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ChangeLog.1.x
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2004-02-10 Geoff Hutchison <ghutchis@wso.williams.edu>
* configure, configure.in: Update with notes on versioning for
shared library support.
* src/Makefile.ac, src/Makefile.in: Apply specific 0:0:0 current
version for shared libopenbabel -- change this as appropriate for
new versions. See libtool manual for more information on what
versions are needed for revisions, backwards incompatibility, etc.
2004-02-18 Michael Banck <mbanck@gmx.net>
* src/pqs.cpp: Include <strings.h>, if available.
2004-02-17 Michael Banck <mbanck@gmx.net>
* configure.in (AC_INIT): Changed PACKAGE_NAME to 'OpenBabel'.
Additionally specifiy PACKAGE_TARNAME as 'openbabel'.
(AM_INIT_AUTOMAKE): Removed deprecated arguments PACKAGE and
VERSION.
(AC_DEFINE_DIR): Use AC_PACKAGE_TARNAME instead of
AC_PACKAGE_NAME.
* configure: Regenerated.
2004-02-10 Geoff Hutchison <ghutchis@wso.williams.edu>
* src/mol.cpp: Documentation updates.
* NEWS, THANKS: Updates for 1.100.2 release.
* aromatic.txt, aromatic.txt: Minor updates for aromaticity of
various heteroatoms.
* element.txt: * Minor documentation update.
2004-02-14 Michael Banck <mbanck@gmx.net>
* src/base.cpp [HAVE_CONFIG_H]: Removed the conditional around
#include babelconfig.h (reverted patch).
* src/bgf.cpp, src/data.cpp, src/gromos96.cpp, src/main.cpp,
src/newmain.cpp, src/oberror.cpp, src/obutil.cpp, src/patty.cpp,
src/pdb.cpp, src/phmodel.cpp, src/povray.cpp, src/residue.cpp,
src/rotor.cpp, src/typer.cpp, src/base.h, src/bitvec.h, src/crk.h,
src/data.h, src/fileformat.h, src/grid.h, src/mol.h,
src/obifstream.h, src/obutil.h: Likewise.
2004-02-13 Michael Banck <mbanck@gmx.net>
* configure.in (AM_INIT_AUTOMAKE): Added 'no-define', to prevent
defines for PACKAGE and VERSION in src/babelconfig.h.in, which
would confuse other projects.
* configure: Regenerated.
* src/babelconfig.h.in: Regenerated.
2004-02-12 Fabien Fontaine <ffontaine@imim.es>
* tools/obgrep.cpp: -t NUM option added to control
the number of match in each molecule
*tools/obprop.cpp: new tools added to compute and print
simple molecular properties for non C++ programmers
2004-02-10 Geoff Hutchison <ghutchis@wso.williams.edu>
* configure, configure.in: Change --enable-shared to the
default. Build shared libraries except where specified by the
user.
2004-02-10 Michael Banck <mbanck@gmx.net>
* test/cmltest/Makefile.am (EXTRA_DIST): Removed auto-generated
.cml files.
* test/cmltest/Makefile: Regenerated.
2004-02-09 Michael Banck <mbanck@gmx.net>
* src/base.cpp [HAVE_CONFIG_H]: New conditional, wrap babelconfig.h
#include into it.
* src/bgf.cpp, src/data.cpp, src/gromos96.cpp, src/main.cpp,
src/newmain.cpp, src/oberror.cpp, src/obutil.cpp, src/patty.cpp,
src/pdb.cpp, src/phmodel.cpp, src/povray.cpp, src/residue.cpp,
src/rotor.cpp, src/typer.cpp, src/base.h, src/bitvec.h, src/crk.h,
src/data.h, src/fileformat.h, src/grid.h, src/mol.h,
src/obifstream.h, src/obutil.h: Likewise.
2004-02-09 Michael Banck <mbanck@gmx.net>
* src/base.cpp: Include babelconfig.h.
* src/base.h: Likewise.
* src/crk.h: Likewise.
* src/data.h: Likewise.
* src/fileformat.h: Likewise.
* src/main.cpp: Likewise.
* src/oberror.cpp: Likewise.
* src/residue.cpp: Likewise.
2004-02-08 Geoff Hutchison <ghutchis@wso.williams.edu>
* src/mol.cpp, src/qchem.cpp, src/gaussian.cpp, src/report.cpp:
Improved support for spin multiplicity and total charge --
calculate from atomic formal charges and spin multiplicities where
not specified.
* Doxyfile, src/base.cpp, src/base.h, src/binary.cpp,
src/binary.h, src/chains.cpp, src/chains.h, src/data.h,
src/generic.cpp, src/generic.h, src/grid.h, src/mol.h,
src/oberror.h, src/obifstream.h, src/obutil.h, src/parsmart.h,
src/parsmi.cpp, src/pdb.cpp, src/phmodel.cpp, src/phmodel.h,
src/residue.cpp, src/rotor.cpp, src/typer.cpp, src/typer.h:
Updated documentation for generation by doxygen.
