2007-07-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/Makefile.am, src/Makefile.in: Bump library version for 2.1.1
release.
2007-07-05 Chris Morley
* src/formats/inchiformat(WriteMolecule): downgraded the InChI
message "Tetrahedral stereo info not available" to obInfo,
since it arises from the workings of the the opaque OB chirality
system. Also added the molecule number for identification.
* src/GUI/OBGUI.cpp, tool/babel.cpp: added &std::cout to the
call to OBConversion::Write() for the APIInterface, because the
previous NULL value was causing it to be ignored. This meant
that ---errorlevel wasn't working, as again found by Noel.
2007-07-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mdlformat.cpp (MDLFormat::ReadMolecule): Add
additional error and warning messages, including a check if the
atom/bond block doesn't work. Fixes crash reported by Joe Bedell,
Sigma-Aldrich.
* Makefile.am, Makefile.in: Skip INSTALL.Windows, deleted by
Chris.
2007-07-04 Chris Morley
* src/finger3.cpp: Trim firts line which decided format of
patterns.txt. In Windows there was trailing \r which caused
none of the patterns to be read, as found by Noel.
2007-07-04 Chris Morley
* src/formats/smilesformat.cpp(CreateSmiString): call
FindClosureBonds even when all atoms are chiral.
(GetSmilesElement): only call GetChiralStereo when
atom has is specified clockwise or anticlockwise, not just chiral.
2007-07-02 Noel O'Boyle <baoilleach@gmail.com>
* include/oberrors.h: Fixed typo in Doxygen
2007-07-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, */Makefile.in: Updated with patch from
Jean Brefort. Adds new --with-pkglibdir flag to facilitate
packaging with versioned format directories.
2007-07-01 Chris Morley
* src/obconversion.cpp(InstallStreamFilter): test for non-zero
pInFormat to avoid crash with no input.
* src/formats/gamessformat.cpp: Test for "$END" now works on $END$.
Put size test first. Fixes bug #1738005 and probably #1745066.
* INSTALL.Windows: deleted obsolete file
2007-06-30 Chris Morley
* src/formats/smiles format.cpp(GetSmilesElement):do not always
output atoms in 2D molecules in bracket form if the chirality
is not specified (fix for bug #1738355)
* src/GUI/OBGUI.cpp: small change to About text
2007-06-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/pdbformat.cpp: Fix for PR#1705895 -- check for
string length before trying to read the 3rd character. Causes
crash on Windows.
* scripts/Makefile.*: Fix for change in Ruby build script.
* src/formats/gaussformat.cpp (and others): Fix for
PR#1737209. Return false for reading a molecule with no atoms. In
these formats, empty molecules are invalid.
2007-06-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/obenergy.cpp, tools/obminimize.cpp: Minor feature request
1722878 to add hydrogens before running force field
calculations for Chris Swain.
2007-06-24 Geoffrey Hutchison <babel@geoffhutchison.net>
* NEWS: Update for upcoming 2.1.1 release.
* src/formats/pdbformat.cpp (ReadMolecule): Add a new OBPairData
for any record we don't currently parse. This way all data is
preserved.
* src/formats/mol2format.cpp: Fix PR#1739905. Add warning if
elements cannot be interpreted as atom types correctly (e.g., this
GaussView file). Instead, attempt to interpret as element names.
* data/types.txt: Fix two HO typing errors, which masked this
bug.
* scripts/openbabel-ruby.i: Fix module declaration -- really
OpenBabel.
* tools/obminimize.cpp: Minor fix requested by Chris Swain --
allow setting output format using -o flag.
* tools/obfit.cpp: Add RMS output to standard error.
2007-06-23 Noel O'Boyle <baoilleach@gmail.com>
* scripts/*.i (except Perl, which was already done): Added
groupcontrib.h and updated wrapper code
* scripts/python/Pybel stuff:
Added calcdesc() method to Molecules for descriptor calculation
Added update() method to MoleculeData
Convert to string before setting a value in MoleculeData
Updated tests, and API docs
2007-06-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, Makefile.*: Updates from the Cygwin
ports project for better compatibility (e.g., shared format
modules on Cygwin). Thanks to Yaakov of Cygwin ports and Noel.
2007-06-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/chemdrawcdx.cpp: Fix a Universal binary problem on
Mac OS X. We cannot rely on an autoconf test since the compiler is
run twice: for ppc and i386. Thanks to Mike Stump from Apple for
help.
* scripts/java/: Updated classes for vectors of rings and vectors
of strings.
* Makefile.am, Makefile.in: Update for Chris's removal of the
windows directory below.
2007-06-05 Chris Morley
* src/formats/smilesformat.cpp(PaseSmiles):ignore any char<0
Caused crash in isspace() in Visual C++8. Fixes bug
#1730132 for this compiler at least.
* windows/: Delete. This should have gone before because we are
no longer supporting VC++6.
* src/GUI/OBGUI.cpp(OnGetInputFile): Delete | wxHIDE_READONLY
so that compiles with v2.8.3 of wxWidgets.
2007-06-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/cansmilesformat.cpp (AddHydrogenToChiralCenters):
Fix PR#1700301. Never attempt to create atoms while iterating
through the molecule. Safer technique -- keep a list of atoms to
add hydrogens, add in a separate step.
(AtomIsChiral): Fix PR#1699418. When determining chiral
information for canonical SMILES, make sure to check if the atom
is 3D. Otherwise it will never have wedge/hash bond flags.
* src/mol.cpp (DeleteHydrogens): Update to fix PR#1704551 with H-H
bonds not deleted.
* src/formats/smilesformat.cpp: Add warning message for unmatched
ring closures described below.
* configure, configure.in: Bump to 2.1.1 version.
2007-06-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* Doxyfile: Bump to 2.1.1 and add search engine support.
* src/formats/smilesformat.cpp: Fix bug reported by Craig with
un-matched ring closures. These should now always be rejected,
since _rclose will not be empty.
* test/files/invalid-smiles.txt: Add ring closure tests from
Craig.
* test/mol.cpp: Add test for H-H deletion bug reported by Donald,
PR#1704551.
2007-06-01 Noel O'Boyle <baoilleach@gmail.com>
Final changes for Windows release of OBPython 1.2
* windows-vc2005/OBPython/setup.py: bumped version up to 1.2
* scripts/python/pybelapi.py: updated API docs
2007-05-30 Chris Morley
* include/openbabel/base.h(tokenize): Add \r to default
delimiters in the two functions. Now Windows or old Mac files
(esp data files) should be read properly.
Cures bug #1727333, I hope.
2007-05-30 Chris Morley
* src/fingerprint.cpp(Tanimoto): return 0.0 if no bits set.
Should cure bug #1728410.
2007-05-30 Chris Morley
* include/openbabel/lineend.h: remove sync()call from destructor
so that can delete in OBConversion's destructor after
istreams have gone.
* include/openbabel/obconversion.h, *src/obconversion.cpp
Add InstallStreamFilter() and call from Read() and Convert().
I hope this will cure the Windows Python bug, and is a neater
method all round.
2007-05-25 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/xml/cdxmlformat.cpp: don't clear the molecule
before writing. [#1725343]
2007-05-14 Chris Morley
* src/obconversion.cpp(Read, Convert): Do not install a
FilteringInputStreambuf if stream already contains one. This
solves my problem with multiple reads on the same input stream.
2007-05-13 Chris Morley
* src/obconversion.cpp(Read): Ensured that FilteringInputStreambuf
is used. Previously it wasn't, which could cause errors
except with unix reading unix files.
2007-05-12 Noel O'Boyle <baoilleach@gmail.com>
* SWIG interface files: Added template for vectors of strings
* pybel.py: Added informats and outformats, dictionaries corresponding
to the supported input and output formats
2007-05-11 Jean Brefort <jean.brefort@normalesup.org>
* include/openbabel/format.h: add missing new line (makes gcc happy).
* src/formats/xml/cmlformat.cpp: ditto.
2007-05-10 Noel O'Boyle <baoilleach@gmail.com>
* pybel.py: Added support for unitcell, and deletion of OBPairData
(need to update the tests and the API docs)
2007-05-08 Chris Morley
* include/openbabel.h/base.h, src/base.cpp: corrected
bug in DeleteData(OBGenericData*) which is the probable
cause of bug #1715092. Added new function DeleteData(string)
which makes it easier to use.
Moved the declarations for Tokenize and Trim from mol.h to
base.h so that they could be used more widely. Maybe there is
an even better home.
2007-05-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/*.i: Added casting from OBGenericData to OBUnitCell.
2007-05-08 Noel O'Boyle <baoilleach@gmail.com>
* scripts/*.i: added a template for a vector of OBRing*
which is required for OBMol.GetSSSR()
2007-05-08 Noel O'Boyle <baoilleach@gmail.com>
* scripts/*.i: added a method to cast OBGenericData to
OBPairData.
* scripts/python/pybel.*: added dictionary-like support for
accessing molecule data, and updated the tests and the API
documentation.
2007-04-30 Chris Morley
* NSIS installer script: Add some extra data files, replaced
*.* which was causing extra files to be copied, and deleted
HKCU/SoftwareOpenBabelGUI/ on uninstall.
As used in OpenBabel2.1.0_Windows_Installer.exe
2007-04-26 Noel O'Boyle <baoilleach@gmail.com>
* NSIS installer script: Updated to install the MS VC++
run-time installer
2007-04-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure, configure.in: Bump version to 2.1.1b1.
* */*.cpp, include/*.h: Warning fixes contributed by Jean Brefort.
2007-04-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/inchi/strutil.c: Bug reported on the InChI mailing
list.
* src/formats/inchiformat.cpp: Bug caught during ChemSpotlight
testing -- some files don't have chirality information (e.g., 3D
files but with 0.0 coordinates throughout). Warn and give up.
2007-04-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* NEWS: Minor fixes for 2.1.0 final release.
2007-04-05 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* data/psa.txt: corrected smiles for 3-rings.
* src/groupcontrib.cpp: call ConvertDativeBonds before assigning
contributions, is needed for TPSA (e.g. [N](-*)(=*)=* ). Update to
documentation.
* include/openbabel/groupcontrib.h: documentation update.
2007-04-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/residue.h: Undo previous change. Rich Apodaca
suggested some SWIG-fu instead.
* scripts/ Update accordingly. Includes ruby changes, new README
and examples.
2007-03-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/base.cpp: Additional "What's new" documentation for 2.1
release.
* include/openbabel/residue.h: Hide some residue names (e.g.,
_1MG) from SWIG wrappers -- such constants are not valid symbols
in some languages like Ruby.
* scripts/ Update accordingly.
2007-03-29 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/: Updated interface wrappers, including new Java
README. (Java is confirmed to work on Mac OS X.)
