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ChangeLog
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2012-08-20 Paolo Tosco <paolo.tosco@unito.it>
* src/formats/mol2format.cpp: added a check for N.4 nitrogens
(fixes PR#3557898)
2012-06-09 Paolo Tosco <paolo.tosco@unito.it>
* src/kekulize.cpp: reverted the r4862 patch to kekulize.cpp;
the incorrect aromaticity perception of oxonium salts concerned
only the MOL2 format, so the fix was applied to mol2format.cpp
instead
* src/formats/mol2format.cpp: added a check to improve downstream
aromaticity perception on charged molecules containing oxygen
2012-06-07 Paolo Tosco <paolo.tosco@unito.it>
* include/openbabel/atom.h: added protos for CountFreeSulfurs() and
IsThiocarboxylSulfur() functions which are equivalent to
CountFreeOxygens() and IsCarboxylOxygen() and address
(di)thiocarboxyl groups
* src/atom.cpp: added the CountFreeSulfurs() and
IsThiocarboxylSulfur() functions
* src/forcefields/forcefieldmmff94.cpp: added some additional
checks to make MMFF94 atom type assignment more robust
* src/formats/mol2format.cpp: added some checks to improve downstream
aromaticity perception on charged molecules containing nitrogen,
oxygen and sulfur
* src/kekulize.cpp: added a check to fix incorrect perception of
aromatic oxonium and thionium cations
2010-10-29 Konstantin Tokarev <annulen@yandex.ru>
* scripts/CMakeLists.txt: fixed behavior of build system if some of
JNI dependencies were not found
2010-10-29 Konstantin Tokarev <annulen@yandex.ru>
* scripts/CMakeLists.txt: added dependency 'openbabel' to target
'_openbabel' (Python bindings)
On non-Windows platfroms Python module is linked by custom script
which is not aware of target dependencies. This change fixes parallel
build
2010-10-24 Jean Brefort <jean.brefort@normalesup.org>
* data/space-groups.txt: fixed space group 104 (missing transfoms).
2010-10-14 Jiahao Chen <jiahao@mit.edu>
* src/charges/qeq.cpp,src/charges/qtpie.cpp: Added documentation.
* data/qeq.txt: Simplified parameter file format.
There is an upper bound on the screening radius that is constrained by
the atomic hardness parameter. (These parameters are not entirely
independent.) If this constraint is violated, i.e. radius * hardness <
sqrt(2/pi) a.u., then it is possible to get infinite charges for
certain geometries. For now, the screening radius using the Gaussian
orbitals (in this code) is taken to be the same as the screening radius
for Slater orbitals in the original QEq specifications, except when the
constraint is violated, in which case the radius is reduced to the
largest possible radius satisfying the constraint. To do this properly,
a reparameterization of the methods are required, but this should
suffice for not producing ridiculous charge predictions.
2010-09-30 Chris Morley
* src/alias.cpp: Use MCDL for expanding aliases in 2D mols, since
builder seems now only to generate 3D coords. Add dummy connection to
alias before generating 3D coords to improve geometry, but still not
quite right for NO2. Fixes #3077897
* src/mcdlutil.cpp: small doc change
* src/config.h.cmake: MSVC build: enable warning on unreferenced
formal parameters and disable warning on forcing int etc. value
to bool 'true' or 'false' (performance warning). Should reduce number
of warnings.
2010-09-29 Noel O'Boyle
* src/formats/smilesformat.cpp: Handle cis/trans stereo involving ring
closures. Handle errors in specifying cis/trans stereo in general and
involving ring closures.
2010-09-23 Noel O'Boyle
* src/math/align.cpp, align.h: Add OBAlign::GetRotMatrix()
* test/aligntest.cpp: Add basic test for GetRotMatrix()
2010-09-23 Chris Morley
* src/fingerprints/finger2.cpp: generate detailed fragement info
and output via new DescribeBits function, as suggested by Noel.
* include/openbabel/fingerprint.h: make Flags interface writeable.
* src/fingerprint.cpp(FastsearchIndexer): set fingerprints
FPT_NOINFO flag to save time (FP2).
* src/fingerprints/finger3.cpp,src/formats/fingerprintformat.cpp:
minor format changes to DescribeBits output.
2010-09-19 Noel O'Boyle
* src/formats/inchiformat.cpp: Handle atoms with tet chirality due to
lone pairs.