2004-02-07 Michael Banck <mbanck@gmx.net>
* src/math/matrix3x3.h [ __sgi]: Removed and...
[HAVE_IOSTRAM], [HAVE_FSTREAM]: Replaced with this.
* src/math/vector3.h: Likewise.
* src/base.cpp [#include <iostream>]: Removed and...
[HAVE_IOSTREAM, HAVE_IOSTREAM_H]: Replaced with this.
* src/base.h: Likewise.
* src/crk.h: Likewise.
* src/data.h: Likewise.
* src/fileformat.h: Likewise.
* src/main.cpp: Likewise.
* src/mol.h: Likewise.
* src/oberror.cpp: Likewise.
* src/oberror.h: Likewise.
* src/obutil.h: Likewise.
* src/residue.cpp: Likewise.
* src/base.cpp [#include <fstream>]: Removed and...
[HAVE_FSTREAM, HAVE_FSTREAM_H]: Replaced with this.
* src/binary.h: Likewise.
* src/crk.h: Likewise.
* src/data.h: Likewise.
* src/fileformat.h: Likewise.
* src/main.cpp: Likewise.
* src/mol.h: Likewise.
* src/residue.cpp: Likewise.
2004-02-06 Geoff Hutchison <ghutchis@wso.williams.edu>
* Doxyfile, doc/Doxyfile-man: Updated for 1.100.2 release and for
newer doxygen versions.
* src/base.cpp: Doxygen doc updates. Should produce links to key
classes in intro page.
* src/base.h, src/generic.cpp, src/mol.cpp, src/mol.h,
src/math/matrix3x3.cpp, src/math/vector3.cpp: Documentation updates.
* src/data.cpp, src/data.h, src/extable.txt, src/extable.h,
src/fileformat.cpp, src/fileformat.h: Updates for PQS format,
contributed by Pawel Wolinski <pwolinsk@uark.edu>.
* src/pqs.cpp: New code, as above.
* src/typer.h: Turn on root-atom detection via SelectRootAtoms.
* test/smartstest.txt, test/attype.00.smi: Add new tests for ring
and SMARTS testing.
* test/ringresults.txt, test/smartsresults.txt: Regenerated.
2004-02-06 Michael Banck <mbanck@gmx.net>
* src/cml.cpp (debug): Fix loop control variable j.
Contributed by Francesco Bresciani <fbresciani@users.sourceforge.net>.
2004-02-04 Fabien Fontaine <ffontaine@imim.es>
* tools/obgrep.cpp: -n option added to print
the name of the matched molecules only
2004-02-02 Geoff Hutchison <ghutchis@wso.williams.edu>
* src/mdl.cpp (WriteSDFile): Add support for wedge/hatch, as
contributed by Eugen Leitl.
* src/typer.cpp: Remove debugging information used for
SelectRootAtoms development. (oops!)
* configure, aclocal.m4, */Makefile.am, */Makefile.in: Regenerated
using autoconf 2.59, automake 1.8.2, libtool 1.5.2 to prevent recent
problems linking on Mac OS X.
2004-01-31 Michael Banck <mbanck@gmx.net>
* src/crk.cpp (WriteCRK): Rename loop variable from n to m.
Contributed by Chris Morley <c.morley@gaseq.co.uk>.
2004-01-27 Michael Banck <mbanck@gmx.net>
* configure.in: Rename defined directory DATADIR to BABEL_DATADIR,
to avoid problems with other programs. Closes: #885828.
* configure: Regenerated.
* src/babelconfig.h.in: Regenerated.
* src/bondtyper.cpp: Rename _dir from DATADIR to BABEL_DATADIR.
* src/data.cpp: Likwise.
* src/pdb.cpp: Likewise.
* src/phmodel.cpp: Likewise.
* src/rotor.cpp: Likewise.
* src/typer.cpp: Likewise.
2004-01-16 Michael Banck <mbanck@gmx.net>
* test/Makefile.am (TESTS): Run test-scripts with absolute path
$(top_srcdir)/test/, as they are not present in the current
directory when building in a builddir.
(SUBDIRS): New directive, including cmltest.
* test/Makefile.in: Regenerated.
* test/cmltest/Makefile.am: New file.
* test/cmltest/Makefile.in: New file, autogenerated.
* configure.in (AC_OUTPUT): Added test/cmltest/Makefile.
* configure: Regenerated.
2004-01-16 Michael Banck <mbanck@gmx.net>
Second and last pass of test-suite-in-builddir handling, fixing
the shell scripts.
* test/cml.sh: Export $srcdir and $builddir for use in the called
scripts. Prepend $cmltestdir to avoid absolute pathnames.
* test/cmltest/test.sh: Define $builddir and specify path to the
babel executable from there. Replace every absolute pathname
with relative ones.
* test/roundtrip.sh: Likewise.
