2002-12-6 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* Doxyfile, README, configure.in, configure: Rename version to
1.100.
* doc/FAQ: Update with a few minor corrections -- synched with
website.
* THANKS: A few omissions -- synched with website.
* src/mdl.cpp, src/smi.cpp: Throw errors if the molecules are too
large, rather than segfault. In MDL, this seems to be a problem
inherent in the file format. For SMI, this seems to be a recursion
problem.
* src/mol.cpp: Take out the "quick-and-dirty" aromatic pass, it's
too rough to be useful. I need to figure out how to pass off the
rough structure to the Kekulize routines.
* src/types.txt, src/types.h: Make sure there's a default type for
an "N" atom, caught by roundtrip testing from PDB files. Fix typo
for O.co2 v. Oco2 external type. Also add XYZ forms for all atoms.
2002-12-5 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* Doxyfile: Update for 1.99.1 release.
* Makefile.in (dist): Make sure to remove autom4te.cache, etc.
* THANKS: Plenty of contributors to this next release!
* configure.in: When searching for the "ar" program, remember that
Solaris has it in /usr/ccs/bin, so we should check there and fall
back to the user's $PATH if it's not found.
* configure: Regeneratre using autoconf-2.56.
* src/mol.h: Add OBAtom::GetAtomicMass(), which will eventually
allow for isotope-labeled atoms.
* src/atom.cpp: Implement it.
* src/mol.cpp (GetMolWt): Write using above.
* src/cml.cpp: For the moment, turn off debugging output. (This
should really go through a filter to allow users to see it if
needed.)
* src/data.cpp (GetAtomicNum): Have D and T atoms return for
hydrogen. Eventually needs to support isotopes!
* src/element.txt, src/element.h: Update with current IUPAC
masses.
* src/extable.txt, src/extable.h: Make sure all extensions are
lowercased--since all comparisons are done this way. Fixes bug
with GROMOS96 translation.
* src/fileformat.h, src/fileformat.cpp (ReadMolecule): Fix thinko
with BGF format--call the proper procedue.
(WriteMolecule): Write Box format with a default size. (!!)
* src/bgf (ReadBGF): Cleanups found from roundtrip testing. Make
sure bond records are parsed correctly and run atom types through
the element table rather than the type table.
(WriteBGF): Change remark to "Open Babel" rather than "Babel" so
people know who created the bugs. ;-)
* src/gromos96.cpp: Use "Open Babel" as above.
* src/pdb.cpp (WriteDelphiPDB, WritePDB): Make sure we have a
proper line length. Bug discovered via roundtrip testing (and our
complaints about short CONECT lines).
* src/povray.cpp: Don't attempt to get a hostname--this introduces
all sorts of portability problems. Also use the atomic symbol
rather than the atom type. Less flexible, but POV-Ray doesn't like
some symbols in atom types (e.g. period in O.co2).
* src/report.cpp: Add report on chiral atoms. (Probably needs some
improvement still.)
* src/types.h, src/types.txt: Add missing types, notably for Ar
and B2, uncovered via roundtrip testing to the c3d file formats.
* src/xed.cpp: Fix segfault caused by improper iteration over
bonds. Uncovered via roundtrip testing.
2002-12-3 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/data.cpp (ParseLine): Fix bug that ignored the first
non-comment line.
2002-12-2 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* Makefile.in, src/Makefile.in, src/math/Makefile.in,
test/Makefile.in: Makefile changes to ensure the src/math
directory is called for all targets (including "clean") and
testing data files are only copied when needed for $(builddir) !=
$(srcdir).
* src/mol.h: Fix typo in OBMol documentation.
* src/mol.cpp: Add quick-and-dirty aromatic marking.
2002-12-1 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/bond.txt: Data file for functional group recognition in bond
order typing (currently unused).
* src/*.txt: Update with headers, including copyright notice.
* src/data.cpp: Ignore comment characters (including copyright
notice).
* src/pdb.cpp: Fix bug with reading in residue data--the source
file is called resdata.txt, not residue.txt.