2007-03-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp: Make sure to always return from any
exception. Otherwise we could crash running code.
* src/formats/mdlformat.cpp: Avoid infinite loop in
ParseAliasText.
* src/formats/acrformat.cpp: Minor formatting change.
* test/Makefile.am, test/Makefile.in, test/wrapper.sh: Add
inchiwrite tests to suite.
* test/inchiwrite.cpp, test/inchi.pl: Formatting to integrate into
Perl "prove" test suite.
2007-03-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/obprop.cpp (main): Fix PR#1688251 with while/for loop on
CML files. Thanks to Tapani Kinnunen for the report.
* src/formats/mol2format.cpp: Fix problem reported by Noel with
"USER_CHARGES" appearing instead of Gasteiger.
* src/data.cpp, src/groupcontrib.cpp: Fix doxygen warnings.
* include/openbabel/groupcontrib.h: Documentation fixes.
* NEWS: Minor fixes.
* doc/*.1, doc/*.html: Documentation updates.
2007-03-24 Benoit Jacob <jacob@math.jussieu.fr>
* include/openbabel/atom.h, src/atom.cpp: Change SetVector to
const parameter.
2007-03-23 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/psa.txt, data/mr.txt, data/logp.txt: Small changes -- DOS
to UNIX line endings.
* test/Makefile.am, test/Makefile.in: Make sure to add inchiwrite
to compile list.
* test/wrapper.sh: Add notes on passing arguments to "prove."
* tools/obprop.cpp: Fix formatting problems - PR#1685879, reported
by Tapani Kinnunen.
* src/formats/mol2format.cpp: Add new -xl flag to output "ligand
only" data (i.e., no residue info). Fixes PR#1683788.
* src/formats/smilesformat.cpp: Fix PR#1680070 with output of
chiral root (first) atoms. Really need to clean up BuildTree()
since that if() statement is messy, but works for 2.1 release.
2007-03-23 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* data/psa.txt: Added ";heavy", fixes the logp_psa test.
* tools/obprop.cpp: Function string sequence(OBMol) was not returning
any string.
2007-03-22 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefield.cpp: When determining length, if two atoms are
really close, add a small random separation (~0.1Ang). Fixed
PR#1684479.
2007-03-22 Chris Morley
* windows-vc2005: Simplified projects to OpenBabelDLL with driver
programs for commandline, GUI, and Python interface.
* include/openbabel/forcefield.h: So that the Python build
in Windows will work, added a dummy function so that the
compiler will really make some functions of the templated class
OBIter<OBForceField> which SWIG is expecting. The needs to be
done properly, but needed to get it working for the 2.1 release.
* include/openbabel/obconversion.h and src/obconversion.cpp:
added the patches supplied by Jerome Pansanel for providing a
list of available formats.
2007-03-20 Chris Morley
* src/formats/xml/cmlformat.cpp: Add code to write W and H in
bondstereo. Ensure <bondStereo> is written in array form.
Mods inDoAtoms to read the right set of atom coordinates.
Add option to write bonds as aromatic.
2007-03-19 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp: Amend yesterday's change to address double
free() bug, PR#1683541. Still don't like this, as it could leak
the zip_istream we create.
* src/parsmart.cpp: Fix PR#1683890 for SMARTS pattern 'x' with no
number. Default is "at least one ring bond."
* test/files/smartstest.txt, test/files/smartsresults.txt: Update
for above. 'x' pattern and 'x0' pattern.
2007-03-19 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/mol.cpp: OBMol::DeleteAtom - Moved DeleteAtom to *after* the
EndModify call. At this point the atom is already removed from the _vatom
vector. OBMol::DeleteBond - Moved DeleteBond to *after* the EndModify
call. At this point the bond is already removed from the _vbond vector.
2007-03-18 Chris Morley
* src/formats/mdlformat.cpp: Added support for atom aliases when
reading. It's not much described in the main MDL specification,
so this implementation is just adequate to handle the InChI
samples, where for some reason, this antiquated feature is
used in several molecules.
* src/formats/inchiformat.cpp(ReadMolecule): Now reads implicit
H isotopes.
(WriteMolecule): rewrote option to not display routine warnings.
* test/: Added inchiwrite.cpp, two NIST sample molecule sets and
annotated results sets.
* src/formats/getinchi.cpp: Added declaration of GetInChI().
* src/canon.cpp (FixCisTransBonds): changed | to || in if statement
* src/forcefield (GenerateCoordinates): initialize torang to 0,
to avoid compiler warning. This variable doesn't seem to be
doing much but please could somebody check this is ok.
2007-03-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/mol.cpp (Separate): Add support for copying, updating
OBChiralData. Fixes PR#1680730.
* src/obutil.cpp: Fix typo in yesterday's change.
* test/logp_psa.cpp: Update to output predicted values, even if
they match.
* src/obconversion.cpp: Make sure to declare the new readbuf
outside of the if() scope.
2007-03-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/molchrg.cpp: Add new OBPairData descriptor "PartialCharges"
to express origin as Gasteiger charges.
* src/formats/qchemformat.cpp, src/formats/mopacformat.cpp,
src/formats/gamessformat.cpp, src/formats/gaussformat.cpp:
Set PartialCharges descriptor to express origin as Mulliken
charges.
* src/formats/mol2format.cpp: Use above.
* src/*: Strip out 0.0f and similar floating-point casts,
extending yesterday's changes with forcefield.cpp. Defensive
programming against similar floating-point issues.
2007-03-16 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/atom.h, include/openbabel/mol.h: Fix
PR#1626789 with large PDB files. Fixes regression to 2006-09-25
changes supporting >2^16 atoms or bonds.
* src/mol.cpp(EndModify): Ensure idx is unsigned (to match atom indexes).
* include/openbabel/chains.h, src/chains.cpp: Make sure atomids is
int, not short. Atom IDs can go up to a full unsigned int.
* src/formats/chemdrawcdx.cpp: Some code cleanups, including use
of obErrorLog.
* src/forcefield.cpp: Fix PR#1680717. Seems to be an issue with
floating-point roundoff. When 0.0f and similar tags were removed,
works great.
2007-03-16 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/groupcontrib.cpp, include/openbabel/groupcontrib.h: General
class to handle group contribution algorithms (LogP, TPSA, MR, ...).
Also contins OBLogP, OBPSA and OBMR. Should these simple classes be
bundled in a OBDescriptors class?
* src/logp.cpp, src/psa.cpp, include/openbabel/logp.h,
include/openbabel/psa.h: moved to groupcontrib.cpp/h
* data/mr.txt: data for molecular refractivity.
* test/logp_psa.cpp: forgot to commit.
2007-03-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/inchiformat.cpp, src/formats/cmlformat.cpp: Fix compile
problems with GCC and last changes. (Return value from
OBChiralData should be assigned to a full object.)
* src/obconversion.cpp, src/obconversion.h: Tackle some gzip
problems, including PR #1617838. We need to be sure we don't try
to gzip twice. Create a zip_istream pointer, then free it as
needed.
* scripts/*: Updated for recent library changes.
2007-03-13 Chris Morley
* src/formats/inchiformat.cpp: Add bond stereo handling to
ReadMolecule(). Correct 0D stereo in reading and writing.
Remove the waring message about stereochemistry. Apart from
a few special cases, e.g. allenes, 'either' parity, I think
the InChI writing and reading is now ok., but still more
testing needed...
TestFormat messages improved.
* src/formats/xml/cmlformat.cpp: Correct handling of 0D
atomParity on reading and writing.
* src/GUI/optswx.cpp: Added documentation
2007-03-13 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefields/forcefieldghemical.cpp: Fix 1,4-scaling problem.
2007-03-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefields/forcefieldmmff94.cpp: Switch pow() to use
doubles to prevent compile problems on older Linux/GCC systems.
Switch to using OpenDatafile.
* src/logp.cpp, src/psa.cpp: Switch to use OpenDatafile() call.
* src/fingerprints/finger3.cpp: Likewise.
* src/forcefields/forcefieldmm2.cpp,
src/forcefields/forcefieldghemical.cpp: Likewise.
* src/formats/xml/Makefile.am, src/formats/xml/Makefile.in: Fix
problems with compiling XML formats on Mac OS X.
* include/openbabel/Makefile.am: Make sure to include psa.h and
logp.h in distribution.
* src/data.cpp: Move comments to provide better documentation for
OpenDatafile. Switch OBGlobalDatabase::Init to OpenDatafile.
* include/openbabel/data.h: Add envvar argument to OpenDatafile.
* config.sub, config.guess, configure, Makefile.*: Update with
automake-1.10 and autoconf-2.61.
2007-03-13 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* tool/obminimize.cpp: added '-sd', '-cg', '-c criteria' options
* doc/obminimize.1: update for added options (man pages for obenergy
and obminimize are also on wiki now)
2007-03-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mopacformat.cpp: Added patch #1676963
for MOPAC 2007 output format. Thanks to 'dn2010.'
(Daniil Bratashov). Solves PR#1654907.
* src/formats/qchemformat.cpp: Added support for keywords.
* src/formats/acrformat.cpp: New format, contributed by Daniel
Mansfield.
* src/formats/Makefile.am, src/formats/Makefile.in: Add acrformat.
* src/formats/gaussformat.cpp: Add feature to write bonds,
contributed by Daniel Mansfield.
* src/formats/fchkformat.cpp: Add initial support from Maxim
Fedorovsky. (Maxim's contribution also supported vibrational data
using Eigen and matrix operations.)
* include/openbabel/generic.h, src/generic.cpp: Include
OBVibrationData class (even if the matrix operations to use it
aren't in Open Babel yet).
* tools/obprop.cpp: Additional properties, including canonical
SMILES and InChI. Fixes request PR#1620842.
* THANKS: Work on updates for 2.1 release.
* NEWS: Likewise.
2007-03-11 Chris Morley
* src/data/atomtyp.h: Aggressive simplification of
IMPVAL for oxygen and new value for Si. Read and test with
/test/files/FormulaTest.smi. Solves bugs 1635901 and
1474930
* include/openbabel/forcefield.h: Remove unused
#ifndef isnan
2007-03-11 Chris Morley
* src/formats/inchiformat.cpp: Moved handling of InChI
options to new subroutine and it added options to
ReadMolecule().
In WriteMolecule() removed deletion of OBChiralData and
re-zeroed z coords, so that OBMol is unchanged.
* src/GUI/OBGUI.cpp, OBGUI.h: Made default ostream a
stringstream which is written to textbox at end. Solves
bugs 1596906 and (probably) 1669973.
Added facility for copying output to input.