2004-01-13 Michael Banck <mbanck@gmx.net>
First shot at making a test-suite run from a build-directory
possible.
* test/Makefile.am (AM_CPPFLAGS): Added -DTESTDATADIR, pointing
to $(srcdir)/test, where the test-suite data files are located.
* test/Makefile.in: Regenerated.
* test/ringtest.cpp: Use strings to handle the filenames. If
TESTDATADIR is defined, prepend it to the filename. Transform
the string to a char* when calling SafeOpen().
* test/smartstest.cpp: Likewise.
* test/unitcell.cpp: Likewise.
2003-12-17 Fabien Fontaine <ffontaine@imim.es>
* src/typer.cpp (AssignImplicitValence)
Fix protonation of amines bug due to spin multiplicity assignment
move spin multiplicity lines of CM to OBMol::AssignSpinMultiplicity();
Add spin multiplicity flag and related functions in mol.h
2003-12-08 Fabien Fontaine <ffontaine@imim.es>
* src/mol.cpp (DeleteNonPolarHydrogens): uncomment "IncrementMod();"
to avoid _c initialization when Deleting atoms
2003-12-01 Michael Banck <mbanck@gmx.net>
* src/data.cpp (GetExtension): Make sure that the returned long
description stays defined by copying it into a static string.
Contributed by David Mathog <mathog@mendel.bio.caltech.edu>.
* (GetDescription): Likewise.
2003-12-01 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/pdb.cpp, src/mol2.cpp, src/gromos96.cpp:
Residue perception via OBChainsParser turned on, contributed by
Malcolm Gillies.
* src/atom.cpp(GetResidue): Call SetChainsPerceived--ensures that
chain perception code will not be called repeatedly on failure,
contributed by Malcolm Gillies.
* src/crk.h, src/crk.cpp: New files for Chemical Resource Kit
support, contriubted by Alex Clark <a.clark@bendcable.com>.
* src/Makefile.am, src/Makefile.in: As above.
* src/data.cpp, src/data.h, src/extable.txt, src/fileformat.cpp,
src/fileformat.h: Changes to support read/write CRK files.
* src/mol.h: Fix mistake in HasAromaticBond() -- aromatic bonds
are "5", not "4"!
* src/bond.cpp(IsTriple): New method for triple bonds.
* src/typer.h: Add new SelectRootAtoms method (defaults to off)
contributed from JOELib.
* src/typer.cpp(SelectRootAtoms): Implement it, as ported from
Joerg Wegner's JOELib Java code.
(AssignAromaticFlag): Use SelectRootAtoms -- if
avoidInnerRingAtoms is set to false, same as previous code.
* test/attype.00.smi: Add new test patterns from JOELib tests.
* test/smartstest.txt: Add new pattern from JOELib tests.
* test/ringresults.txt, test/smartsresults.txt: Regenerate using
current code (i.e. do not use SelectRootAtoms code yet).
2003-11-22 Michael Banck <mbanck@gmx.net>
* src/povray.cpp (CalcBoundingBox): Decouple declaration of
`unsigned int i' from the for-loop. Contributed by Chris
Morley.
* src/Makefile.am (libopenbabelinclude_HEADERS): Added
babelconfig.h
* src/Makefile.am (EXTRA_DIST): Removed newmain.cpp, bondtyper.cpp
and bondtyper.h for now.
* configure.in (AC_CHECK_HEADERS): Added iostream and fstream.
They seem to be not always present on Irix.
(AC_HEADER_TIME): New macro.
(AC_CHECK_TYPES): New macro, checking for clock_t.
(AC_CHECK_FUNCS): New macro, checking for rint.
* configure: Regenerated.
* src/babelconfig.h.in: Regenerated.
* src/bitvec.h, src/grid.h, src/obifstream.h: Include
babelconfig.h.
[__sgi]: Removed, and ...
[HAVE_IOSTREAM]: Replaced with this.
* src/main.cpp [__BORLANDC__]: Removed strncasecmp function.
* src/mol.h [WIN32]: Removed, and ...
[!HAVE_RINT]: Replaced with this.
* src/obutil.h: Include babelconfig.h.
[WIN32] (include time.h): Removed, and ...
[TIME_WITH_SYS_TIME, HAVE_SYS_TIME_H]: Replaced with this.
[WIN32] (clock_t): Removed, and ...
[HAVE_CLOCK_T]: Replaced with this.
* src/obutil.cpp: Include babelconfig.h.
[WIN32]: Removed, and ...
[HAVE_CONIO_H]: Replaced with this.
* src/mol.h: Move #include for babelconfig.h to the top.
2003-11-21 Fabien Fontaine <ffontaine@imim.es>
* src/typer.cpp (AssignImplicitValence): SetAromaticPerceived flag on
to ensure that the aromatic typer is not called when assigning
implicit valence, and check if implicit valence has already been
assigned
*src/mol.h SetFlags function added
2003-11-17 Michael Banck <mbanck@gmx.net>
* src/chemtool.cpp (WriteGX): Replaced round(x) with
floor(x + 0.5) as round() does not seem to be available on all
systems.