2002-11-28 Vincent Favre-Nicolin <vincefn@users.sf.net>
* src/obutil.cpp(CartesianToInternal): Fix the conversion
from cartesian to Internal coordinates. The previous code
prevented atom 3 to be bonded with atom 1, and any
atom with idx>3 to be bonded with atom 1 or 2, which does
happen sometimes...
2002-11-27 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/atom.cpp(MemberOfRingSize): New method -- if atom is in a
ring, return size. (Need to fix to designate *which* ring if in
multiple.)
(SetHybAndGeom): Fix to use scaled bondlengths for aromatic,
double and triple bonds and adjust expected bond angles if in a
ring.
* src/mol.cpp: Add << and >> convenience functions based on
OBFileFormat objects.
* src/ghemical.cpp: Fix header line for new "gpr" extension.
* src/povray.cpp: New file, contributed by Steffen Reith to output
POV-Ray scene files.
* src/data.cpp, src/data.h: Add POV file type.
* src/extable.txt, src/extable.h: Likewise.
* src/fileformat.cpp, src/fileformat.h: Likewise:
* src/Makefile.in: Add povray.cpp.
* doc/README.dioxin.pov, doc/README.povray, doc/babel31.inc,
doc/dioxin.mol2, doc/dioxin.pov: New files.
2002-11-25 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/mol.cpp, src/mol.h: Add back << and >> convenience functions
derived from OBFileFormat methods.
(PerceiveBondOrders): Fix bug introduced with previous change--do
not add multiple bonds to an atom already with them. (Causes a
problem with allene, but this is a rarer situation than the
reverse.)
* src/pdb.cpp (WritePDB, WriteDelphiPDB): Fix ATOM records with
correct specification. Should fix problems with 5-digit atom
numbers, PR#633719, reported by Kristian Rother.
2002-11-20 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* configure: Update with new autoconf-2.56
* src/Makefile.in, src/math/Makefile.in, test/Makefile.in: Remove
redundant '/' in path for $(builddir) variable.
* src/data.cpp: Remove references to depreciated strstream.h
header.
* src/data.h: Likewise.
* src/mol.cpp: Add "flat ring" pass for 5-member and 6-member
rings. Ensures that these are all marked as potential sp2
hybrids. Also prevent adding 4 bonds to nitrogen, for now.
* src/extable.txt, src/extable.h: Update with new Ghemical
extension .gpr (same format though).
2002-10-11 Michael Banck <mbanck@gmx.net>
* src/math/Makefile.in: New file.
* configure.in, src/Makefile.in: Adjust accordingly.
2002-09-19 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/aromatic.h, src/aromatic.txt: Remove selenium aromatic
pattern for now. Fixes test/smartstest error on
LABOTEST_LT-2_FE_546.
* src/c3d.cpp, src/chains.cpp, src/cml.cpp, src/data.cpp,
src/jaguar.cpp, src/main.cpp, src/mol.cpp, src/oberror.h,
src/pdb.cpp, src/phmodel.cpp, src/ring.cpp, src/smi.cpp,
src/xyz.cpp, src/math/matrix3x3.cpp, test/matrixtest.cpp,
test/ringtest.cpp, test/smartstest.cpp: Warning fixes contributed
by Erik Kruus.
2002-09-16 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/report.cpp: Fix bug noted by Markku Laukkanen, where the min
variable would roll past the maximum number of atoms in a
molecule.
* src/cml.cpp (debugMolecule): Add default dimension. Contributed
by Francesco Bresciani.
* src/obutil.cpp (InternalToCartesian): If vector input is empty,
quit early. Contributed by Francesco Bresciani.
* src/oberror.h, src/oberror.cpp: Namespace fixes to handle
problems on gcc-3.1 as reported by Austin Acton and Andrea Tasso.
2002-09-07 Michael Banck <mbanck@gmx.net>
* Replaced $DEST with $DESTDIR and $bindir
2002-08-30 Stefan Kebekus <kebekus@users.sourceforge.net>
* src/math/matrix3x3.cpp, src/math/matrix3x3.h added methods, in
particular for eigenvector calculations. Modified the API slightly.