* src/GUI/optswx.cpp,stdwx.cpp:Leave header files in src/GUI
2007-03-10 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/psa.h, src/psa.cpp, src/Makefile.am,
src/Makefile.in, data/psa.txt: Added OBPSA class.
* tools/obprop.cpp: Added PSA property.
* test/logp_psa.cpp: LogP and PSA test for 3 molecules.
2007-03-10 Chris Morley
* src/formats/inchiformat.cpp(WriteMolecule): For 2D molecules
use a modified CalculateChiralVolume() to add psueudo z
coordinates, rather than using InChI's 2D bond stereo method.
I think we are close to getting the InChI write stereochemistry
right at last, but systematic checking needed.
* include/openbabel/chiral.h, src/chiral.cpp
(CalculateChiralVolume): add backwards-compatible extra
parameter to facilitate use of pseudo z coordinates.
* src/formats/cansmilesformat.cpp(BuildCanonTree): two more
instances of the bug corrected yesterday.
2007-03-10 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure, configure.in: Bump for 2.1.0b7 snapshot.
* Doxyfile: Bump version for eventual 2.1.0 release.
* src/*, src/formats/*: Add OBGenericData::SetOrigin calls to
provide attribution to sources of data: file input, user input,
perceived, etc.
* tools/obfit.cpp: Likewise.
2007-03-09 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/logp.h, src/logp.cpp, src/Makefile.am,
src/Makefile.in, data/LogP.txt:
Added OBLogP class (see mailing list).
* tools/obprop.cpp: Added LogP property.
2007-03-09 Chris Morley
* src/formats/cansmilesformat.cpp(BuildCanonTree):The insert in
line 893 invalidates iterator ai. Add a line so that the subsequent
test (outside the loop) does not crash my debug build but always
is false - no push_back. Solves bug 1650790. I hope that Craig or
somebody can check whether the cannonical SMILES output is still ok.
2007-03-09 Donald E. Curtis <dcurtis3@sourceforge.net>
* include/obiter.h: added deconstructor functions. Lack of these can
cause problems when using the FOR_*_OF_* macros.
2007-03-08 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* forcefield.h/cpp: documentation update.
2007-03-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/smilesformat.cpp: Fix problem with "invented" stereo
from 2D files -- make sure to check bond torsion ~0.0 and
~180.0. Fixes PR#1663814.
* doc/*.1: Initial cleanups of man pages, including new pages for
obenergy, obminimize, and obrotamer.
* Doxyfile-man: Update to point to new babel location.
* src/chains.cpp: Fixing bug with chain perception related to
PR#1626789, and 1577248. Setting visit flags skipped
marking some atoms as members of residues.
* test/residue.cpp: Add new tests for PR#1577248.
* data/types.txt, data/types.h: Add Lp atom type for Sybyl based
on PR#1672575.
2007-03-08 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/obutil.cpp: moved IsNan() to here. Hopefully this will eliminate
the problem with non C99 compatible compilers.
* src/forcefield.cpp: update documentation + small optimization
changes.
* include/openbabel/forcefield.h: update documentation (in progress).
* tools/obenergy.cpp: Added man page.
* tools/obminimize.cpp: Added man page.
2007-03-07 Chris Morley
* src/for,ats/smilesformat.cpp(FixCisTransBonds): replace
bitwise | by logical ||.
I guess if (v1 < 2 || v1 > 3 || v2 < 2 || v2 > 3) was meant.
* include/openbabel/base.h(GetData(DataOrigin), base.cpp:
This was returning a reference to a local object.
Return a copy of it instead.
* src/formats/inchiformat.cpp: Reformat Description().
In WriteMolecule, modify bond stereo to work with new Up/Down
usage.
* src/formats/xml/cmlformat.cpp: For reading and writing,
modify bond stereo to work with new Up/Down usage.
Now writes bondStereo elements in array form.
2007-03-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/obdoc.cpp: Update for wiki format to facilitate updates
after 2.1 release.
* src/formats/pdbformat.cpp: Mark that chain/residue
perception is not needed. Make sure that code anticipates atoms
with no residue.
* src/data.cpp (OBResidueData): Anticipate that some atoms will
have no residue.
* src/formats/mopacformat.cpp: Add keyword support, fix problem
with writing molecules (i.e., molecule was cleared before
cartesians written).
* src/formats/smilesformat.cpp, src/formats/mol2format.cpp,
src/formats/xml/cmlformat.cpp, src/formats/carformat.cpp,
src/formats/cifformat.cpp, src/formats/fastaformat.cpp,
src/formats/gaussformat.cpp, src/formats/gamessformat.cpp,
src/formats/alchemyformat.cpp, src/formats/cansmilesformat.cpp:
Clean up descriptions and indentation.
2007-02-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefield.cpp, src/forcefield.h: Cut out some compiler
warnings from GCC. Remove is14(), already available through
OBAtom::IsOneFour.
* src/forcefields/forcefieldghemical.cpp: Make sure to return from
all functions.
* src/dlhandler_unix.cpp: Use global loading. May improve script
language interface on Linux.
* include/openbabel/base.h, src/base.cpp: Support for filtering
OBGenericData based on the source.
* include/openbabel/generic.h, src/generic.cpp: Likewise.
* test/files/smartsresults.txt: Fix results based on Craig's
SMARTS changes today.
2007-02-28 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp: Replaced isnan() by OBIsNan().
2007-02-28 Craig James <cjames@emolecules.com>
* src/formats/smilesformat.cpp: Fixed PR#1663854 "Canonical SMILES
gives incorrect cis/trans" in cansmilesformat.cpp, also fixed the
same problem in smilesformat.cpp.
* Disabled SMARTS parsing of cis/trans '/' and '\', these are
temporarily treated as ordinary single bonds, due to severe bug
in SMARTS matching. See PR#1663730, this is a temporary workaround.
2007-02-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mol2format.cpp: Fix PR#1666406 with mis-typed Sybyl
atom types.
* data/types.txt, data/types.h: Likewise.
2007-02-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/inchiformat.cpp: Fix compile problems on GCC.
* src/mol.cpp: Fix PR#(PR#1665519) with AddHydrogens when no
conformers are available.
* Doxyfile: Remove babelconfig and config from header list.
* src/patty.cpp: Mark as deprecated.
* src/fingerprint.cpp, src/mol.cpp, src/typer.cpp
src/parsmart.cpp, : Documentation updates.
* include/obmolecformat.cpp, src/formats/obmolecformat.cpp,
include/openbabel/xml.h, include/openbabel/typer.h,
include/openbabel/parsmart.h, include/openbabel/rand.h,
include/openbabel/mol.h: Likewise.
2007-02-26 Chris Morley
* src/formats/inchiformat.cpp(WriteMolecule): Mods to 0D and 2D
stereochemistry; more to be done, work in progress.
Added Option to use InChI options.
* src/formats/mdlformat.cpp(ReadMolecule):Use the content of
any "NAME"(case independent) property as OBMol title if there
is not already one.
* src/format/xml/cmlformat.cpp, xml.cpp(GetContent): Add Trim()
after several cases of xmlTextReaderConstValue to remove any \n
* src/obconversion.cpp(Convert): Add test for pInFormat to avoid
crash with erroneous input.
* src/mol.cpp(Separate): Copy dimension to each fragment.
2007-02-26 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/mol.cpp: OBMol::AddBond() / OBMol::DeleteBond()
Bond indexing starts at one. Had to undo the change made by Tim and
correct the fix on 2007-01-07 as a result of the bulk resizing.
2007-02-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/ring.cpp (FindRings): Don't return early if all atoms are
visited. Some atoms may be in multiple rings and will be visited
more than once on a graph traversal.
2007-02-25 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/mol.cpp: OBMol::DeleteBond()
_vbond.erase(_vbond.begin() + bond->GetIdx());
Since _vbond indices start at 0 and bond->Getdidx() indices start at
1, the line is replaced by:
_vbond.erase(_vbond.begin() + bond->GetIdx() - 1);
2007-02-25 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/forcefield.h: comment out Description() (comply
with new pluginiter).
* obmm, obenergy, obminimize, obgen: comment out the use of
Description().
2007-02-25 Chris Morley
* windows-vc2005/OpenBabelDLL: Updated OpenBabelDLL.vcproj.
Temporarily added OpenBabelDLL.dll and OpenBabelDLL.lib
(without forcefield)
* include/openbabel/kinetics.h, lineend.h, pluginiter.h:
documentation changes.
2007-02-25 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/ring.cpp: Added a check in FindRings to make sure the depth is
not larger than the number of atoms we have. (see mailing list)
2007-02-24 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp: Added ConjugateGradientsInitialize() and
ConjugateGradientsTakeNSteps(). ConjugateGradients() still exists and
uses these two new function.
Idem for SteepestDescent.
2007-02-24 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/mol.cpp: changes OBMol::NewBond, fixes PR#1666785. AddBond() was
resizing the _vbond vector and NewBond() used push_back to add items.
This created a gap bewteen the bonds added by NewBond() and AddBond().
The FOR_BONDS_OF_MOL iterator expects all bonds to be at the begin of
the vector. Note: this also fixes the initial problem with the
OBAngleData and OBTorsionData.
* test/addhydrogens.cpp: added/deleted... (was used for debugging)
* src/forcefield.cpp: changes "*logos << ..." to OBFFLog(...)
* src/forcefields/forcefieldghemical.cpp: changes "*logos << ..." to
OBFFLog(...)
2007-02-23 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* data/ghemical.prm: Final update. All molecules from the validation
ste are given correct atom types and charges.
* src/forcefields/forcefieldghemical.cpp: Calculated energies comply
with those from ghemical except for 1,4-scaling. Ring atoms are not
always scaled in ghemical, not sure why.
* src/forcefield.cpp: Added OBFFLog, fixes PR#1664279. (tested, but
needs to replace all "*logos << ..." lines)
Moved IsInSameRing from OBForceFieldMMFF94 to OBForceField.
Test molecule from PR#1665765 minimizes correctly, but added cutoff
accuracy to make sure.
* tools/obmm.cpp: Added commands for DelHydrogens, GenerateCoordinates,
SystematicRotorSearch and NumConformers.
* include/openbabel/forcefield.cpp: Added a definition for isnan.
(should be replaced with a better method in the math class??)
2007-02-22 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/mol.cpp: Added SetParent call to NewBond function. Should resolve
segfault issues related to bug 1665519.
2007-02-21 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/mol.cpp (NewBond): Fix PR#1665649. Make sure to set the
parent of a newly-created bond.
* test/mol.cpp: Add test for above.
* src/formats/Makefile.am, src/formats/Makefile.in: Fix linking
problems on Linux discovered by Craig.
2007-02-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/*.i, scripts/*: Add access to OBForceField classes and methods.