2003-11-13 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* test/attype.00.smi, test/smartstest.txt: Updated with tests from
SMARTS bug reports PR#776094 and 796649. (Not problems in the
current CVS code, but added as new test cases anyway.)
* test/ringtest.cpp, test/smartstest.cpp: Allow generation of the
results files.
* test/ringresults.txt, test/smartsresults.txt: Generated from
above. (Current implementation validates previous results as well
as new patterns above.)
* src/atomtyp.txt: Add Sybyl typing for phenol oxygens and ester
sp3 oxygens.
* src/aromatic.txt: Remove phosphole from aromatic patterns, add
selenophene. (Phosphole is a classic non-aromatic system due to
the non-planar P atom.)
* src/aromatic.h, src/atomtyp.h, src/extable.h: Autogenerated.
2003-11-12 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* configure, */Makefile.in: Regenerated using automake-1.7.8,
autoconf-2.58, libtool-1.5. (Should solve problems with CVS
versions needing to call autoconf/automake due to timestamps.)
Added AM_MAINTAINER_MODE.
* aclocal.m4: Put this back in CVS so aclocal isn't needed to
generate from CVS.
* src/Makefile.am: Add back targets for generating binary .h files
from the appropriate .txt data files.
* src/parsmi.cpp: Back out Chris Morley's SMILES extensions for
radicial centers--current causes many SMILES/SMARTS errors.
* test/main.cpp, test/roundtrip.cpp: Add comments on additional
tests needed soon. (These are all in the project tracker for
Release-2.0 roadmap too.)
* test/smartstest.cpp: Improve debugging information on
errors--give the first atom matching if we have a match, even if
it's not the number of matches expected by the results.
* test/test-set.sh: Only mention running the test if the test
directory is there.
2003-11-11 Michael Banck <mbanck@gmx.net>
* configure.in (AC_CHECK_HEADERS): Removed checks for some C++
Standard Library headers (algorithm vector map list iostream
fstream deque). They are essential for openbabel and we don't
even exit if ./configure does not find them, let alone work
around them missing. So in effect, the checks were just wasting
CPU cycles until now. stream and strstream are still checked.
* configure: Regenerated.
* src/babelconfig.h.in: Regenerated.
2003-11-11 Michael Banck <mbanck@gmx.net>
* configure.in (AC_REPLACE_FUNCS): New directive, including
snprintf and strncasecmp for now.
* configure: Regenerated.
* src/babelconfig.h.in: Regenerated.
* src/Makefile.am (libopenbabel_la_LIBADD): Added @LTLIBOBJS@.
(babel_LDADD): Added @LIBOBJS@.
* src/Makefile.in: Regenerated.
* src/mol.h [!HAVE_SNPRINTF] (snprintf): New declaration.
[!HAVE_STRNCASECMP] (strncasecmp): Likewise.
* src/snprintf.c: New file, taken from Mark Martinec.
* src/snprintf.h: New file, taken from Mark Martinec.
* src/strncasecmp.c: New file, taken from gnulib.
2003-11-10 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/main.cpp: Silently ignore cases with 0 atoms in a
molecule. This is frequently due to trailing empty lines in a file.
* test/Makefile.am: Separate the tests in obtest into distinct
programs and tests for a more accurate "make check" result.
* test/main.cpp, test/matrixtest.cpp, test/ringtest.cpp,
test/smartstest.cpp: Ditto.
* test/cml.sh: Skip the test in "make check" if the directory
doesn't exist.
* test/test-set.sh: If the test-set directory exists, then run it,
otherwise skip the test.
2003-11-10 Michael Banck <mbanck@gmx.net>
* src/math/Makefile.am (AM_CPPFLAGS): New directive, adding
$(top_srcdir)/src to includes to make building in a seperate
build-directory possible.
* test/Makefile.am (AM_CPPFLAGS): Likewise.
* tools/Makefile.am (AM_CPPFLAGS): Likewise.
2003-11-08 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* configure, */Makefile.in: Updated with current autoconf, automake.
* src/cml.cpp: Add OB_VERSION const to use BABEL_VERSION
definition (automagically updated from babelconfig.h).
* src/extable.txt: Add .ins ShelX extension.
* test/cml.sh, test/cmltest/roundtrip.sh, test/cmltest/test.sh:
Shell scripts to run the CML test suite.
* test/smartstest.cpp: Add more debugging information if SMARTS
tests fail.
* src/shelx.cpp: Changes suggested by Louis Ricard
<louis.ricard@polytechnique.fr> to fix several ShelX bugs.
* src/atom.cpp, src/mdl.cpp, src/mol.h, src/parsmi.cpp, src/smi.cpp,
src/typer.cpp: Support for radical centers, contributed by Chris
Morley <c.morley@gaseq.co.uk>.