* src/mol.cpp, src/obutil.cpp removed a couple of undocumented
mathematical methods that were never used. Make mol use the
eigenvector functions from the matrix class now.
* test/matrixtest.cpp test suite for matrix algebra and eigenvector
calculations
* src/oberror.cpp, src/oberror.h introduced a generic error class
2002-08-27 Stefan Kebekus <kebekus@users.sourceforge.net>
* test/main.cpp, test/ringtest.cpp, test/smartstest.cpp resolved
namespace problems for the tests. The test compile now, but show
errors.
2002-08-25 Michael Banck <mbanck@gmx.net>
* Changed charge to int (gaussian.cpp) and divisor/exponent to
double (c3d.cpp) in order to compile on g++-3.2
2002-08-19 Stefan Kebekus <kebekus@users.sourceforge.net>
* src/xyz.cpp more bugfixing. The translator behaves now smarter
when interpreting the title and the atom types.
2002-08-16 Stefan Kebekus <kebekus@users.sourceforge.net>
* src/pdb.cpp re-wrote routine to read CONECT records. That
(hopefully) fixes a number of bugs in the earlier version
(inability to read 5-digit serial numbers, accidently reading salt
bridges as connects, etc.)
2002-08-15 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/pdb.cc: Fix ParseConectRecord to make sure we don't read
beyond the vs.size().
2002-08-14 Stefan Kebekus <kebekus@users.sourceforge.net>
* src/xyz.cpp Set molecule title to the string that is read from
the second line of the file. Set atom type strings to strings read
from the file. The reading method now prints +extensive+ and
+detailed+ warnings to cerr if is xyz file is bad.
2002-07-26 Stefan Kebekus <kebekus@users.sourceforge.net>
* src/math/matrix3x3.cpp added a few method useful in symmetry
detection
2002-07-30 Michael Banck <mbanck@gmx.net>
* src/gaussian.cpp: Last atom was written twice
2002-07-26 Stefan Kebekus <kebekus@users.sourceforge.net>
* added documentation
2002-07-24 Michael Banck <mbanck@gmx.net>
* src/gaussian.cpp: Added some comments/warnings; changed multiplicity
calculation to use abs(charge) instead of charge
* src/Makefile.in: splitted CXXFLAGS into CXXFLAGS, DEFS and INCS
2002-07-22 Michael Banck <mbanck@gmx.net>
* src/gaussian.cpp: Fixed WriteGaussianCart() hopefully:
- calculate charge and mulitiplicty (the latter being quite shakey
ATM)
- do away with the zero after the atom type
- don't reference coordinates, write them straight after the atom type
- add a blank line at the end
* configure.in: Added --enable-doxygen configure option. If enabled,
search for doxygen and print an URL if not found
* configure: Updated for new configure.in
2002-07-18 Stefan Kebekus <kebekus@users.sourceforge.net>
* isolated the 3-dimensional vector and matrix classes, gave them
less ambigous names, and put them into a directory "math". Added
an access function to the vector class.
2002-07-12 Stefan Kebekus <kebekus@users.sourceforge.net>
* added documentation to the Vector class, made some functions
inline, and commented out some methods of the vector class
whose names I found misleading, and which were never used anyway.
* src/Vector.cpp, src/Vector.h: added documentation to the Vector
class, made some functions inline, and commented out some methods
of the vector class whose names I found misleading, and which were
never used anyway.
* configure.in: configure now warns if doxygen is not present
* configure: Updated with autoconf 2.52d.
2002-07-09 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/fileformat.h, src/mol.h, src/binary.h: Fix missing std:: in
headers, which causes problems with namespace-compliant
compilers. Should fix PR #578522.
* src/residue.cpp: Add missing "using namespace std," which also
caused problems with namespace-compliant compilers.
* src/pdb.cpp: For now, disable bond order perception--prevents
problems with PDB residues observed by Richard Gillian.