* tools/obprop.cpp: Remove "test" methods, introduced sometime
since the last release.
* tools/obmm.cpp: Make sure to set the OBForceField log to prevent
crashes (e.g., PR#1664279).
* Doxyfile: Bump version number to 2.1.0b6 for new snapshot.
* configure.in, configure: Bump to 2.1.0b6 for new snapshot.
* src/forcefield.cpp, tools/obrotamer.cpp: Update to use
std::vector instead of arrays.
* src/rotamer.h, src/rotamer.cpp: Update documentation to use
std::vector. Fixes compile problems on Windows.
AddRotamer(std::vector) New method for above.
* src/base.cpp: Documentation updates.
* src/canon.cpp, src/forcefield.cpp: Likewise.
* include/openbabel/ring.h, generic.h, pluginiter.h, canon.h,
forcefield.h, lineend.h: Likewise.
* src/all.h, src/formats/all.h, src/Makefile.am, src/Makefile.in,
src/formats/Makefile.am, src/formats/Makefile.in: Update to allow
using precompiled headers again.
* src/canon.cpp, src/formats/cansmilesformat.cpp: Fix crash caused
by linking problem. CanonicalLabels() moved to the Open Babel namespace.
2007-02-20 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp: UpdateCoordinates now 'knows' about conformers
and selects the correct one before returning.
* tools/obminimize.cpp: Implemented (was copy of obmm).
2007-02-18 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp: Added vector analysis methods
VectorLengthDerivative(), VectorAngleDerivative(),
VectorTorsionDerivative()
Removed SetEnergyCalculated and related methods for the moment.
* src/forcefields/forcefieldghemical.cpp: Updated to use the vector
analysis methods.
* src/forcefields/forcefieldmmff94.cpp: Updated to use the vector
analysis methods.
* tools/obgen.cpp: Added -ff option.
* tools/obenergy.cpp: Added. Calculate the energy of a molecule.
* tools/obminimize.cpp: Added. Minimize the energy of a molecule.
2007-02-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/typer.cpp: Fix PR#1594657 -- long recursion for large
multi-ring systems like fullerenes. This started by two calls to
CheckAromaticity, including one allowing recursion depth of
20. Discussion with Henry Rzepa suggested 14 as a reasonable
cutoff.
* src/forcefields/forcefieldmmff94.cpp: Fix compilation problem
with call to NumericalDerivative.
2007-02-17 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/forcefield.h: Some doxygen comments updated.
* src/forcefield.cpp: Added SystematicRotorSearch(), uses RotamerList
class to rotate all torsions, select the best conformation (lowest
energy) and minimize it (1000 steps).
SteepestDescent(int steps, int method) and
ConjugateGradients(int steps, int method):
the "int method" argument is added, can be set to
OBFF_ANALYTICAL_GRADIENTS (default) or OBFF_NUMERICAL_GRADIENTS.
Added ValidateGradientError(vector3 &numgrad, vector3 &anagrad):
calculate the difference in % between the analytical and numerical
gradient.
NumericalDerivative(OBAtom *atom, int terms) and
GetGradient(OBAtom *a, int terms):
the added argument terms can be set to OBFF_ENERGY (total gradient,
default), OBFF_EBOND (gradient for bond stretching), ... (Mainly used
for ValidateGradients
* src/forcefields/forcefieldghemical.cpp: All analytical gradients are
now correct (errors can still be minimized by limiting the number of
devisions etc...) ValidateGradients also compares gradients for
individual energy terms.
Electrostatic term implemented.
* data/ghemical.prm: Added charge parameters.
* tools/obgen.cpp: Changed to SystematicRotorSearch().
* tools/obmm.cpp: Added help command.
2007-02-17 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/chemdrawcdx.cpp: don't center molecules.
2007-02-16 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/obmolecformat.cpp: make it compile again (gcc-4.1.2).
2007-02-15 Chris Morley
Sorry that incomplete code keeps escaping. I'll put up Separate
code now, although the performance for 0D stereochemistry (sigh)
needs sorting out. Fulfills Feature Request 1581542
* include/openbabel/obiter.h, src/formats/obiter.cpp: Extend
OBMolAtomDFSIter operator* to return NULL to indicate end of a fragment.
Add parameter to constructor allow the iteration to start at any atom.
* include/openbabel/mol.h, src/formats/mol.cpp: Add API function
OBMol::Separate() to return disconnected fragments in OBMol vector.
* include/openbabel/obmolecformat.h, src/formats/obmolecformat.cpp:
Code for applying Separate() in conversion process.
Also, add ReadNameIndex() for indexing names in multiobject files.
Requires further testing.
* src/formats/transform.cpp: Added options --separate and
renamed -j as --join. (-j still works)
2007-02-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefields/forcefieldmm2.cpp,
src/forcefields/forcefieldmmff94.cpp: Remove exit() calls in favor
of error messages and default return values. Fixes PR#1650132.
* src/forcefields/forcefieldghemical.cpp: Add default
electrostatic function (return 0.0) to fix compilation error.
* tools/obmm.cpp: Add cg command for conjugate gradients.
2007-02-15 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/obconversion.h: Removed OBConversion:: before
CheckForUnintendedBatch(...); to fix compilation error.
* src/forcefield.cpp: Added/Updated LineSearch, SteepestDescent,
ConjugateGradients. Also added the same functions as Validate... to
test the implementation for x^2 + 2 y^2.
Added bool is14(OBAtom *a, OBAtom *b). Should move to atom.cpp??
Started working on DistanceGeometry (needs more sophisticated matrix
operations than OB currently supports).
* src/forcefields/forcefieldghemical.cpp: Now uses
OBFFXXXCalculationYYY to improve performance. All energy functions have
analytical derivatives. Small corrections to the energy expressions to
match energies produced by ghemical, added 14-scaling for non bonded
energy terms. Different bondtypes in ghemical.prm are no longer
ignored. Added ValidateGradients().
* src/forcefield/forcefieldmmff94.cpp: Continue work on MMFF94 to
comply with the validation suite.
Added ValidateGradients().
2007-02-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/obmolecformat.cpp: Comment out sections of
ReadChemObjectImpl -- looks like code from Chris invoking
OBMol::Separate().
2007-02-13 Chris Morley
Clear OBMol objects by default at start of ReadMolecule.
* include/openbabel/base.h: Add CastAndClear().
* src/*format.cpp(ReadMolecule): Replace dynamic_cast by a call
to CastAndClear().
* include/openbabel/obconversion.h, src/obconversion.cpp
(Read, ReadString, ReadFilemove): Remove clearFirst parameter,
since it is no longer needed.
2007-02-13 Chris Morley
* include/openbabel/obconversion.h, src/obconversion.cpp:
Corrected bug 1657817 - wrong name for batch conversion
of one file - which was due to misinterpretation as
splitting operation. Solution requires that the base name
for output files splitting is not empty - not a big constraint.
Added extra warning messages and checks in
CheckForUnintendedBatch(). Made this function and
BatchFileName() and IncrementedFileName() protected.
2007-02-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/cansmilesformat.cpp
(OBMol2Cansmi::AddHydrogenToChiralCenters): Fix PR#1658317 with
chirality on last atom. Switched iterator to use obiter.h macros.
* configure.in, configure, src/config.h.in: Add big-endian,
little-endian check, which defines WORDS_BIGENDIAN for
chemdrawcdx.cpp (and other binary formats in the future).
* src/formats/chemdrawcdx.cpp: Solve compilation problems with
previous change. (endian.h and byteswap.h are GNU and Linux
extensions.) Requires declaration of WORDS_BIGENDIAN in
babelconfig.h (as above for Unix).
* src/Makefile.am, include/openbabel/Makefile.am,
src/obconversion.cpp: Remove references to newline.[h, cpp].
* include/openbabel/lineend.h: Add std namespace declarations to
solve compilation problems with GCC.
* include/openbabel/ring.h, src/ring.cpp: Documentation updates,
added new constructor to simplify OBRingSearch::SaveUniqueRing().
* src/generic.cpp, include/openbabel/generic.h: Change reference
of DataSource to DataOrigin, as suggested by Noel.
* include/openbabel/bitvec.h: Fix bug (and documentation) with
FirstBit().
* include/openbabel/obutil.h: Fix GCC compile warning.
* test/cansmi.cpp: New test program for Canonical SMILES format.
* test/wrapper.sh, test/Makefile.am, test/Makefile.in: Use it.
* data/types.txt, data/types.h: Fix PR#1650239 with incorrect
Sybyl Mol2 atom types.
2007-02-11 Chris Morley
Replaced filter for line endings with a version which works
with fastsearch. Solves bug 1617324.
* include/openbabel/newlinebuf.h and src/newlinebuf.cpp:
replaced by include/openbabel/lineend.h
* src/obconversion.cpp: code in Convert() and Read() replaced.
Removed peek() in the Convert()loop. This was needed for
some other mod, which has probably not yet been committed.
This is not causing any problems for me, but is rather
central to the conversion process.
Added some documentation on GetOutputIndex.
2007-02-08 Noel O'Boyle <baoilleach@gmail.com>
* scripts: Regenerated bindings for scripting languages
2007-02-07 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/chemdrawcdx.cpp: make it work on little-endian
machines.
2007-02-02 Chris Morley
* include/openbabel/mol.h: Remove definition of Separate()
which was added prematurely.
2007-02-05 Noel O'Boyle <baoilleach@gmail.com>
* scripts: Removed %apply of OUTPUT and regenerated scripts
2007-02-02 Chris Morley
* windows-vc2005/Distribution: remove the Windows DLLs added
yesterday.
2007-02-01 Chris Morley
* windows-vc2005/Distribution: add some Windows DLLs for the
installer.
2007-01-31 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/canon.h, src/canon.cpp: Add canonical
numbering code from Craig James. (Eventually needs integration
into other methods -- these duplicate since they support
fragments.)
* src/formats/cansmilesformat.*: Add CANSMI format for Canonical
SMILES output. Eventually needs better integration into current
SMI format rather than duplication.
* src/Makefile.* include/openbabel/Makefile.*: Add above files.
2007-01-27 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/cdxmlformat.cpp: add support for formal charges.
2007-01-26 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/xml/cdxmlformat.cpp: fixed issues in writing
multi-molecules files.
2007-01-26 Chris Morley
* src/obconversion.cpp, include/openbabel/obconversion.h: Mitigate
some of the uncertainties in writing multi-molecule files.
pointed out by Jean Brefort, including bug 1644241.
Added SetLast as an alternative name for SetOneObjectedOnly.
Added documentation to GetOutputIndex().
2007-01-25 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/xml/cdxmlformat.cpp: scale bond lentghs to 30 (using the
first molecule) and enable write support.