Changes contributed by Malcolm Gillies <malcolm.b.gillies@anu.edu.au>
* src/pdb.cpp: (ReadPDB) BUG: OBMol::ConnectTheDots() fails inside a
OBMol::BeginModify()/OBMol::EndModify() pair, as OBMol::Has3D() will
always return false. Rearrange to avoid this.
Use ATOM/HETATM record element name information in columns
76-77 to determine element type when possible and necessary.
(WritePDB) BUG: writing of ATOM records could fail due to use of
strncpy to copy atom and residue names (i.e. lack of null termination)
Write HETATM records instead of ATOM records if
res->IsHetAtom(atom)==true
2003-10-22 Fabien Fontaine <ffontaine@imim.es>
Added tools directory: contains utilities using libopenbabel
* tools/obgrep.cpp: SMART molecule grep
* tools/obfit.cpp: align molecules on SMART substructures
* tools/obrotate.cpp: rotate a tortional bond matching a SMART
* src/mol2.cpp (ReadMol2): Continue reading untill EOF or next
MOLECULE record to avoid 'error: has zero atoms!' message
2003-10-20 Fabien Fontaine <ffontaine@imim.es>
* src/patty.h Istype function added
* src/patty.cpp (read_rules) (assign_rules) : memory
allocation changed
2003-10-03 Michael Banck <mbanck@gmx.net>
* src/atom.cpp (GetDistance): New method.
* (GetAngle): Likewise.
* src/mol.h: Declare them.
2003-09-25 Michael Banck <mbanck@gmx.net>
* src/mol.h (_internals): New protected class attribute.
(GetInternalCoord): New declaration.
(SetInternalCoord): New method.
(BeginInternalCoord): New method for iterating over _internals.
(NextInternalCoord): Likewise.
* src/mol.cpp (GetInternalCoord): New method.
2003-09-21 Peter Murray-Rust <pm286@cam.ac.uk>
* src/cml.cpp: removed inconsistences between atomRef, atomRef1,
atomRef2, and atomRefs2 attributes.
* test/cmltest/cs2a.cml: changed atomRefs1 and atomRefs2 attributes
to atomRef
* test/cmltest/test.bat: minor edits to allow echo
2003-09-14 Michael Banck <mbanck@gmx.net>
* src/povray.cpp: Removed getlogin() declaration.
(OutputHeader): Removed log_name, don't output login name in
Povray header.
2003-09-13 Michael Banck <mbanck@gmx.net>
* src/chemtool.cpp: New file.
* src/Makefile.am (libopenbabel_la_SOURCES): Added chemtool.cpp.
* src/Makefile.in: Regenerated.
* src/data.cpp (TextToType): Added CHEMTOOL typestring.
* src/data.h (io_type): Added CHEMTOOL.
* src/extable.txt: Added Chemtool writing support.
* src/fileformat.cpp (OBFileFormat::WriteMolecule): Added
WriteCHT function call for CHEMTOOL io_type.
* src/fileformat.h (OBFileFormat): Added WriteCHT() method.
2003-07-02 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/data.cpp (GetAtomicNum): Fix mistake in calls to strcasecmp,
as pointed out by Chris Morley.
* src/math/Makefile.am: Make sure math/matrix3x3.h and
math/vector3.h are installed with a "make install" as reported by
Jean. Fixes PR#761644.
* Makefile.in, src/math/Makefile.in: Regenerate using automake.
2003-06-26 Michael Banck <mbanck@gmx.net>
* NEWS: New file.
2003-06-23 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/main.cpp: Move man documentation to end of file (right
after usage() code) for better "readability". Also make sure that
we quit attempting to read molecules from a file when we find no
atoms. Fixes some problems seen when roundtripping.
2003-06-23 Vincent Favre-Nicolin <vincefn@users.sourceforge.net>
* doc/Doxyfile-man, src/main.cpp, Doxyfile: Added the man page in
doxygen format in main.cpp, for automatic generation of the man
page from the source code, using 'Doxygen Doxyfile-man' in the
doc/ directory. Normal Doxygen run now skips src/main.cpp
2003-06-23 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* doc/babel.1: Update with current command-line options and file
formats.
* doc/FAQ.html, doc/Migration.html: Use HTML versions from the
website rather than text versions.
* doc/Makefile.in, doc/Makefile.am: Update accordingly.
* src/cml.cpp(CleanUp): New method to clean up global vector
variables after ReadCML() and WriteCML() in attempt to fix
PR#736001. Does not change normal command-line path, but should
fix library useage when multiple files may be loaded.
2003-06-22 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/main.cpp: Updated to use OBMolVector for importing multiple
molecules in a file. Emulates behavior of babel, but improvements
are needed. (e.g. some formats like separators if it's a
multi-molecule file.) Also added -f (first) and -l (last)
flags to pick particular molecules. Fixes feature request
PR#575243.
* src/molvector.h, src/molvector.cpp: Add new PushMol method for
adding new molecules to the end of the vector. Improve Write
support and clean up overloaded methods--instead use default
values.