2010-09-19 Chris Morley
* src/ops/opisomorph.cpp: As requested by Douglas Houston, -s option
allows multiple molecules in pattern file (with multiple coloring of
matching substructures); -v (inverse of -s) now uses the same code
and has the same capabilities.
2010-09-19 Chris Morley
* src/depict/depict.cpp: correct position and direction of wedge and
hash bonds. Deduce using TetStereoTo0D. May need further work.
* include/openbabel/depict/painter.h(OBColor): add a few more named
colors, color input from rgb hex (like #8dcb70), and a default color,
in case of typos.
2010-09-19 Chris Morley
* include/openbabel/obconversion.h: expose Count (the input index)
* src/ops/addinindex.cpp, src/CMakeLists.txt: add an op to add Count
to title: --addinindex (Yes, awful names)
* src/obmolecformat.cpp, src/transform.cpp:
rename --addindex to --addoutindex.
src/transform.cpp: -v option does nothing if parameter empty.
(ClassDescription)small documentation changes for -s, -v
2010-09-19 Chris Morley
* src/stereo/perception.cpp(TetStereoTo0D):fix bug which was truncating
the loop without examining all possible bonds.
* include/openbabel/inchiformat.h: correct formating of Description
so will work with GUI (no \n\n inside option list).
* src/formats/inchiformat.cpp: OBBond instead of OBEdgeBase, which
was removed a million years ago.
2010-09-17 Noel O'Boyle
* src/math/align.cpp, test/aligntest.cpp: Correct dumb error in
final line of calculation of RMSD.
2010-09-15 Noel O'Boyle
* src/builder.cpp: When correcting stereo on rings, handle the case of
the lone pair. Thanks to Peter Lavin for reporting.
2010-09-15 Noel O'Boyle
* src/formats/smilesformat.cpp: Handle chiral S with a lone pair in
the SMILES writer. Fixes PR#3058701. The test cases in the previous
commit log message should actually be C[S@](=O)Cl, etc. to be
chemically correct.
2010-09-14 Noel O'Boyle
* src/formats/smilesformat.cpp: Handle chiral S with a lone pair and
in general, the situation where a chiral atom has a lone pair.
Test cases: C[S@](Br)I, [S@](C)(Br)I, C[C@-](Br)I, C[S@](=O)(=O)Cl.
2010-09-14 Noel O'Boyle
* CMakeLists.txt: As discussed on list, don't build all bindings when
RUN_SWIG=ON (building some bindings may cause errors). Instead, the
option ALL_BINDINGS=ON will build all bindings.
2010-09-10 Noel O'Boyle
* src/formats/pdbqtformat.cpp: Remove "ent" designation as this is
already used by the .pdb file format.
2010-09-09 Noel O'Boyle
* scripts/python/pybel_py*.x.py: Synch with cinfony. Add support for
MCDL 2D coordinate generation when calling 'draw()'. MCDL is the
default. To use OASA, specify method="oasa".
2010-09-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/base.h: Add new UNUSED() macro for unused
parameters.
* include/openbabel/forcefield.h: Use it.
* src/kekulize.cpp: Decrease recursion level from 31 to
24. Prevents some crashing / "infinite" loops on large fused-ring
systems.
* src/formats/pdbqtformat.cpp: Add new format from Stuart
Armstrong, InHiBOx.
* src/formats/CMakeLists.txt: Ditto.
2010-08-26 Noel O'Boyle
* src/formats/mdlformat.cpp: Chris beat me to one fix (see below), but
I also added code to handle unspecified cis/trans stereo
* test/testsym.cpp: Correct test results and add some new ones for the
-as option (with 0D MDL).
2010-08-26 Chris Morley
* src/depict/depict.cpp(DrawMolecule): fix so works with empty molecules
* src/formats/gamessukformat.cpp: fix typo
* src/formats/mdlformat.cpp: -as needs OBConversion::INOPTIONS
* src/obmolecformat.cpp: make -C option work again
2010-08-24 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/generic.h, src/generic.cpp: Improve on
functionality for OBOrbitalData -- including convenience functions
for loading lists of orbital energies.
* src/formats/gamessformat.cpp: Use it (closed-shell
calculations for now).
* src/formats/gaussformat.cpp: Grab new "z-matrix orientation"
coordinates given sometimes by Gaussian 09. Also add some
OBOrbitalData support.
2010-08-24 Chris Morley
* src/format/mdlformat.cpp: add -aP format to read only title
and properties only. Speeds up filtering of sdf datasets based on
their properties.