2002-07-01 Richard Gillian <reg8@users.sourceforge.net>
* src/main.cpp: Add -hpH to use the "adjust pH" setting for adding
hydrogens.
* src/mol.cpp: When adding hydrogens, if the parent atom is part
of a residue, copy this information to the new atoms.
* src/mol2.cpp: Write residue types and original atom names for
the atoms if they exist.
2002-07-01 Stefan Kebekus <kebekus@users.sourceforge.net>
* Doxyfile: New file, configuration for Doxygen API documentation.
* configure: Updated with autoconf 2.52d.
* Makefile.in: Added automatic API documentation generation. Use
"make apidoc".
2002-06-29 Vincent Favre-Nicolin <vincefn@users.sourceforge.net>
* src/mol.h: Give sample documentation from the primer for
OBResidue, OBAtom and OBMol.
* src/ring.h: As above for the OBRing class.
2002-06-28 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* configure.in, configure, src/Makefile.in: Adjust for various
removed (unused) files.
* src/fileformat.cpp, src/fileformat.h: Use a const char * title
and declare ReadMolecule and WriteMolecule methods static to allow
calling w/o needing to instantiate a specific OBFileFormat object.
* src/*.cpp: Adjust all ReadFile methods to use const char* title,
as above.
* src/atom.cpp, src/binary.cpp, src/binary.h: Fixes imported from
OELib.
* src/generic.cpp, src/generic.h: Add support for torsion and
angle data and associated handlers for OBGenericData.
* src/main.cpp: Remove obsolete headers.
* src/mol.cpp, src/mol.h: Add OBMol::FindTorsions method to fill
the OBTorsionData in a molecule. Remove the confusing OBPose
class. (Conformers are conformers and not managed by a separate
class.) Remove residue code, which has migrated to residue.cpp.
* src/obutil.cpp: Remove unused code.
* src/pdb.cpp: Add OBSerialNums, imported from OELib.
2002-06-11 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/Makefile.in: Add proper commandline for new bin2hex for
PhModelData. Remove smarts.* from file lists.
* src/Vector.cpp: Import changes contributed by Open
Eye--improvements in random vector and matrix methods.
* src/*.h: Improve top comment to refer to Open Babel and update
copyright dates. Add uniform #ifdef symbols to prevent clashing
with external header files.
* src/alchemy.cpp, src/atom.cpp, src/balst.cpp, src/chains.cpp:
Updates to cut down on buffer overflows, to begin addressing
PR#565413.
* src/data.cpp: Make OBExtensionTable types uniform. Make sure
\0 is inserted in the proper place in the buffer when reading from
the dataptr in OBGlobalDataBase::Init(). Fixes PR#567420.
* src/fileformat.cpp: Use updated io_type declarations.
* src/types.txt: Reformat to remove trailing whitespace and make
spacing uniform. (Attempt to minimize problems with reading using
OBTypeTable.)
* src/obutil.[h,cpp]: Remove SmartsLexReplace, which is now
migrated to parsmart.[h,cpp].
* src/parsmart.[h,cpp]: Updated version from code contributed by
Open Eye. Includes caching and RestrictedMatch method and seems to
solve memory leak problems in older version. Solves PR#536943 and
#564096. Includes code from smarts.* files.
* src/phmodel.cpp: Update to work with new SMARTS parser.
2002-06-07 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* Makefile.in: Make sure directories are properly created on "make
install" which fixes PR#565412.
* src/Makefile.in: Add support for rebuilding the binary data
headers when needed. Also generates library first, then just links
this into main.o for the program. Also as above.
* src/bin2hex.pl: Import a revised version contributed by Open
Eye.
* src/atomtyp.txt, src/extable.txt, src/types.txt: Ditto.
* src/aromatic.h, src/atomtyp.h, src/element.h, src/extable.h,
src/phmodel.h, src/resdata.h, src/types.h: Generate using new
bin2hex.pl.