* src/*.txt: Updated copyright information.
* src/*.cpp, src/*.h: Ditto. (As needed)
2003-06-15 Michael Banck <mbanck@gmx.net>
* src/pdb.cpp (WritePDB): Cast atom->GetValence() to int to avoid
signed/unsigned comparison.
* src/ring.cpp (OBRingSearch::RemoveRedundant): Remove register
attribute for i and j to suppress a warning.
(OBRingSearch::AddRingFromClosure): Remove unused parameter
`int level'.
* src/ring.h (AddRingFromClosure): Remove unused parameter `int'.
* src/povray.cpp (OutputMoleculeBonds): Remove unused parameter
`OpenBabel::OBMol mol'.
2003-06-15 Geoff Hutchison <hutchisn@chem.northwestern.edu>
Updated to latest autoconf, libtool, automake versions to fix a
few minor bugs and add libtool-1.5 Mac OS X support.
* depcomp, ltmain.sh, missing, config.guess, config.sub: Update
with latest GNU versions.
* src/Makefile.am: Remove main.cpp from targets for library and
make sure only one set of headers exists.
* configure: Regenerated with autoreconf.
* */Makefile.in: Regenerated with autoreconf.
* openbabel.pc.in: Fix minor typo.
* *.cvsignore: Add new libtool-generated files.
2003-06-15 Michael Banck <mbanck@gmx.net>
Added pkg-config support, thanks to Jean Bréfort.
* openbabel.pc.in: New file.
* configure.in: Add openbabel.pc to AC_OUTPUT.
* configure: Regenerated.
* Makefile.am: Install openbabel.pc in $(libdir)/pkgconfig.
* Makefile.in, doc/Makefile.in, src/Makefile.in, src/math/Makefile.in,
src/windows/Makefile.in, test/Makefile.in: Regenerated.
* ChangeLog: Fixed a wrong filename in the last entry, minor
corrections.
2003-06-15 Michael Banck <mbanck@gmx.net>
Switch to automake.
* configure.in: Add automake macros, remove some obsolete legacy
stuff (AC_PATH_PROG(AR), $top_builddir, AC_PROG_RANLIB), enable
libtool.
* configure: Regenerated.
* Makefile.am, test/Makefile.am, doc/Makefile.am,
src/Makefile.am, src/windows/Makefile.am, src/math/Makefile.am:
New files.
* doc/Makefile.in, src/windows/Makefile.in: New files,
autogenerated.
* Makefile.in, test/Makefile.in, src/Makefile.in,
src/math/Makefile.in: Regenerated.
* src/babelconfig.h.in: Regenerated.
2003-06-10 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/Makefile.in: Remove cwrap.h and cwrap.o as these have been
removed.
* src/mol.cpp (ConnectTheDots, PerceiveBondOrders): Make sure
these don't try to run on 2D structures, fixing bug reported by Jean.
Remove a variety of compilation warnings.
* src/cacao.cpp, src/data.cpp, src/mpqc.cpp, src/povray.cpp:
Remove unused variables.
* src/mopac.cpp: Switch to unsigned int to remove comparison warning.
* src/obutil.h, src/obutil.cpp: New IsNear and IsNearZero
functions to compare floating-point numbers instead of unreliable
== operator. Ensures numbers are closer than a user-specified epsilon.
* src/mol.cpp, src/mol2.cpp, src/molchrg.cpp,
src/math/vector3.cpp: Improve reliability of floating point
comparisons. Replace == operator compares with new IsNear and
IsNearZero functions.
(vector3.cpp probably should replace == operators as well.)
2003-06-09 Michael Banck <mbanck@gmx.net>
* src/main.cpp:
- Renamed usage() to help() and added a new method
usage() with a terse usage output and a pointer to help().
- Added -H switch for help().
- Reformatted usage() and help() output a bit.
- Print out an 'unrecognized option' error message when
option parsing fails, in addition to usage().
2003-06-09 Michael Banck <mbanck@gmx.net>
* src/main.cpp: Added a pointer to the Mailing-List for sending
bug-reports to the end of usage().
2003-06-03 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/mol.h: Add OBBond::UnsetKekule for PerceiveBondOrders support.
* src/mol.cpp (PerceiveBondOrders): Add aromatization pass to
complete the implementation of Roger Sayle's algorithm. This
implementation is rather naive--it types rings, then passes back
to Kekulize. Still works pretty well.
2003-06-02 Geoff Hutchison <hutchisn@chem.northwestern.edu>
Lots of minor bugfixes from the past few weeks.
* src/element.txt, src/element.h: Update phosphorus covalent
radius as suggested by Jean Brefort (PR# 743730).
* configure.in: Set "bug report" e-mail address, remove custom
openbabel_version variable and change AC_CHECK_HEADER calls to
AC_CHECK_HEADERS to gracefully fail and set appropriate HAVE_
macros in babelconfig.h.