* src/ops/opisomorph.cpp: "extract" parameter on -s option to
retain only matched atoms. Useful for preparing templates for
--gen2D
* src/alias.cpp(FormulaParse): return false when lower case letter
encountered. Reduce chance of misinterpretation in this backstop
function.
* src/depict/depict.cpp: output D and T
* src/formats/gaussformat.cpp: fix bug with diatomics looking for
"Rotational Constants" when ther is only one.
* windows-vc2008/Distribution/NSISScriptToCreateInstaller.nsi:
put shortcut to babel guide to http://baoilleach.webfactional.com
for the time being.
2010-08-23 Noel O'Boyle
* src/formats/mdlformat.cpp: Make the "s" option work by resurrecting
some old code I had written and then subsequently removed. Atom
parities will now be used for 0D structures, but only if "s" is
specified.
2010-08-23 Noel O'Boyle
* include/openbabel/stereo/stereo.h, perception.cpp: Add doxygen docs
for TetStereoTo0D and change return value to bool.
2010-08-23 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.cpp (GetAtomicNum): Handle "Hl" hydrogen label from CIF
PR#3048959. Add warning when an unknown element label is provided.
* src/parsmart.cpp, include/openbabel/parsmart.h: Add thread-safe
SMARTS matching API, PR#3949927, thanks to David Koes.
* src/formats/mol2format.cpp: Disable tellg/seekg forwarding,
which is very slow with gzip-compressed mol2.gz
files. PR#3048758.
* src/formats/outformat.cpp: Handle new GAMESS-US/WinGAMESS output
files.
* src/kekulize.cpp: Add deeper recursion for aromaticity/kekule
determination. Solves a number of semi-rare molecules with 6+
fused 6-membered rings.
* test/files/forcefield.sdf: Fix Esomeprazole molecule -- not
protonated. This caused an impossible aromatization issue.
* test/files/*results.txt: Regenerate forcefield results.
2010-08-22 Noel O'Boyle
* scripts/CMakeLists.txt: Should have been using STREQUAL
not EQUAL when comparing strings. The Ruby bindings (among
others) were not being installed to the correct location.
2010-08-22 Chris Morley
It's a bit late for new features but the value of this one
shows up when writing command-line documentation.
* include/openbabel/obconversion.h, src/obconversion.cpp
(FullConvert,OpenAndSetFormat): When file name starts with -:
it is treated as SMILES and put in a stringstream rather being
used to open a ifstream.
* tools/obabel.cpp: pass through files starting with "-:", e.g.
obabel -:CN2C(=O)N(C)C(=O)C1=C2N=CN1C -ocan
Multiple use also possible. Not enabled in babel, but could be.
* src/obconversion.cpp: Comment out line end buffer deletion,
so cml conversion works but still have memory leak.
2010-08-19 Noel O'Boyle
* scripts/CMakeLists.txt: Get rid of return() statements by
reorganising logic. The way it was, if there was a problem
with the Python bindings, it would never make it to the
Java bindings, etc.
Now each set of bindings has two 'if' statements: the first
decides whether or not to try to compile the bindings; the second
actually does it (running SWIG if requested beforehand).
2010-08-19 Chris Morley
* windows-vc2008/Distribution/NSISScriptToCreateInstaller.nsi:
add the forgotten DLLs. Seems ok on XP but uninstall leaves some
folders in Windows 7.
2010-08-18 Chris Morley
* src/formats/fastsearchformat.cpp: make work with deprecated -S option
(-s is now an op and op names are case insensitive).
* tools/obabel.cpp: catch error when output specification missing
Remove messageSummary, which is really needed only when debugging.
Still in babel.
* src/formats/svgformat.cpp: small description change
2010-08-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/xyzformat.cpp (OpenBabel): Add parsing of 5th column
as partial charge -- supported by Jmol and others.
2010-08-18 Tim Vandermeersch
* include/openbabel/isomorphism.h, src/isomorphism.cpp: Use VF2
algortihm for finding isomorphisms and set this as default algorithm.
The class performes good enough for general purpose now and is
comparable in speed with the current smarts matching algortihm.
* include/openbabel/query.h, src/query.cpp: Make sure aromaticity is
handled correctly.
* test/automorphismtest.cpp, test/isomorphismtest.cpp: Add some more
tests.