2002-06-06 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/main.cpp: Add support for -iMIME or -oMIME <mime_type>
input. This should facilitate use for web applications (e.g. as a
pass-through filter to other programs).
* src/data.h, src/data.cpp: Add methods
IsReadable/IsWritable(io_type).
2002-05-30 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/mol.h, src/atom.cpp (HasNonSingleBond): Add new method to
simplify and optimize bond typing code.
* src/mol.cpp (PerceiveBondOrders): Use it.
* src/cml.cpp: Fix problems with arrays of OBAtom* since these
cause casting problems in ISO C++. Still has a number of "missing
return" warnings, though these shouldn't cause problems.
2002-04-23 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/hin.cpp (ReadHIN): Fix bugs in reading HyperChem files as
contributed by Tommi Hassinen.
2002-04-16 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/qchem.cpp: Fix conversion from internal coordinates at the
end of a geometry optimization (silly thinko, forgot to convert
from deg. to rad. for angles).
2002-04-12 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/bin2hex.pl: Set output header files to be "static const
char" instead of plain char. Should prevent some clobbering,
e.g. PR #543314.
* src/aromatic.h, src/atomtyp.h, src/element.h, src/extable.h,
src/phmodeldata.h, src/resdata.h, src/types.h: Generate as above.
* src/aromatic.txt, src/atomtyp.txt, src/phmodel.txt: Change
"OELib" in headers to "Open Babel."
* src/data.h: Make all _dataptr members "const char" and set
ParseLine() methods to operate on const char*.
* src/data.cpp, src/pdb.cpp, src/phmodel.cpp, src/rotor.cpp,
src/typer.cpp: As above.
* src/mol.h: Set tokenize() declarations to operate on const
char*.
* src/tokenst.cpp: As above.
2002-04-05 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/parsmart.cpp: Added some defensive programming when calling
delete, also set the pointer to NULL.
* src/parsmart.h: Add constructor and destructor to
OBSmartsParser.
* src/smarts.h: Add full destructors for OBEdge, OBNode.
* src/smarts.cpp: As above. Should solve memory leaks, PR #508056.
2002-03-30 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/*.h: Update headers to use std:: namespace to refer to
vectors, strings, pairs, streams, etc.
* src/*.cpp: As a first stage in full namespace support, add a
full "using namespace std;" (to be followed eventually with only
importing the necessary namespace portions.
2002-03-27 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/cml.cpp: Fix use of strcmp() in code in favor of strncmp()
to prevent buffer overflow. Fixes problems with 2D/3D export.
2002-03-26 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/cml.cpp: New CML support, including built-in XML parser,
contributed by Peter Murray-Rust.
* src/Makefile.in: Add cml.cpp to list to support CML compilation.
* src/data.h, src/data.cpp: Add CML file type.
* src/extable.txt, src/extable.h: Update to add in .cml files.
* src.fileformat.cpp, src/fileformat.h: Add in support for CML
read/write as well as passing options to WriteMolecule methods.
* src/main.cpp: Add support for passing output options (currently
only XML/CML) to export methods.
* src/aromatic.txt: Enable support for recognizing Se in aromatic
rings. (Uncommon, but I've been doing work with selenophene
recently.)
* src/pdb.cpp (ParseConectRecord): Fix bugs in CONECT records with
PDB files. Would only read first 4 columns and wouldn't handle
multiple bonds. Fixes PR #529744. Use PerceiveBondOrders() when
using ConnectTheDots() for missing bonds.
* src/ghemical.cpp: Add error checking for reading bonds. Don't
assume the # of bonds given in the header is correct.
* src/mol.cpp: Check to see if a bond exists before adding
it. (Prevents a bond addition (a,b) followed by (b,a).)
2002-02-22 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/Makefile.in: Add viewmol.o.
* src/viewmol.cpp: New code to read/write ViewMol files as ported
from the GPL'ed patch sent by J?rg-R?diger Hill.
* src/data.h, src/data.cpp, src/extable.txt, src/extable.h: Add
ViewMol format and enable Chem3D and derived formats.