* configure, src/babelconfig.h.in: Updated using autoreconf.
* src/data.cpp, src/povray.cpp: Update to use sstream if present
and strstream if not.
* src/main.cpp: Add support for centering coordinates as well as
checking for 2D vs. 3D coordinates when calling WriteMolecule.
* src/mol.cpp (Kekulize): Remove 255 atom limit discovered by
Frank Schmitt. (Some limit is reasonable, but SMARTS matching
should be better about matching non-Kekulize'd structures.)
* Makefile.in: Use standard PACKAGE_VERSION instead of
openbabel_version.
* src/Makefile.in: Get rid of bitgrid.[cpp,h] and version.h.
* src/base.cpp: Minor documentation updates.
* src/extable.txt, src/extable.h, src/fileformat.cpp,
src/fileformat.h: Add in preliminary hooks for ShelX support.
* src/shelx.cpp, src/bondtyper.h, src/bondtyper.cpp: New files.
* test/unitcell.cpp: Make sure to initialize variables.
* test/roundtrip.cpp: Use babelconfig.h instead of version.h.
2003-04-22 Michael Banck <mbanck@gmx.net>
Switch to autoheader.
* configure.in:
- Added AC_CONFIG_HEADER(src/babelconfig.h), along with
two cosmetic changes.
- Define BABEL_VERSION and DATADIR directly. DATADIR is
$datadir/openbabel (i.e. $pkgdatadir in automake) as before,
$datadir can be specified normally as option to ./configure.
* configure: Regenerated
* acinclude.m4: New file for local m4-files, it currently has
AC_DEFINE_DIR (used in order to define DATADIR) as content.
* src/Makefile.in: Removed DEFS=-DDATADIR.
* src/math/Makefile.in: Likewise.
* src/babelconfig.h.in: Initial autogenerated version
* src/bgf.cpp, src/gromos96.cpp, src/newmain.cpp, src/patty.cpp,
src/pdb.cpp, src/phmodel.cpp, src/rotor.cpp, src/typer.cpp:
Added #include "babelconfig.h", removed #include "version.h" where
applicable
2003-04-13 Michael Banck <mbanck@gmx.net>
* config.guess, config.sub, ltmain.sh: Updated to current FSF
versions
2003-03-26 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/bondtyp.txt, src/bondtyp.h: Files for the PerceiveBondOrder
functional group typing.
* Src/Makefile.in: Add rules for generating bondtyp.h from the
text file.
2003-03-18 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/configure.in, src/configure: Update with "1.100.1" version
number for now.
* test/roundtrip.cpp (main): Improve usability by making BOX and
SMI file types special cases. (Hard to compare atoms and coords
for them.)
* src/pdb.cpp (WritePDB): Make sure two-character elements end up
in the correct columns even with residue information.
(ReadPDB): Refer to the original text (with spaces) before
deciding if an atom type is a two-character element or a one-char
element.
* src/*.h, *.cpp: Switch from float to double throughout. Improves
accuracy significantly in coordinate transformations.
* src/binary.cpp (PackCoordinate, UnpackCoordinate): Make sure to
cast to float before packing for compatibility with file format.
2003-03-17 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/cml.cpp: Fix unused declarations that cause problems with
the xlC compiler reported by Markku Laukkanen.
* src/pdb.cpp (WritePDB): Make sure strings are null-terminated
and convert element name to upper-case for the column 77-78 entry.
2003-03-15 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/cacao.cpp (SetHilderbrandt): Fix one coredump found on
roundtrip testing and add notes on what needs to be fixed for an
iron-clad version of this.
* src/hin.cpp (ReadHIN): Fix bugs uncovered in latest roundtrip
testing. Some lines are exactly 11 tokens long and this should not
stop the parsing.
* src/viewmol.cpp (ReadViewMol): Remove loop attempting to find
the first part of the file -- causes problems since two lines
instead of one are read off the top.
2003-03-14 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* test/roundtrip.cpp: Detect cases where files have no atoms.
* test/Makefile.in: Add targets to create roundtrip program.
* src/cacao.cpp (ReadCaccrt): Add an obUnitCell object to the
molecule for keeping track of unit cell data. Call
ConnectTheDots() and PerceiveBondOrders().
(WriteCaccrt): If obUnitCell data exists, output unit cell data.
* src/dmol.cpp (ReadDMol): Read $cell vector section if it exists.
(WriteDMol): Write unit cell data if it exists.
* src/parsmi.cpp (ParseComplex): Add isotope information where
available.
(ParseSmiles): Fix segfault in test file caused
by white-space character ending SMILES string. Ignore them and
continue.
* src/generic.cpp (OBUnitCell::ctor): Make sure to set the generic
data type and string.
* src/generic.h (OBUnitCell): Add space group storage as a string.
* src/mopac.cpp (ReadMOPAC): Remove debugging output left
inadvertantly.