2010-08-16 Chris Morley
* include/openbabel/math/vector3.h,src/math/vector3.cpp: add new
function, Point2Line()
* windows-vc2008/Distribution/NSISScriptToCreateInstaller.nsi: mods
to make help file local, add java bindings. Version 2.3.0rc
* doc/OpenBabelGUI.html, windows-vc2008/Distribution/ToolsPrograms.txt,
src/ops/xout.cpp,src/ops/partialcharges.cpp: documentation updates
2010-08-16 Noel O'Boyle
* include/openbabel/math/vector3.h: The components of a vector3 were
unaccessible from Python, so I've added GetX(), GetY() and GetZ(). The
exisintg x() method returns a reference to _vx (i.e. a pointer) and so
couldn't be used from Python.
2010-08-13 Chris Morley
* tools/obabel.cpp: by its design obabel cannot use multiple
concatenated single-character options. Ensure single ones with
an unregistered number of parameters work correctly.
* src/formats/fastsearchformat.cpp: extra error handling
2010-08-13 Chris Morley
* src/formats/inchiformat.cpp(ReadMolecule):Use GetStructFromINCHI
and not GetStructFromStdINCHI so can read both standard and
non-standard InChIs. Make error handling more robust.
2010-08-13 Noel O'Boyle
* src/mol.cpp: HasHydrogens() never returned True as the flag was
being cleared in AddHydrogens(). Reported by Alex Henderson on
openbabel-devel. Now fixed.
2010-08-13 Noel O'Boyle
* src/forcefield.cpp: Fixed a problem with invalid pointers in
WeightedRotorSearch that was resulting in weird geometries. I think I
introduced this problem back in May. Also noticed that the final
conformer returned had an off-by-one error. I think I also introduced
this problem at the same time.
2010-08-12 Chris Morley
* src/ops/opisomorph.cpp: make more robust to errors like a missing
file.
* src/descriptor.cpp: allow descripor parameters to be in quotes.
* src/formats/mdlformat.cpp: change the new -at option to -aT
because FastSearchFormat already uses -at.
* src/ops/xout.cpp, src/GUI/OBGUI.cpp: change the name of the op
xout to 0xout so that it is executed before other ops.
* src/GUI/optswx.cpp(SetOptions): ignore entries with both
checkbox and editboxes unless checked.
2010-08-12 Noel O'Boyle
* src/stereo/perception.cpp: CisTransFrom3D was not able to handle
deviations from ideal angles. Replaced existing method with one based
on the signed distance to the plane through the double bond at right
angles to the stereo unit.
* src/math/vector3.cpp, vector3.h: Move body of Point2Plane into new
function Point2PlaneSigned. Point2Plane now just returns
fabs(Point2PlaneSigned).
2010-08-09 Chris Morley
* src/formats/gaussformat.cpp:Comment out inconsistent use of
OBMol::SetEnergy(double).
The use of this needs to be agreed.
2010-08-10 Tim Vandermeersch
* include/openbabel/rotor.h, src/rotor.cpp: Add method to fix bonds
and mark fix atoms as deprecated. Update documentation.
* include/openbabel/conformersearch.h, src/conformersearch.cpp: Use
OBAlign with symmetry and update documentation.
* test/rotortest.cpp: Some OBRotor and OBRotorList unit tests.
2010-08-10 Noel O'Boyle
* src/builder.cpp, include/openbabel/builder.h: Add a Set/Unset method
for keeprings. This allows the user to keep the ring conformation from
the input molecule (this only makes sense if it's a 3D structure to
begin with).
2010-08-09 Chris Morley
* src/mcdlutil.cpp: fix to bug #3041650 (2D coordinates with
disconnected molecules), provided by Sergei Trepalin.
2010-08-09 Noel O'Boyle
* test/aligntest.cpp: Enable all parts of the alignment test
* src/math/align.cpp, include/openbabel/math/align.h: Use Tim's work
on masked isomorphisms. Small speedups in caching and matrix code.
All of the alignment tests now pass and do so quickly.
2010-08-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/CMakeLists.txt: Patch from Wayne Volkmuth to fix use of
PYTHON_PREFIX PR#3038634.
* scripts/openbabel-csharp.i: Fixed moduleclass error broken with
upgrade to SWIG 2.0.0.
* src/formats/moldenformat.cpp: Add "molf" extension found with
some example files.
2010-08-03 Chris Morley
* src/ops/opisomorph.cpp:-s replacement. Is used instead of
original in transform.cpp. Takes a SMARTS string as before,
but also a molecule file when the matching is done by Tim's
new isomorphism code which is less restrictive, e.g. bug#3029478
Also will color the substructure, mainly for svgformat.