* src/c3d.cpp: Clean up Read methods to match normal declarations.
* src/fileformat.h, src/fileformat.cpp: Enable Read/Write for
Chem3d1, Chem3d2, Mmads and ViewMol formats.
* src/main.cpp: Add support for using '--' to read from STDIN and
output to STDOUT. Tackles request #519085.
2002-02-17 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* README, configure.in, configure: Update for next snapshot of
1.99.1.
* src/Makefile.in: Add -I(builddir) to ensure that
configure-generated version.h is included.
* src/alchemy.cpp, src/amber.cpp, src/balst.cpp, src/box.cpp,
src/cacao.cpp, src/car.cpp, src/ccc.cpp, src/dmol.cpp,
src/feat.cpp, src/gamess.cpp, src/gaussian.cpp, src/hin.cpp,
src/jaguar.cpp, src/mopac.cpp, src/mpqc.cpp, src/nwchem.cpp,
src/qchem.cpp, src/report.cpp, src/unichem.cpp, src/xyz.cpp:
Make sure that SetTitle() is called with the default title if the
format doesn't have a title, do not set atom types unless the
format supports them (the internal atom typer is better), and for
formats without bond information, call the new
mol.PerceiveBondOrders() method.
* src/mol.h, src/mol.cpp: Rename PerceiveBonds in favor of
more accurate PerceiveBondOrders(). Make sure that
auto-hybridization is turned off while bond orders are being
perceived and then let it run afterwards.
2002-02-16 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/mol.cpp (PerceiveBonds): Improve accuracy by picking the
closer atom (shorter bond) when there are two atoms with equal
electronegativities.
* src/main.cpp: Add -v flag to give version information but not
the whole usage report.
* src/base.h, src/binary_io.h, src/bitvec.h, src/commandline.h,
src/ctransform.h, src/data.h, src/fileformat.h, src/grid.h,
src/matrix.h, src/mol.h, src/obutil.h, src/smarts.h: Remove
"using" statements from header files which pollute namespace of
user code. Fixes PR#493388.
2002-02-14 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/data.h, src/data.cpp: Add MIME support to
OBExtensionTable. Progress towards feature request #511533.
* src/extable.txt, src/extable.h: As above (using as much from the
current Chemical MIME page as possible).
* src/mol.h, src/mol.cpp (PerceiveBonds): Add preliminary support
for assigning bond orders based on Roger Sayle's "Cruft to
Content" algorithm. Still needs functional group and aromatic ring
recognition passes. Progress towards feature request #514589.
<http://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html>
* src/mopac.cc: Fix bugs in read/write methods as pointed out by
Radek Liboska. Should solve PR #515884.
* src/atom.cpp (GetType): Fix bug with atom typing by assigning
the ATN type of an atom if the atom typer didn't pick one before.
* src/gamess.cpp, src/xyz.cpp, src/unichem.cpp, src/ghemical.cpp:
Don't try to translate atom types as this causes problems. (Works
cleanly now that the GetType() bug is fixed.)
2002-02-13 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/data.cpp, src/data.h, src/element.txt: Added support for
electronegativity of elements. (Needed for assigning bond types,
among other things.)
* src/element.h: Regenerate using bin2hex.pl.
* src/ghemical.cpp: Don't try to type atoms, it only causes
problems with the internal atom typing.
2002-02-07 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/Makefile.in: Add c3d.cpp to the compilation list.
* src/obutil.cpp: Migrate quat.c code here temporarily.
* src/mol.cpp, src/mol.h: Resolve problems with declarations of
old quat.c code since they now fall under OpenBabel namespace.
2002-02-01 Michael Banck <mbanck@gmx.net>
* test/Makefile.in, src/Makefile.in: Delete Makefile when calling
distclean target.
* Makefile.in: Fix install target to create the $(mandir) directory.
2002-02-01 Michael Banck <mbanck@gmx.net>
* Makefile.in: Added manpage to install target.
