
	build dynamic file format modules when shared libraries are also
	enabled.

	* scripts/*: Update SWIG modules using SWIG 1.3.26rc1.

	* src/formats/smilesformat.cpp: By default, add implicit hydrogens
	when reading SMILES files.

	* tools/obprop.cpp: No need to add hydrogens to SMILES files, as
	above.

	* src/formats/carformat.cpp: Modifications to better handle
	multiple-molecule CAR files, as suggested by Jean Dessolin.

	* test/roundtrip.cpp: Refined error messages to report molecule
	number and file number (1 vs. 2).

2005-09-29  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* data/types.h: Updated (as below).

	* src/zipstream.h, src/zipstream.cpp: Updated with cleaned-up
	versions from OpenSG project. Added method to add gzip header
	after creating stream.

	* src/obconversion.cpp: Clean up WriteString() and WriteFile()
	methods to use Write() -- eliminates duplicated code. (Maybe
	Convert should use Read() and Write() similarly.) Now works
	correctly with gzip output.

	* src/dlhandler_unix.cpp: Update to fix crashing bugs with global
	loading of OBConversion::LoadFormatFiles().

	* configure, configure.in, */Makefile.am, */Makefile.in: Update
	for new snapshot, minor fixes for distribution.

	* Doxyfile, src/base.cpp: Update for eventual 2.0.0 release.

2005-09-17  Chris Morley  <c.morley@gaseq.co.uk>

	* src/formats.mpdformat.cpp: Nick England's format for printing
	atom types added  (Slightly modifed option handling.)

	* data/types.txt: Extended. types.h not yet updated.

2005-09-14  Chris Morley  <c.morley@gaseq.co.uk>

	* src/main.cpp(main): line 322 Mods to place * correctly 
	when file name has *.gz

	* src/obconversion.cpp, obconversion.h: Removed dummy
	instance which was causing trouble and called LoadFileFormats()
	from the initialisation of a static variable. Removed call to
	LoadFileFormats in constructor.

	* src/obconversion.cpp: Added -z option and code for zipstream
	output in Convert() and Write(). But ozipstream seems not to be
	working properly at present. 
	Messed around with ReadString()	and ReadFile(). 

2005-09-14  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/obconversion.cpp: Only use dummy instance on WIN32 or when
	not using dynamic modules (e.g., CygWin).

	* src/zipstream.cpp, src/zipstream.h: Changes to compile on
	GCC. (Hopefully it will *still* compile on VC6.)

2005-09-14  Chris Morley  <c.morley@gaseq.co.uk>

	* src/obconversion.h, obconversion.cpp(Read): Make non-templated
	and move to .cpp; Add zipstream code to Read and Convert,
	
	* src/OBConversion.cpp: Add global dummy instance, so that format 
	files are loaded. (A better way to do this needs to be found.)
	
	* src/zipstream h, zipstream.cpp: changed to compile on VC6! 

2005-09-12  Geoffrey Hutchison  <babel@geoffhutchison.net>

	* src/zipstream.h, src/zipstream.cpp: Modified classes (updated to
	compile in GCC) to support gzip/zlib compression streams.

	* configure.in, configure, src/Makefile.am, */Makefile.in: Add
	support for conditional compilation of code depending on zlib. (i.e.,
	zipstream.cpp).

	* src/obconversion.cpp (FormatFromExt): Change to detect .gz
	extension and look for previous extension.

2005-09-11  Geoffrey Hutchison  <babel@geoffhutchison.ne