* src/CMakeLists.txt: add the above file
* src/formats/fastsearchformat.cpp: rearraged to use the new -s
as the main target specification.
2010-08-03 Noel O'Boyle
* include/openbabel/generic.h: Don't clone OBRingData when copying a
molecule. If you do, you'll end up with two RingDatas because one will
already exist due to Kekulize() in EndModify() in operator= in OBMol.
Having more than one RingData causes problems as one can become
invalid.
2010-08-02 Chris Morley
* include/openbabel/obmolecformat.h,src/obmolecformat.cpp
(WriteChemObjectImpl) move the option implementation to a
separate function so that it can be used externally...
* src/formats/svgformat.cpp: ...like here.
2010-08-02 Chris Morley
* src/descriptors/filters.cpp: add new formula descriptor
* src/transform.cpp: remove --addformula, use --append formula
Make -s option do nothing if parameter is empty.
* src/obmolecformat.cpp: add --addindex
* src/parsmart.cpp:add onceOnly to SMARTS error
2010-08-02 Chris Morley
* include/openbabel/obconversion.h,include/openbabel/op.h,
include/openbabel/plugin.h,src/plugin.cpp,src/obconversion.cpp:
added some extra documentation on the OBPlugin concept and options
as suggested by Hans deWinter
* doc/examples/obfingerprint_getfingerprint.cpp: added an
example file
I haven't got doxygen working yet on my computer (do we really need
latex?) so the formatting of the above may need attention.
2010-08-01 Chris Morley
* data/svgformat.script: make zoom work with Chrome
* src/formats/svgformat.cpp: Make using internal color data the
default.
Use "sans-serif" as the font. Improves appearance in Opera.
2010-07-30 Chris Morley
* tools/obabel.cpp, tools/babel.cpp: allow e.g. '-L formats cml'
in addition to '-L cml' to handle cases where the same name is used
for two plugins of different types.
* src/GUI/OBGUI.cpp: now menu always returns details of plugin of
the correct type.
2010-07-30 Noel O'Boyle
* CMakeLists.txt, src/CMakeLists.txt: Add test for libdl. Now compiles
under FreeBSD (and hopefully the others too). Thanks to Florian Nigsch
for a build machine.
2010-07-30 Noel O'Boyle
* scripts/openbabel-python.i: Revert of r3914 (presumably it was a
mistake to include this file in the commit)
2010-07-29 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/smilesformat.cpp: Add detection for single-character
"bracket" elements, e.g., [n] for a fall-back. Fixes one failure
from sdfcansmi unit test.
* include/openbabel/chargemodel.h: Improved documentation, added
method to retrieve dipole moment (with scaling).
* src/charges/*: Add scaling factors calculated from regression
across NCI, Zinc, and other subsets (~1000 molecules).
2010-07-29 Noel O'Boyle
* include/openbabel/rotor.h: Fix memory leak in AddRotor
2010-07-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/sdfcansmitest.cpp: Added new unit test suggested by TJ
O'Donnell to check for canonical SMILES consistency from a
SDFile. Currently shows 4 / 48 failures.
2010-07-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/CMakeLists.txt: Only link getopt.c if needed. Removes
warnings from Clang and GCC about strlen on non-glibc platforms
(e.g. Mac).
* scripts/openbabel-python.i: Add chargemodel to Python bindings.
* src/mol.cpp (AddHydrogens): Fix crashes exposed by
buildertest. Make sure to clear flags even if we don't
actually add hydrogens.
* test/buildertest.cpp: Add asserts to ensure perception flags are cleared.
2010-07-26 Noel O'Boyle
* CMakeLists.txt, src/formats/CMakeLists.txt: Conditionally compile
gamessukformat.cpp only if MSVC or has regex.h. (Fix for MinGW
compilation)
2010-07-26 Noel O'Boyle
* scripts/CMakeLists.txt, openbabel-python.i: Pass -DHAVE_EIGEN2 to swig
and conditionally generate bindings for conformersearch.h.
2010-07-22 Chris Morley
* src/formats/mdlformat.cpp: right align atom numbers in A line, as
prompted by Igor Filippov.
* include/openbabel/tokenst.h: add functor to help withr deleting
containers of pointers.
2010-07-21 Noel O'Boyle
* include/openbabel/math/align.h: Add Doxygen docs. Update the default
constructor.