2007-01-25 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/xml/cdxmlformat.cpp: add some stereochemistry and initial
write support (not enabled).
2007-01-24 Jean Brefort <jean.brefort@normalesup.org>
* src/formats/xml/Makefile.am: add cdxmlformat.
* src/formats/xml/cdxmlformat.cpp: make it basically work.
* src/formats/xml/xml.cpp: fix a memory leak.
2007-01-23 Donald E. Curtis <dcurtis3@sourceforge.net>
* tools/obmm.cpp: Added check for cin.eof resolving bug 1639880.
2007-01-22 Donald E. Curtis <dcurtis3@sourceforge.net>
* include/openbabel/bond.h: Added const versions of GetBeginAtom and
GetEndAtom.
* include/openbabel/atom.h: Added const version of GetVector. Required
changing _v to mutable.
* src/atom.cpp: Added implementation of GetVector.
* include/openbabel/math/vector3.h: Added const to function definition of
AsArray function.
2007-01-17 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/Distribution: Added all of the remaining files to the
installer script so that you can now make an installer directly after
compiling the relevant projects (OBGUII and OBComLn). Have also
checked in the example files included with the Windows distribution.
2007-01-16 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/mol.h, src/*: Documentation updates.
* include/openbabel/Makefile.am: Make sure pluginiter.h is included.
2007-01-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/snprintf.c: Update with declaration of GPL license in
addition to Artistic. Checked with author:
http://www.ijs.si/software/snprintf/
* configure.in, configure, Makefiles: Bump version number to
2.1.0b5.
* src/forcefields/forcefieldmmff94.cpp: Added stub for
electrostatic calculation. Solves linking problems on Mac OS X.
2007-01-14 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/Distribution: Edited the installer script to make it
easier to set the version number. Also added explicit paths to some of
the DLLs in the SVN repository.
* COPYING: Removed the text after the terms and conditions. This is
the text describing how to apply the license.
2007-01-13 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/Distribution: Added files necessary for creating an
installer using NSIS, an open source software for creating Windows
installers. The current script needs to be edited to be able to pick
up the files from the OpenBabelGUI build.
2007-01-12 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-python.i: quick fix to allow the openbabel module
to be imported without errors. The OBFingerprintIter issue remains
unresolved.
2007-01-09 Chris Morley <ob@gaseq.co.uk>
* scipts/openbabel-python.i: changes to OBFingerprintIter. Not tested
yet!
* include/openbabel/pluginiter.h: comment out PluginIter::Description()
and operator* which are causing problems with the Python build -
I suspect because they are not used in the C++ code.
* include/openbabel/forcefield.h: src/forcefields/forcefieldghemical.cpp,
src/forcefields/forcefieldmm2.cpp: changes to several return values
to avoid compiler errors.
2007-01-08 Chris Morley <ob@gaseq.co.uk>
* include/openbabel/pluginiter.h: correct documentation on
the use of FOR_EACH to iterate over all objects.
2007-01-07 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/mol.cpp: Moved all Destroy* calls to the end of Delete* functions so
that indexes are updated and other meta information.
* src/mol.cpp: NewBond was assigning indexes based on the size of the
_vbond vector but since the vector is incremented in chunks of 100 this
was producing incorrect index numbers. Updated misc docs. Also had a bug
in DeleteBond using the bond variable for more than one purpose (added
bondi for iterator usage).
2007-01-07 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/math/vector3.cpp: Added Point2PlaneAngle(vector3 a, vector3 b,
vector3 c, vector3 d) (moved from OBForceField)
* src/forcefield.cpp: Added logging features
* src/forcefields/forcefieldmmff.cpp: All energy functions except
E_Electrostatic() now use a OBFFXXXCalculationYYY class. Runs much
faster.
* src/formats/mopacformat.cpp: Added MOPAC Internal format (mopin)
* data/exttype.txt: Updated for MOPAC Internal format (mopin)
2007-01-06 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/OBPython/setup.py: Bumped up version number to 1.0.
Added a postinstall script that sets BABEL_DATADIR. Included
zlib1.dll.
* Added windows-vc2005/OBPython/openbabel_postinstall.py: A post
install script that sets the value of BABEL_DATADIR.
* windows-vc2005/OBPython/README.txt: Updated instructions on how to
run setup.py to create the distribution.
2007-01-06 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-[python,java,perl,ruby].i: Added ability to handle
the new pluginiter.h, and in particular, its use in
OBFingerprint.Iter. Also, regenerated all of the dependent files.
* scripts/openbabel-python.i: Removed python code added on 2006-12-20
to set BABEL_DATADIR as it actually had no effect.
2007-01-06 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefields: Ghemical now uses SMARTS for atomtype setting.
* src/forcefields: Added initial MMFF94 implementation. (uses new
OBFFCalculation class for better performance)
* tools/obgen.cpp: Now uses OBForceField::GenerateCoordinates().
* data/: Added SMARTS patterns to ghemical.prm for typing. Added
ghemical.prm to Makefile.*
Added parameters for MMFF94 (files for validating MMFF94 not included)
Data needs forcefield subfolder??
* test/obmmff94validate.cpp: Validate MFF94 using the validation
suite.
2007-01-05 Chris Morley <ob@gaseq.co.uk>
* include/openbabel.residue.h: Added EXTERN macro for global
variables for DLL builds. (Does nothing otherwise).
* Updated OpenBabelDLL project file.
2007-01-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/*.cpp, include/openbabel/*.h: Compiler warning fixes from
Jean Brefort.
* include/openbabel/residue.h, include/openbabel/generic.h: Remove
static declarations for OBGenericDataType and residue properties.
2007-01-05 Chris Morley <ob@gaseq.co.uk>
* include/openbabel/fingerprint.h: Give OBFingerprint a virtual
destructor. Noel found this was why SWIG was failing.
2007-01-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefields/forcefieldghemical.cpp: Fix typo from file
renaming. (Can't use Tripos since that's a copyright.)
* Makefile.in: Regenerate all Makefiles to fix build problems.
2007-01-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/forcefields: New code from Tim for MM2 and Ghemical force fields.
* include/Makefile.*: Updates for Chris's changes earlier today.
* include/inchi/*.c: Moved actual inchi source files back to src/.
* configure, */Makefile.in: Updates for inchi move and forcefield directory.
2007-01-03 Chris Morley <ob@gaseq.co.uk>
* Update Windows project files. But Python SWIG interface isn't
working on Windows.
* Moved libxml and inchi header files to include.
2006-12-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* Doxyfile: Change format slightly for better API documentation.
* src/*, include/openbabel/*: Many API documentation updates.
* include/openbabel/base.h, src/base.cpp (OBBase::Clear): New method in base
class to improve OBConversion::Read() syntax.
2006-12-27 Chris Morley <ob@gaseq.co.uk>
* src/newlinebuf.cpp: Revert to as in rev 1652.
2006-12-22 Chris Morley <ob@gaseq.co.uk>
* include/openbabel/pluginiter.h, fingerprint.h: Modify so that most
of code to implement plugin module behaviour is in pluginiter.h,
making it easy to give this behaviour in future to other classes.
Compatibility for OBFingerprint maintained except for iteration
through fingerprint types which is now in the style of obiter,
hopefully making it compatible with Python (binding not yet done).
* formats/fastsearchformat.cpp: change implementation of F option
to new iteration style.
* src/fingerprint.cpp, include/openbabel/fingerprint.h: remove
the replaced static variable _pDefault and GetNxtFPrt().
Add FastSearch::ReadIndexFile() alterantive to avoid
std::stream parameter which is no good for scripting.
Add FastSearch::FindMatch() which is simialr to Find() but requires
all bits of fingerprint to match.
* src/obconversion.cpp: added NO_NEWLINEBUF to avaoid compiling
newline buf which is currently incompatible with FastsearchFormat
and OBConversion::SkipObjects().
All types of line ending seem to work ok with VC++8 on Windows.
2006-12-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obiter.cpp (OBAtomAtomIter): Fix bug reported by Zhiguo Liu,
with obvious typo.
* src/formats/pdbformat.cpp: Fix atom typing bug reported by
Zhiguo Liu. Fix problems with unknown elements (due to atom
parsing) from PR#1577238.
2006-12-20 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/OBPython/setup.py: Install data files (e.g.
patterns.txt needed for FP3) into site-packages/openbabel_data
* scripts/openbabel-python.i: For Windows installs, set BABEL_DATADIR
to the location into which the binary installer installs the data files
* src/fingerprints/finger3.cpp: Replace instances of "/" by
FILE_SEP_CHAR
2006-12-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/python/setup.py, scripts/perl/Makefile.PL: Updates from
Dominik Mierzejewski to check for src/.libs directories. Prevents
"chicken and egg" problem with what component is built first.
2006-12-16 Noel O'Boyle <baoilleach@gmail.com>
* fingerprint.cpp/.h: Changed the FindFingerprint method to accept
const string& instead of string&. This is necessary for access to this
function from Python.
* scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a method
to Molecule for calculating a molecular fingerprint, handled by a new
Fingerprint class.
2006-12-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, Doxyfile: Bump to 2.1.0b4 for upcoming snapshot.
* src/*.cpp: Update class documentation (for many classes) to
reflect <openbabel/header.h> syntax. Makes API documentation
consistent with usage.
* src/obconversion.cpp, src/obconversion.h: Enable on-the-fly line
ending translation for input. Windows and Classic Mac files should
now translate without problems. Right now, XML files are excluded
through the new READXML flag.
* src/formats/xml: Update for READXML flag and move of xml.h
header.
* include/openbabel/xml.h: Move header for public use.
* src/formats/fastsearchformat.cpp: Add READBINARY flag.
* include/openbabel/Makefile.am, Makefile.in: Fix "make dist"
target to remove generated babelconfig.h header for snapshots and
releases.
* scripts/Makefile.am, scripts/Makefile.in: Make sure to clean
java targets.
* data/mm2.prm, data/Makefile.am, data/Makefile.in: MM2 parameters.
2006-12-15 Chris Morley <ob@gaseq.co.uk>
* tools/babel.cpp, src/obconversion.cpp, src/formats/obmoleculeformat.h:
Move -k option help info into OBConversion::Description, where it can
be used by other front-ends. (The info in help() is specific to the
command-line interface.) Register it as having no parameters.
2006-12-14 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/formats/gaussformat.cpp: Will export "model/basis,method" if keyword
translation is enable however is not tested accurate.
* src/formats/ghemicalformat.cpp: Re-wrote and tested the GAMESS keyword
export.
* src/formats/gamessformat.cpp: Modified keyword import operations.
Should now import the model,basis,method for keywords it knows about.
This method is all statically implemented. We need a new way to do this
translation such as OBKeyword class.