* configure, configure.in, Makefile.in, src/Makefile.in,
src/version.h.in: Put version information in configure.in and made
generated tarballs contain it.
2002-01-24 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* doc/FAQ, doc/babel.1: Minor documentation fixes.
2002-01-21 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* Makefile.in: Fix problems with the dist target.
* configure, configure.in: Add 'top_builddir' macro to know where
objdir is in the case that we're not building in the source
directory.
* src/Makefile.in: Run the library through 'ranlib', which fixes
problems on Mac OS X. Fix problems running 'install' when not
building in the source directory.
* src/unichem.cpp: Fix bug in reading files.
* src/version.h: Set version to 1.99.
* test/Makefile.in: Fix problems with the check target: tests need
to be copied to the build dir if we're not in the source directory.
2002-01-21 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* doc/*: Move documentation to subdirectory--since there will
eventually be more than these few morsels.
* doc/Migration: Add a Migration guide for OELib -> Open Babel changes.
2002-01-20 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* FAQ, README: Added FAQ.
2002-01-20 Michael Banck <mbanck@gmx.net>
* babel.1: Initial import of man page, this is only a rough
draft. Should become babel.1.in perhaps, with the available file
types determined during the build.
2002-01-18 Michael Banck <mbanck@gmx.net>
* Makefile.in, src/Makefile.in: Fixed install target. Removed
Primer.html, bin2hex.pl and GNULICENSE from datafiles. Added
datafiles to install: target.
* Makefile.in, src/data.cpp, src/Makefile.in, src/patty.cpp,
src/pdb.cpp, src/phmodel.cpp, src/rotor.cpp, src/typer.cpp:
Openbabel now first checks for $BABEL_DATADIR, then looks in
${pkgdatadir} and finally uses the compiled-in values to get the
relevant data.
2002-01-16 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/main.cpp: Use the filename as the default filename when
reading molecules.
* src/qchem.cpp: Disable reading final z-matrix--currently
produces very bizzare results for some files.
* test/Makefile.in: Make sure the main program is compiled too.
* test/main.cpp, test/ringtest.cpp, test/smartstest.cpp: Update to
new OpenBabel API. (Took about a minute to change OE->OB and
change to iterate over OBNodeBase and OBEdgeBase.)
* test/smartstest.txt: Get rid of DOS line endings--lines are not
properly read.
2002-01-11 Michael Banck <mbanck@gmx.net>
* src/Makefile.in, test/Makefile.in, Makefile.in: Added
distclean-targets to src and test's Makefiles and removed stamp.h
again (D'OH).
* Makefile.in: Added 'stamp.h' to distclean:-target and renamed
DISTDIR from *openbabel to *openbabel-dist. ('make dist' fried my
CVS-repository because it was named 'openbabel') dist:-target
still does not work properly.
Removed "\" at the end of first line of distclean:-target
2002-01-09 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* */*: Updated build environment with src/ directory and autoconf
configure script. Builds cleanly--haven't tried using the "install
target" The test/ subdir needs fixing to remove OELib references.
2001-12-14 Michael Banck <mbanck@gmx.net>
* Makefile.in: Changed oeutil.* to the new name obutil.*.
2001-12-14 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* */*: Changed OE prefix to OB -- think I got all the cases, but
some may crop up.
Thanks to Michael Banck:
-Added some GNUish files like AUTHORS, etc.
-Added configure.in -- will shortly replace configure script with
an autoconf one.
-Need to decide how to work ChangeLog--should it go before
OELib->OpenBabel change?
* */*: Many changes to namespace and cleanup of API to work with
gcc v. 3. Still need to do big OE prefix cleanup.
2001-11-28 ghutchis <ghutchis@hydra.chem.northwestern.edu>
* configure, data.cpp, dmol.cpp, main.cpp, mol.cpp, Primer.html,
Makefile.in: Fixes from Ghemical and a first start at the "Open
Babel" nomenclature.
2001-11-27 ghutchis <ghutchis@hydra.chem.northwestern.edu>
* Import from OE current CVS. (Last GPL'ed version.)