* src/math/align.cpp: Update the default constructor.
2010-07-21 Noel O'Boyle
* src/formats/povrayformat.cpp: POV-ray format has been neglected for
a long time. Based on Steven Wathen's comments on openbabel-discuss
(28/11/2009), I have gotten it to work. I also added options for
checkerboard, a mirror sphere and sky.
2010-07-21 Noel O'Boyle
* src/CMakeLists.txt: Only compile ops/conformer.cpp and
src/conformersearch.cpp if Eigen2 is found
2010-07-19 Chris Morley
* src/formats/inchiformat.cpp: make suitable for InChI 1.03.
Allow InChI options and re-enable -M and -F options for non-
standard InChI.
* include/openbabel/inchiformat.h: improve Description()
* windows-vc2008/libs/i386/libinchi.dll, libinchi.lib: add
* windows-vc2008/libs/i386/libstdinchi.dll, libstdinchi.lib: remove
* windows-vc2008/default_build.bat: change from libstdinchi.lib
to libinchi
* src/GUI/OBGUI.cpp,src/GUI/OBGUI.h: add menu item to shrink
window to minimum useful size.
2010-07-19 Chris Morley
* include/openbabel/plugin.h: reverted the last change. Something
seems to have gone wrong with the deobfuscation of the MAKE_PLUGIN
macro and was causing a crash in the GUI when formats were changed.
I did not find out the precise cause, but it seemed to be around the
default op. The difficulty of debugging this illustrates that using a
macro here is is not nice; we could do with a more C++ way of making
a plugin. Tim has suggested a possible approach
http://openbabel.org/wiki/Plugins
There is already an annotated version of the contents of the macro
at the end of the op.h, but it might not be up to date.
2010-07-16 Konstantin Tokarev
* New INSTALL file
* include/openbabel/plugin.h: Deobfuscated MAKE_PLUGIN macro
* src/formats/xml/cmlformat.cpp: Save and load bond labels in
CML format
2010-07-13 Chris Morley
Alternative method for read-conformers which maintains
code segregation (no chemistry in OBConversion)
* src/ops/readconformers.cpp: new OBOp to combine multiple conformers
into a single molecule.
* src/obconversion.cpp,src/transform.cpp:comment out read-conformers
code; minor doc mods
* src/obmolecformat.cpp: Change option name from "write-conformers"
to "writeconformers". The - was causing parsing problems in the GUI.
* src/ops/deferred.h,src/ops/sort.cpp: put DeferredFormat in
a new file.
2010-07-13 Chris Morley
* include/openbabel/op.h(OpOptions): ignore ops with
"not displayed in GUI" in the first line of their Descriptions()
* src/ops/conformer.cpp,src/ops/forcefield.cpp,tools/obgrep.cpp:
Add "not displayed in GUI" to some ops which use multiple extra options
that the GUI cannot yet display.
* tools/obgrep.cpp: fix so compiles in MSVC
2010-07-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/buildertest.cpp, src/mol.cpp: Clear flags for SSSR and
Aromaticity after adding hydrogens, as detected by the builder
test. Don't clear these flags in the test anymore.
* test/automorphismtest.cpp, test/aligntest.cpp: Find formats
correctly on UNIX.
* include/openbabel/mol.h: Return FindChiralCenters() to use new
IsChiral().
* scripts/CMakeLists.cpp: Require SWIG 2.0.0.
* src/chiral.cpp: Remove FindChiralCenters().
2010-07-12 Tim Vandermeersch
* Add OBConformerSearch class
* Add OBIsomorphismMapper and OBQuery
* Add --write-conformers option to (o)babel
* Add OpConformer to do conformer searching with (o)babel
* Add OpEnergy and OpMinimize
* Many documentation updates + add examples code (see cmake BUILD_EXAMPLES)
2010-07-10 Chris Morley
* include/openbabel/math/erf.h: local implementation of erf, because
not present in MSVC library.
* src/charges/qtpie.cpp, src/charges/qeq.cpp: use the above for MSVC
builds only, instead of boost.
* CMakeLists.txt: remove MSVC test for boost, which is not used
* windows-vc2008/default_build.bat: Remove absolute path for cmake;
it has to be in PATH now.
Add option for eigen. Eigen directory has to be in a env var.
2010-07-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/buildertest.cpp: Test for Noel's builder/ring.cpp
crash. Currently passes on Mac because of clearing flags. See code
comments for details.