* tools/babel.cpp: Added help information for the '-k' parameter which
attempts to translation keywords along with molecule information.
2006-12-13 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-[python,ruby,java,perl].i: Updated to include all
iterators in obiter.h. Note: there is a problem getting
OBMolPairIter to work even if std_pair.i is included and a template
<int, int> created (compile of openbabel_python.cpp fails in this case
so these additions have not been included).
2006-12-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/babel.cpp: Moved src/main.cpp here -- more consistent with
new directory structure.
* configure, configure.in, src/Makefile.*, tools/Makefile.*: Ditto.
* scripts/: Regenerated files based on Noel's changes today.
* test/files/smartsresults.txt: Updated after Craig's bug-fixes.
* test/cmltest/: Update scripts to handle new location of babel
binary.
2006-12-13 Craig A. James <cjames@emolecules.com>
* src/parsmarts.cpp, src/formats/smilesformat.cpp: Fixed bug in
SMILES parser/writer and SMARTS parser that reversed Cis/Trans
chirality when the "/" or "\" followed an open-parenthesis "("
character. Commented out an unused function from parsmarts.cpp.
Fixed a bug where a semicolon ";" was printed for an aromatic bond
instead of a colon ":" for external bonds.
2006-12-13 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-[python,ruby,java,perl].i: Tidied up the
references to classes in obiter.h (e.g. there's no such thing
as OBResidueBondIter). Added some comments. Added wrappers for Python
to allow iteration over atoms in a molecule, etc.
This involved renaming the original OB method, and replacing
it by a Python class implementing the iterator protocol.
2006-12-12 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-[python,ruby,java,perl].i: Added a line to
create a vector of unisigned ints, required to use the Fingerprint
class. Also, added lines to prevent warnings due to shadowed classes
in obiter.h.
2006-12-10 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel: New directory for public headers. Ensures
internal and external code use the same
#include <openbabel/header.h> syntax.
Also, all related UNIX-based build changes.
2006-12-04 Vincent Favre-Nicolin <Vincent.Favre-Nicolin@ujf-grenoble.fr>
* src/format/ciffformat.cpp: Added new OBFormat-derived class to
handle Crystallographic Information Files. Initial implementation
handles reading & writing atomic coordinates, reading unit cell
and spacegroup name but no interpretation of symmetry is done.
2006-12-04 Benoit Jacob <jacob@math.jussieu.fr>
* src/math/vector3.cpp: optimize createOrthoVector(), update doc.
2006-12-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/generic.h, src/generic.cpp (OBRingData): Add new methods for
iterating over rings. (OBAngleData): Modifications from Tim
Vandermeersch to facilitate iteration over angles in an OBMol.
* src/mol.h, src/mol.cpp (FindAngles()): New method to parallel
FindTorsions() for filling an OBAngleData record in an OBMol,
contributed by Tim.
* src/obiter.h, src/obiter.cpp: New classes and macros, including
FOR_RINGS_OF_MOL, FOR_ANGLES_OF_MOL, FOR_TORSIONS_OF_MOL
FOR_PAIRS_OF_MOL, contributed by Tim.
* src/forcefield.h, src/forcefield.cpp, src/Makefile.am,
src/Makefile.in: New classes for mol. mechanics force fields
contributed by Tim Vandermeersch.
2006-12-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/Makefile.am, test/Makefile.in: Remove outdated vector3 and
matrix tests.
* scripts/: Added fingerprint.h header for direct access to
OBFingerprint classes.
* src/grid.h, src/grid.cpp (OBGrid): New base class, derived from
OBBase to allow conversion to handle grids. Also simplifies
OBFloatGrid and OBProxGrid code.
* src/*: Documentation updates.
* src/formats/xml/cdxmlformat.cpp: New file for ChemDraw CDXML format.
* src/formats/inchiformat.cpp (InChIFormat::ReadMolecule): Fix
compile error with GCC. OBMol::SetTitle() can't handle implicit
string operations.
2006-12-07 Chris Morley <ob@gaseq.co.uk>
* src/formats/inchiformat.cpp: Read capability added using the NIST
code but stereochemistry not yet implemented.
* src/formats/getinchi.cpp: parser to extract InChIs (possibly
split) from other text. Examples in the file.
2006-12-06 Chris Morley <ob@gaseq.co.uk>
* src/formats/mdlformat.cpp: SDFormat and MOLFormat now derived from
base class MDLFormat. SD files now always output with $$$$
(cures bug 1604992), mol files do not output properties.
2006-12-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/math.cpp: Improve speed by switching from endl (causes
flush) to "\n". Make sure to output number of tests 1..testCount.
* test/wrapper.sh: Switch to call new math test program.
2006-12-04 Benoit Jacob <jacob@math.jussieu.fr>
* test/math.cpp: match the Test::Harness output format. Fix a bug
in testEigenvalue.
* src/obutil.h, src/math/vector3.cpp, src/mol.cpp: revert to using
std::min instead of fmin.
2006-12-03 Benoit Jacob <jacob@math.jussieu.fr>
* src/math/vector3.h, src/math/matrix3x3.h,
src/math/vector3.cpp, src/math/matrix3x3.cpp:
--- IMPORTANT: disable floating-point checks and exception-throwing
by default. Now that is compiled only if OB_OLD_MATH_CHECKS is
defined.
--- Fix compilation error on Windows reported by Noel O'Boyle.
(another compilation error on Windows remains to be fixed).
--- Fix some more methods. Now all the floating-point code
should be quite sane.
--- Optimize/simplify several more methods.
--- add matrix3x3::operator*=( const double &), make operator /=
use it.
--- remove #define PI, use the standard M_PI instead.
--- replace #define SQUARE() by a static inline function.
--- remove hyper-dangerous #define x,y,z
* test/math.cpp: extend tests, merge (an improved version of)
matrixtest.cpp. Now math.cpp covers all what vector3.cpp and
matrixtest.cpp did cover, plus a lot more. Geoff: maybe it's time
to remove the tests vector3 and matrixtest?
* test/vector3.cpp: fix bugs, if that still matters.
* src/obutil.h: add note clarifying that to check if x is zero, one
should use IsNegligible( x, 1.0) instead of IsApprox( x, 0.0 ).
* src/rotor.cpp, tools/obxyz.cpp: use M_PI instead of PI.
2006-12-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/*: Cleanups and fixes, including for compilation
problems with Perl. (Derives from some macro expansion for THR.)
2006-12-01 Benoit Jacob <jacob@math.jussieu.fr>
* src/grid.h, src/grid.cpp: In class OBFloatGrid:
cleanup and simplifications, minor optimizations, add a FIXME
comment in operator<< about endianness issues, replace a dangerous
memset by a for loop. (This memset relied on the fact that the
floating-point value 0.0 is represented by the bits 0....0, which
happens to be true, but is not something we want to depend on.
Plus, compilers are/should be clever enough to make the for loop
just as fast.)
2006-11-29 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-python.i: Added some SWIG magic that allows the
creation of a C doubles array. Also added a Python convenience
function that converts a list to a C doubles array. This will allow
users to access functions such as OBMol::Rotate.
2006-11-29 Benoit Jacob <jacob@math.jussieu.fr>
* math/vector3.cpp: fix a bug that I had introduced a few days ago
in createOrthoVector. Thanks go to the new unittests.
* math/matrix3x3.h, math/matrix3x3.cpp: fix some defines in the
same way as in vector3.h, add both constant and non-constant
operator()(int,int) to access the matrix elements easily.
Fix isUnit(), isOrthogonal(), isDiagonal().
* test/math.cpp, test/Makefile.am, test/Makefile.in:
New tests for the math/ subdirectory. Covers the constructors, access
methods, various operators, operations on rows and columns and
(partly, will be completed) the distances/angles/orthogonality stuff.
* src/obutil.h: add new function IsNegligible(), checks whether a is
much smaller than b with given precision.
2006-11-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/obrotate.cpp: Use a simpler implementation with
OBMol::SetTorsion(). (Need to rewrite command-line parsing to
allow setting torsions of all matches, but no time now.)
* tools/obrotamer.cpp, src/Makefile.am, src/Makefile.in: New tool
to generate random rotamers using OBRotamerList and
company. Additional example of using rotamer code.
* src/rand.h, src/obutil.h, src/Makefile.am, src/Makefile.in:
Split out OBRandom to mirror rand.cpp.
* src/rotamer.cpp, src/rotamer.h, src/rotor.h, src/base.cpp:
Documentation updates.
* src/rotor.cpp (OBRotorRules): Make sure Init() is called before
any action, i.e.., GetRotorIncrements(). Fixes a bug uncovered
with obrotamer.cpp
2006-11-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/*.cpp: Update to switch from OBNodeBase and OBEdgeBase
iterators to OBAtom and OBBond respectively. Follows on 2006-11-20
change contributed by Gerd Menche. Switch many iterators to
preincrement for minor optimization.
* tools/*.cpp: Ditto.
* scripts/*: Regenerate for continuing API changes (e.g., vector3,
etc.)
2006-11-27 Benoit Jacob <jacob@math.jussieu.fr>
* src/math/vector3.h, src/math/vector3.cpp: Remove some inline
keywords from yesterday's patch, further optimize
vector3::createOrthoVector().
2006-11-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obutil.h, src/obutil.cpp: Optimizations and improvements
from Benoit Jacob, including documentation clarifications.
* src/math/vector3.h, src/math/vector3.cpp: Optimizations and
improvements, including documentation clarifications. Inline some
small methods, mark 'const' where possible, remove 'friend'
declarations, etc. contributed by Benoit Jacob.
* src/math/matrix3x3.h, src/math/matrix3x3.h: Use it.
* Doxyfile: Update for 2.1.0b3 snapshot and current Doxygen
version (1.5.1).
* src/rotamer.h, src/rotamer.cpp, src/rotor.h, src/rotor.cpp:
First step at documentation updates on rotamer/conformer
generation routines.
* src/fingerprint.cpp, src/tokenst.cpp, src/generic.h: Eliminate
minor Doxygen warnings.
* src/data.h, src/data.cpp (OBTypeTable::Translate): Add new
method for returning the translated string as a value --
simplifies scripting language access.
* src/mol.h: Documentation updates.
2006-11-25 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/OBPython/logo.bmp: Replaced logo with one that Geoff
sent me.
* scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a
.close() method to the Outputfile class of Pybel. This uses the
CloseOutFile() method added by Chris Morley in r1606. This is
necessary to ensure that all tests pass on Windows.
2006-11-24 Chris Morley <ob@gaseq.co.uk>
* src/obconversion.cpp(Write),(Read): Check for stream pointers
being NULL.