2003-03-13 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/generic.cpp, src/generic.h: Add support for retrieving
OBUnitCell data by a matrix3x3 and add a new method
GetOrthoMatrix() for translating from fractional coordinates.
* src/pdb.cpp (WritePDB): Make sure that residue and atom names
are only a maximum length to format columns correctly. Add element
symbol to columns 77 and 78 to better support the current standard.
* src/math/matrix3x3.h, src/math/matrix3x3.cpp (SetRow): New
method to set a row from a vector3.
* src/mpqc.cpp (ReadMPQC): Fix bugs in MPQC output reading,
uncovered by new roundtrip testing.
* src/cacao.cpp (WriteCaccrt): Make sure the buffer is actually
written to the file. Previous output passed roundtrip testing (no
coredumps) but nothing was actually written to the file!
* test/roundtrip.cpp: New file to compare two molecules after
roundtripping. (Perhaps it should be called molcmp?)
2003-03-12 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/pdb.cpp (WritePDB): Make sure that atom type definitions are
written correctly as per the PDB standard. Fixes PR#701620, as
suggested by Christian Hofbauer.
* src/report.cpp: Add support for listing torsion angles. Angle
and torsion data is not the same as in Babel 1.6, but is
coherent. Fixes feature request PR#568088.
2003-03-11 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/generic.h, src/generic.cpp: Add new OBUnitCell generic data
type for storing and converting unit cell parameters.
* test/Makefile.in, test/main.cpp, test/unitcell.cpp,
test/unitcell.txt: New test to confirm that unit cell conversions
occur accurately.
* src/atom.cpp (GetAtomicMass): If an isotope has been set, use
that as the atomic mass. Otherwise stick to the normal average
mass.
* src/isotope-small.txt, src/Makefile.in, src/isotope.h: Smaller
set of isotopes for generating default data to minimize growth in
executable size.
2003-03-10 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/generic.h: Add new data type "slots" to obDataType enum.
* src/pdb.cc (class OBSerialNums): Use new obSerialNums enum,
rather than overriding user-defined obData# slots. These should
only be used by user-level code, not by Open Babel internal code.
2003-03-10 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/atom.cpp (GetType): Fix compilation error when copying in
"D" atom type for a deuterium atom.
* src/mol2.cpp (ReadMol2): Read residue information if available,
along with atom IDs and residue number. Should address feature
request PR#697614 submitted by Claudio Cavasotto.
* src/mol.h, src/mol.cpp: Add API support for a molecular total
charge.
2003-03-06 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/Makefile.in: Add support for the isotopes.txt -> .h
conversion.
* src/mol.h: Add support for storing atomic isotopes and
"exact mass" methods.
* src/mol.cpp (GetExactMass): New method, using isotope table.
* src/atom.cpp: Add support for atomic isotopes, including
modifications to SetType methods to ensure deuterium isotopes
translate into the correct type.
* src/data.h, src/data.cpp: Add new OBIsotopeTable for obtaining
exact masses of given element/isotope combinations.
(OBElementTable::GetAtomicNum): Expand to return isotope for the
case where a "D" or "T" symbol is passed to the table.
* src/isotope.txt, src/isotope.h: Update to include atomic numbers
at the beginning of each line so ParseLine() knows "where it is."
* src/report.cpp: Add output of molecular weight and exact mass.
2003-03-02 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/mopac.cpp (ReadMOPAC): Fix problems with MOPAC partial
charges not translating to other formats. (PR#660364)
2003-02-28 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/mol.h: Add new method OBAtom::SamllestBondAngle().
* src/atom.cpp: Implement it.
* src/mol.cpp (ConnectTheDots): Improve bonding by checking for
small bond angles while removing long bonds.
* src/pdb.cpp: Do not attempt to add alpha-peptide
bonds. ConnectTheDots is much better at this and doesn't attempt
to add strange very long-range bonds.
2003-01-17 Geoff Hutchison <hutchisn@chem.northwestern.edu>
* src/base.cpp: Add introduction to documentation.
* src/mol.cpp: Don't attempt to use Kekulize or Begin/EndModify to
detect aromaticity.
* src/phmodel.txt, src/phmodeldata.h: Add histidine transformation
and unused tryptophan transformation to help with problems
observed by Richard Gillian (PR#575964).
* src/resdata.txt src/resdata.h: Fix incorrect bond orders for ARG
residue. (PR#575964).
* test/matrixtest.cpp: Make matrix test a bit more verbose to make
debugging problems on non-Intel platforms easier. (Relates to
PR#647417). Problem derives from numerical accuracy, but loosening
tolerance to 2e-6 solves the problem.
2003-01-15/16 Peter Murray-Rust <pm286@cam.ac.uk>
Vincent Favre-Nicolin <vincefn@users.sourceforge.net>
* Changes to compile using the free Borland C++ compiler 5.5.1:
a few fixes ISO C++ fixes, some #if's and added makefiles (bc32.mak)
2003-01-06 Geoff Hutchison <hutchisn@chem.northwestern.edu>