2010-07-08 Chris Morley
* src/ops/sort.cpp(Do): replace stringstream by istringstream.
A reference to stringstream is apparently not a reference to istream
in g++, although is is in MSVC.
2010-07-07 Chris Morley
* include/openbabel/descriptor.h, src/descriptor.cpp:
Allow descriptors to have a parameter. External code which
defines new descriptors will need modifying (an extra parameter
on three functions. External code which just uses descriptors
is compatible.
* include/openbabel/groupcontrib.h,src/descriptors/groupcontrib.cpp,
src/descriptors/cansmidescriptor.cpp,src/descriptors/inchidescriptor.cpp,
src/descriptors/smartsdescriptors.cpp: make compatible.
* src/ops/sort.cpp: mods so that a parameter will be recognised
* src/descriptors/filters.cpp: make compatible and add a useless example
(commented out) which uses a parameter.
2010-07-07 Noel O'Boyle
* windows-vc2008/include/*, windows-vc2008/libs/i386/*: Add include
files and compiled libraries from bsd-xdr (required for xtcformat.cpp
under MSVC). BSD license.
* src/formats/CMakeLists.txt: Use the xdr library when compiling with
MSVC
* windows-vc2008/default_build.bat: Set the location of the xdr
library
* CMakeLists.txt: Ensure that the cmake configure finds the xdr
include files under MSVC
* src/formats/xtcformat.cpp: Rename 'small' to 'small_' as small is a
typedef for 'char' under MSVC (or something like this)
2010-07-07 Noel O'Boyle
* CMakeLists.txt, src/formats/xtcformat.cpp,
src/formats/CMakeLists.txt: Check for rpc/xdr.h and conditionally
compile xtcformat.cpp. (In preparation for MSVC support...)
2010-07-06 Noel O'Boyle
* src/formats/gamessukformat.cpp, CMakeLists.txt: Enable GAMESS-UK
format under MSVC (uses std::tr1::regex instead of regex.h)
2010-07-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/inchi103, src/formats/inchi103: Import final InChI 1.03
release.
2010-07-06 Noel O'Boyle
* include/openbabel/forcefield.h: Fix memory leak identified by VLD
2010-07-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefields/forcefielduff.cpp: Revert changes and parse
extra parameters for now.
* doc/Doxyfile: Renamed from Doxyfile.in (not generated by
autoconf anymore). Generate ob.tag file for projects generating
doxygen documentation with Open Babel symbols (e.g., Avogadro).
* src/oberror.cpp: Fix from Seth Alves to initialize stream
buffers (from Valgrind).
2010-07-05 Konstantin Tokarev <annulen@yandex.ru>
* THANKS, authors.txt: Added myself to contributors
2010-07-04 Noel O'Boyle
* src/formats/*format.cpp: Added text from wiki formats [F-Z] to their
Descriptions in the .cpp file.
2010-07-03 Chris Morley
* src/GUI/optswx.cpp: can use "not displayed in GUI" in option
list in Description()
* include/openbabel/depict/painter.h add operator += for OBColor
* include/openbabel/depict/depict.h,svgpainter.h,
src/depict/depict.cpp, src/depict/svgpainter.cpp: add option
for internalColor on atoms and bonds (by OBPairData)
* src/formats/svgformat.cpp:add option to display internalColor
Remove "Additional Option" in Description
* src/formats/xml/cmlformat.cpp: read and write color on bonds
* src/ops/substructdata.cpp:add new op --ss which is like -s but
colors the substructure
2010-07-02 Noel O'Boyle
* include/openbabel/base.h: Add OBAPI declaration to new global
function OBReleaseVersion()
2010-07-01 Noel O'Boyle
* src/formats/*format.cpp: Added text from wiki formats [A-F] to their
Descriptions in the .cpp file. I added some markup to CML and
Fastsearch.
2010-07-01 Konstantin Tokarev <annulen@yandex.ru>
* src/confi.h.cmake: Added macros OB_VERSION_CHECK and OB_VERSION
2010-06-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefield.cpp: Set fixed atom constraints on rotor rules
during rotamer/conformer searching, from Chris Wassman.
* include/openbabel/base.h, src/base.cpp: Add OBReleaseVersion()
global function, as suggested by Tobias Schmidt for code detection
of versions and features. (Most useful from scripting interfaces,
which won't have BABEL_VERSION as a macro.)