* src/obconversion.h, src/obconversion.cpp: Added CloseOutFile()
at the suggestion of Noel O'Boyle.
2006-11-24 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005: added libxml2.dll (taken from Chris' Windows OB GUI
distribution)
* windows-vc2005/OBPython/logo.bmp, setup.py: new files added that
allow the creation of a Windows OB scripting installer
* windows-vc2005/OBPython/Readme.txt: Updated with instructions on
running setup.py
2006-11-23 Chris Morley <ob@gaseq.co.uk>
* windows-vc2005: Added OBPython project to allow OB to be used
form Python on Windows.
* src/parsmart.h(SmartsLexReplace), src/ring.h(CompareRingSize):
Added OBAPI to declarations of these exported global functions.
2006-11-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/atom.h, src/base.h, src/bond.h, src/residue.h, src/mol.h,
src/ring.h, src/mol.cpp, src/base.cpp, src/obiter.h: Remove
OBNodeBase, OBEdgeBase, and OBGraphBase classes, contributed by
Gerd Menche.
* tools/obprop.cpp: Ditto. Example of changing iterators to new format.
* scripts/*: Updated based on above changes.
* src/formats/xml/cmlformat.cpp: Change size_t to
string::size_type to be sure of 64-bit correctness.
2006-11-17 Chris Morley <ob@gaseq.co.uk>
windows-vc2005: Added projects for OpenBabelDLL, OBComLn, and OBGUII
2006-11-18 Michael Banck <mbanck@gmx.net>
* test/textbuffer.cpp: Do not include "zipstream.h" if HAVE_LIBZ is
not defined. Do not check for a gzip'd input stream if HAVE_LIBZ is
not defined.
2006-11-18 Noel O'Boyle <baoilleach@gmail.com>
* scripts/python/testpybel.py: Needed to relax one of the tests of
molecular weight, as it was failing for the OB2.1b2 snapshot (there
must have been some changes to the atomic masses). Also,
corrected tolerance tests to use the absolute value of the difference
rather than the actual value.
2006-11-18 Noel O'Boyle <baoilleach@gmail.com>
* scripts/python/setup.py, pyopenbabel.py, testpyopenbabel.py,
pyopenbabelapi.html: Changed all references to pyopenbabel to pybel
(new name). Also, corrected minor typo in docstring in pybel.py.
2006-11-17 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/cmlformat.cpp: mods to input and output properties
with the title attribute on <property>, as requested by Carsten Niehaus.
2006-11-17 Chris Morley <ob@gaseq.co.uk>
* src/formats/turbomoleformat.cpp: Added input and output options to
read and write in Angstroms (default is bohr).
Modified WriteMolecule() so that the use of strlwr doesn't corrupt
etab. (Was apparent only in GUI where etab persists between molecules.)
* src/obconversion.cpp: changed some results of string finds to
std::string::size_type.
2006-11-15 Noel O'Boyle <baoilleach@gmail.com>
* scripts/python/pyopenbabel.py: Updated to be consistent, fast, pass
all unit tests, and to have API documentation in docstrings.
* scripts/python/testpyopenbabel.py: Added complete coverage unit tests
for pyopenbabel.py.
* scripts/python/test/*: Removed previous attempts at testing
* scripts/python/pyopenbabel.txt: Removed previous attempts at
providing documentation (we now have a wiki, and API documentation)
* scripts/python/head.sdf: Added small test file, used by
testpyopenbabel.py.
* scripts/python/pyopenbabelapi.html: Added API documentation for
pyopenbabel.py, automatically generated using "pydoc -w"
2006-11-09 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/formats/gamessformat.cpp: Gamess output parsing now only gathers
run information from the input deck rather than gather all and defaults
from gamess. we may need to reconsider this in the future or add an
option for it.
2006-11-08 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/formats/gamessformat.cpp: Bug fixes after further testing.
* src/formats/gamessformat.cpp: For now keywords are in uppercase. This
needs to be decided on by the dev community and will be discussed with
the gamess developers for gamess-specific keywords.
* src/formats/ghemicalformat.cpp: Read GAMESS info from the "gamess"
namespace
* src/generic.h: Added GetData(const char *s) to OBSetData
so that you can retrieve data from a const char rather than
having to instanciate a string.
* src/formats/gamessformat.cpp: More improvements on reading generic
computational meta data. (added runtyp / dfttype / basis). Also modified
the location of gamess extra information. GAMESS now stores it's
information in an OBSetData with attribute "gamess" which is part of the
molecule.
2006-11-07 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/cmlformat.cpp(WriteMolecule): Output new
namespace URL rather than the old one.
* src/obutil.cpp" Remove static from Solvelinear() and
SolveQuadratic() so that would compile on VC8.
* windows-vc2005/babelconfig.h: Extra macro definitions.
* windows-vc2005/libinchi.dll, windows-vc2005/libinchi.lib:
1.01 versions from NIST
2006-11-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/main.cpp, src/obutil.cpp, src/fingerprints/finger3.cpp,
src/format/fastsearchformat.cpp: Patch from Martin Vogt to address
PR#1590609. Crashes due to incorrect handling of string parsing on
64-bit platforms.
2006-11-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, Makefile.in: Add back support for
optional compile of wxWidget GUI in src/GUI.
* scripts/*: Split openbabel.i into individual copies for each
language.
* scripts/java/*: Initial attempt at a java interface from SWIG. Untested.
2006-10-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/molreport.cpp: New psuedo-format to generate atom
and bond information as suggested by Rich Apodaca. Addresses
PR#1587499.
2006-10-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/openbabel.i, scripts/*: Updated with changes from Martin
Vogt to fix break (likely dating back to header split of atom.h,
bond.h, residue.h).
2006-10-20 Chris Morley <ob@gaseq.co.uk>
* src/formats.xml/xml.cpp (ReadChemObject): added extra error
message and convert the rest to use obErrorLog.
* src/formats/mdlformat.cpp: modify description to work around
bug in wxWidgets radiobuttons.
2006-10-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.h, src/obconversion.cpp: Make sure to free
streams created using ReadString, ReadFile, or WriteFile()
methods. Fixes PR#1578916.
2006-10-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/chemdrawcdx.cpp: Fixed corruption of 2D coordinates
caused by attempted conversion from CDX scale to Angstroms. Fixes
PR#1576703.
* configure.in, configure, Makefile.*: Bump to version 2.1.0b2 for
next snapshot (now using autoconf-2.60).
* data/*, src/fingerprints/finger3.cpp: Rename pattern file to
SMARTS_InteLigand.txt.
* src/obiter.h: Fix GCC warning reported by Carsten.
* src/formats/*format.cpp: Update chemical MIME types,
specification URLS and extensions from the chemical MIME project:
http://sf.net/projects/chemical-mime
* scripts/openbabel.i: Add output string for
OBTypeTable::Translate().
* scripts/*: Regenerate.
* test/textbuffer.cpp, test/vector3.cpp: New tests for newline
translation and vector3 manipulations.
2006-09-30 Chris Morley <ob@gaseq.co.uk>
* src/formats/fastsearchformat.cpp(ReadChemObject):
Output message with the properties of the index if no
SMILES structure provided.
* src/fingerprint.h: Added FastSearch::GetIndexHeader()
Reformat tabs.
2006-09-30 Chris Morley <ob@gaseq.co.uk>
* src/formats/chemdrawcdx.cpp (Flags): added NOTWRITABLE
* src/formats/fastsearchformat.cpp: Made timing of indexing
work properly.
* src/oberror.cpp(ThrowError) : return immediately if _logging is
false; do not add to list of messages.
* src/generic.cpp(GetLatticeType, GetSpaceGroupNumber) : ensured
all paths returned value to avoid compiler warning (no real effect)
2006-09-27 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/generic.h: Updated OBSetData to initialize to correct
OBGenericDataType enumeration.
* src/formats/ghemicalformat.cpp: GPR format now exports GAMESS
information correctly if it exists as part of the molecule.
2006-09-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/ruby: Add new ruby interface -- probably needs to be
moved to allow compilation into main libopenbabel.
* scripts/*: Updated for above changes.
2006-09-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/base.h, src/atom.h, src/bond.h: Update internal atom
indexing to use an unsigned int, rather than short. Fixes
PR#1556819, caused by large molecules (i.e. >2^16 atoms or bonds).
* src/newlinebuf.h, src/newlinebuf.cpp: Fix bugs uncovered during
ChemSpotlight testing. Now appears to smoothly handle old Mac OS
9, DOS, and Unix line endings with no problems.
* src/generic.h, src/generic.cpp: Incorporate patches from Carsten
for lattice type and space groups.
* src/formats/chemdrawcdx.[h, cpp]: New format code for ChemDraw
CDX binary code, contributed by Fredrik Wallner.
* src/formats/Makefile.am, src/formats/Makefile.in: Update for
above.
* tools/obgen.cpp, tools/Makefile.am: New "obgen" tool for
creating simple 3D coordinates for SMILES and other 0D
formats. Contributed by Tim Vandermeersch.
2006-09-06 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/generic.h: Added new OBGenericData subclass: OBSetData
2006-08-30 Donald E. Curtis <dcurtis3@sourceforge.net>
* src/mol.cpp: Added OBMol::CreateResidue() function.
2006-08-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/inchi/: Update InChI library with final release of
1.0.1. Need to update configure script to detect libinchi version
to only build newer revisions when needed.
2006-08-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/smilesformat.cpp (ParseComplex): Ensure complex
expressions end in a ']' character. Added patch from Nick England
for handling chiral output using OBChiralData. Should fix
PR#1508741.
* test/files/invalid-smarts.txt: Add additional complex expression
for tests.
* src/generic.cpp (OBUnitCell): Update lattice detection to use
IsApprox instead of IsNear.
* src/mol.cpp (PerceiveBondOrders): Ditto.
2006-08-04 Chris Morley <ob@gaseq.co.uk>
* src/kinetics.h(OBRateData): Change constructor to fit in with
the recent change in OBGenericData constructor.
2006-08-03 Chris Morley <ob@gaseq.co.uk>
* src/formats/smilesformat.cpp (ParseSimple)(ParseComplex)
Removed extension labelled "is this safe" and added support for
* and [*] as wildcard elements. arom = false was also needed.
* src/kekulize.cpp(getorden): Treat Te (atNo=52) the same as Se.
Allows c1cc[te]c1 to be interpreted as better rubbish.
2006-08-02 Chris Morley <ob@gaseq.co.uk>
* src/formats/smilesformat.cpp (ParseSimple)(ParseComplex)
Accept, with a warning, the illegal aromatic elements
b [si] [ge] [sb] [bi] [te] [sn]
2006-07-21 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/cmlformat.cpp (BeginElement): Make sure to call
BeginModify() on a <molecule> tag, since EndModify() is already
called. Fixes PR#1512054 and probably PR#1523956.