2010-06-29 Chris Morley
* tools/babel.cpp, tools/obabel.cpp: -H no longer lists all formats
(As suggested by Noel)
* include/openbabel/plugin.h: correct small error causing warning
* src/format.cpp, src/plugin.cpp: small formatting changes in List
output.
2010-06-29 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/charges/qeq* src/charges/qtpie* data/qeq.txt: Move QEq and
QTPIE parameters to the data file. Parameters are possibly suspect
for non-standard elements. Jiahao Chen will send revised versions later.
* data/UFF.prm: Remove QEq parameters -- not used by UFF.
2010-06-29 Noel O'Boyle
* CMakeLists.txt: Avoid warnings with MinGW when compiling the exes
2010-06-29 Noel O'Boyle
* src/formats/*format.cpp, src/formats/xml/*format.cpp: Edit some
Descriptions() to replace Input with Read and Output with Write. Also
uppercased any "options" to "Options".
2010-06-29 Noel O'Boyle
* src/formats/xml/cmlformat.cpp: Partial fix for chiral N problems.
See PR#3022295.
2010-0628 Chris Morley
* include/openbabel/depict/depict.h, src/depict/depict.cpp:
Use a bitset for options like drawTerminalC, so that extendable
while binary compatible. Add a few more options display options.
* src/formats/svgformat.cpp: add a few more display options.
Augment Description() as a possible prototype for Noel's more
formatted documentation.
2010-0628 Chris Morley
* src/GUI/optswx.cpp: when using Description() strings to construct
GUI option checkboxes, ignore lines with 4 or more leading spaces
within each option list. Allows better formatted documentation, as
proposed by Noel.
* src/formats/*format.cpp: remove remaining continuation characters
in Description()s and replace by concatinated ""..." ""..."
2010-06-24 Chris Morley
* src/formats/mdlformat.cpp:Prevent unnecessary error message with
blank line at end of SDF file.
2010-06-23 Noel O'Boyle
* src/kekulize.cpp, include/openbabel/mol.h: Fix compilation errors
with MSVC (and replace some Tabs with whitespace)
2010-06-23 Tim Vandermeersch
* src/ring.cpp: LSSR selection seems to work now. It is based on
lemma 1 from the Vismara paper. (See source for complete reference)
* src/obiter.cpp, src/ring.cpp: Ring sets should no longer be
acquired using OBMol::GetData(OBGenericDataType::RingData). Ring
sets now have the correct "SSSR"/"LSSR" attribute set.
* src/kekulize.cpp: Use LSSR.
* test/lssrtest.cpp: Add tests for LSSR composition. All unit tests
pass except for smarts (was broken before) and py_kekulize. I'm not
sure why the last test fails but the stored results might need updating?
2010-06-22 Tim Vandermeersch
* include/openbabel/mol.h, src/mol.cpp: Add LSSR, add aromaticity
changes from Craig.
* src/ring.cpp: Add LSSR (FindLSSR, GetLSSR, ...)
* src/kekulize.cpp: Changes to aromaticity from Craig James. Still
uses SSSR.
* test/CMakeLists.txt, test/lssrtest.cpp: Add unit test for LSSR.
The test reorders the atoms and checks if the same rings are found.
Currently used aromatics.smi, attype.00.smi and nci.smi. All 1327
test cases pass. (old ring & aromatics test still pass. py_kelule
test fails though.)
2010-06-21 Noel O'Boyle
* src/builder.cpp: Fix bug when correcting tet stereo where there is
an Implicit H
2010-06-20 Noel O'Boyle
* src/formats/pdbformat.cpp: the_res not NULL-terminated. Resulted in
junk output after residue name in PDB files.
2010-06-20 Noel O'Boyle
* src/formats/mol2format.cpp: Removed obsolete code that was causing
performance problems on large files (e.g. proteins). Fixes
bug #3018188
2010-06-19 Chris Morley
* src/formats/mdlformat.cpp: Added warning message when reading
misformed files with too many atoms or bonds. Bug #2971865
2010-06-18 Noel O'Boyle
* doc/Doxyfile.in: Update to Doxygen 1.7.0 and turn SEARCHENGINE on.
* doc/api-style.css (removed), doc/api-header.html: Old style file
removed as out-of-date with respect to
Doxygen 1.7.0 (instead, the automatically generated doxygen.css is used)
2010-06-17 Noel O'Boyle
* src/stereo/perception.cpp: Fix to previous commit for Linux.