2006-07-21 Chris Morley <ob@gaseq.co.uk>
* src/obconversion.cpp(AddChemObject): remove compiler warning by
returning Count!=0 rather than Count.
* src.obutil.cpp(IsApprox): replaced fmin, which is not known to
MS compiler, with std::min.
2006-07-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/internalcoord.h: New header to encapsulate OBInternalCoord.
* src/Makefile.am, src/Makefile.in, src/mol.h: Updates for above.
* src/obutil.h: Remove old-style casts, and minor documentation
updates.
* src/data.h, src/generic.cpp, src/generic.h, src/math/vector3.h
src/obiter.h: Update to use initialization lists more
consistently.
* src/formats/inchiformat.cpp: Use obiter classes to remove
shadowed temporary variables.
* src/typer.cpp: Fix bug with aromatic typer claiming errors on
blank lines.
* src/data.cpp: Fix bug with reading data files from versioned
directories.
* data/phmodel.txt, data/phmodel.h: Fix bug with seed charge on
hydroxamic acid reported by Noel.
2006-07-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/math/vector3.h, src/math/vector3.cpp: (IsApprox) Add new
method to compare vectors based on approximate floating-point
comparisons, rather than potentially dangerous == and !=
operators.
* src/chiral.cpp: Use vector3::IsApprox instead of ==.
* src/residue.cpp, src/bond.cpp, src/atom.cpp, src/bond.h: Add
back needed headers for compilation, removed with yesterday's
change dividing up mol.h
2006-07-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/atom.h, src/bond.h: New headers to encapsulate OBAtom and
OBBond interfaces, respectively.
* src/bond.cpp: Switch #include of mol.h to new header.
* src/atom.cpp: Ditto. (SetHybAndGeom): Fix missing break
statement, uncovered using AntiC static analysis program.
* src/Makefile.am, src/Makefile.in: Make sure to include above in
distributions.
* src/residue.h, src/residue.cpp: Move OBResidue class declaration
from mol.h.
* src/mol.h: Remove OBAtom, OBBond, and OBResidue, as above.
* src/obutil.h, src/obutil.cpp: Add IsApprox() and CanBeSquared()
contributed by Benoit Jacob.
* src/math/vector3.h, src/math/vector3.cpp: Add new implementation
of vector3::normalize and createOrthoVector, contributed by Benoit.
2006-07-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp, src/main.cpp: Remove unneeded semicolons,
which prevent compilation with GCC at high warning levels.
* src/mol.h: Remove extra OBMol:: specification -- prevents
compilation with GCC and confuses Doxygen.
* src/gaussformat.cpp: Add -xk and -xf write options to output
supplied keywords to Gaussian input. Allows batch output of files
with the same options.
* src/gamessformat.cpp: Ditto. Add contributions from Donald
Curtis for reading GAMESS input files.
2006-06-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/chains.cpp: In TracePeptideChain and TraceNucleicChain, test
for atom visit before recursing. Otherwise, leads to an infinite
loop and crash. Fixes PR#1515198, reported by Noel.
2006-06-29 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure, configure.in: Fix logic in last change.
* Doxyfile: Update to grab obmolecformat.h now in src/format/.
* src/*.cpp, src/*.h, src/formats/*.cpp:
Cleanup #includes for iostream, fstream -- only use iostream when
needed (i.e. for cout, cerr, cin, clog declarations).
* src/all.h, src/formats/all.h: Trim precompiled header templates
to most common headers.
* src/patty.cpp: Remove unused "COMPILE_PATTY_MAIN" #ifdef.
* src/chiral.cpp: Remove unused floating-point methods.
* src/rand.cpp: Remove unused #ifdef DEBUG code.
* src/parsmart.cpp, src/formats/crkformat.cpp: Update calls to
printf with calls to obErrorLog.
* src/obutil.cpp (InternalToCartesian): Check index requests to
avoid requesting past the vector end.
(#ifdef): Remove ifdef, leave code for roots.
* src/formats/ghemicalformat.cpp: Remove dummy atoms, which can
cause problems. Mark all aromatic bonds as bondtype 'C'.
* test/files/attype.00.smi: Add unspecified chiral alkane for @?
SMARTS testing.
* test/files/formalchargeresults.txt, test/files/ringresults.txt,
test/files/formularesults.txt, test/files/smartsresults.txt:
Update for changes to attype.00.smi using generate.sh.
* test/Makefile.am: Cleanup.
2006-06-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure, configure.in, src/all.h, src/formats/all.h,
Makefile.in: Add experimental support for precompiled headers with
GCC, using the --enable-precompiled-headers flag to the configure
script. Haven't performed much timing/optimization -- appears to
help about 10-12%.
* src/base.h, src/mol.h, src/obconversion.h, src/generic.h:
Warning eliminations and documentation improvements from Carsten.
* src/obiter.cpp: Further improvements to documentation on DFS and
BFS iterators.
* src/chains.cpp: Updated call to fprintf(... stderr) to use
modern OBMessageHandler.
* scripts/*: Regenerate for latest header changes.
* Doxyfile, doc/api-style.css: Updated for doxygen-1.4.7 and new
style changes.
2006-06-28 Chris Morley <ob@gaseq.co.uk>
* src/obiter.cpp: Some of the examples wouldn't compile - need
&*a rather than a in parameter calls. Added comment in all the
examples. I ran into this personally with FOR_NBORS_OF_ATOM(b, &*a)
but haven't tested the similarly modified OBResidue example.
* src/formats/mdlformat.cpp(GetTimeDate): Change second parameter
which was corrupting output of mol file line 2.
2006-06-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obiter.cpp: Add improved documentation on DFS and BFS atom
iterators. Fix bug with disconnected fragments uncovered with unit
testing.
* test/iterators.cpp, test/wrapper.sh, test/Makefile.am,
test/Makefile.in: New test for atom and bond iterators.
2006-06-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/base.h src/generic.cpp, src/generic.h, src/mol.h,
src/bond.cpp: Documentation changes, including several from Carsten.
* src/*.cpp: Remove un-needed header #includes turned up by a
script adapted from KDE suggested by Carsten.
2006-06-23 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obiter.h, src/obiter.cpp: Add depth-first and breadth-first
search iterators for atoms through an OBMol. Fixes feature request
PR#1273213.
* src/bitvec.h: Minor cleanup of #include paths.
2006-06-22 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/generic.h, src/generic.cpp (OBUnitCell): Add lattice type
definition, requested by Carsten Niehaus and add GetCellVolume()
method contributed by Carsten.
* src/newlinebuf.h, src/newlinebuf.cpp: New "filtering streambuf"
class to filter line-endings, e.g. \r\n or \r -> \n expected by
much of the code. Fixes PR#1510008 and goes towards feature
request PR#1499615. Currently unused until testing is complete.
* src/Makefile.am, src/Makefile.in: Add newlinebuf.
2006-06-21 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/mol.h, src/atom.cpp (CountRingBonds): New method to return
the number of explicit ring connections to an atom.
* src/parsmart.h, src/parsmart.cpp: Add support for Daylight 'x'
primitive for total # of ring connections using above method.
* test/files/smartstest.txt, test/files/smartsresults.txt:
Test 'x' patterns above.
* scripts/*: Regenerate to add new OBAtom::CountRingBonds()
method.
* src/formats/xyzformat.cpp (WriteMolecule): Only output "Energy" in
title if it's nonzero. General cleanup.
2006-06-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/smilesformat.cpp: Allow use of H atoms for a root
atom when used in a cis/trans "/" or "\" specification. Make sure
to output [H] atoms when in a cis/trans specification. Fixes
PR#1508783. Fix part of PR#1508741 -- chiral atoms should be fine
as root nodes (which preserves the ordering).
* src/parsmart.cpp: Add support for @? matching unspecified chiral
centers. Fixes PR#1364638. Add support for [H] explicit hydrogen
atoms, fixing PR#1463791.
2006-06-19 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/files/invalid-smarts.txt: Add invalid ring closure bond
specifications suggested by Craig in PR#1503849.
* src/parsmart.cpp: Fix PR#1503849 for invalid SMARTS ring
closures -- check both beginning and end bond specifications for
the closure. Uses new function EquivalentBondExpr to test if
two bond specifications are equivalent.
Fix part of PR#1506408 for SMARTS matching @ and @@ atom
specifications.
* src/formats/smilesformat.cpp: Fix cis/trans problem with
PR#1506408 -- IsUp/IsDown parsing support in SMILES was
inconsistent with mol.h and parsmart.cpp. "/" is Up "\" is Down.
* test/files/smartsresults.txt: Regenerate using above changes.
* src/kekulize.cpp: Fix PR#1504089 by adding a special case to
prevent double bonds between aromatic S-S systems, which is
unneeded to show aromaticity.
* test/wrapper.sh: Add smilesmatch to list to prevent regression
on PR#1506408.
* test/ringtest.cpp, test/smartstest.cpp: Correct minor errors in
finding filenames and result generation.
* test/files/nci.smi: Add new test SMILES file.
* test/smilesmatch.cpp: Use it.
2006-06-15 Chris Morley <ob@gaseq.co.uk>
* src/formats/smilesformat.cpp(ParseSmiles): when using
extension and bond is doubled, add
UnsetImplicitValencePerceived() so that implicit hydrogens are
recounted.
* src/formats/smilesformat.cpp(GetSmilesElement): ensure explicit
hydrogens are always written with bracketed atoms (esp when
charged; [OH3+] was being output incorrectly).
* test/files/FormulaTest.smi: Added. Contains several small
molecules to test SMILES input, implicit hydrogen detection
and elemental formula generation.
2006-06-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/base.h, src/base.cpp: Add "const" qualifiers to
OBGenericData methods.
* src/mol.h: Add documentation, including patch contributed by
Carsten Niehaus.
* scripts/*/*.cpp: Regenerated using SWIG for above changes.
* test/invalidsmiles.cpp, test/files/invalid-smiles.txt: New
test. Check to see that invalid SMILES are properly rejected.
* test/smilesmatch.cpp: New test. Check to see if SMILES strings
match themselves using SMARTS.
* test/Makefile.am, test/Makefile.in, test/wrapper.sh: Add
invalidsmiles and smilesmatch to test list.
2006-06-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/parsmart.cpp: Completely reject dot-disconnected SMARTS
e.g. "C.C" which currently are unimplemented and can cause
crashes, e.g. PR#1505711.
* src/obutil.cpp (SafeOpen): Make filename arguments "const".
* test/*.cpp: Update to use new SafeOpen prototypes and remove
old-style casts to (char*) to remove const.
* test/invalidsmarts.cpp: New test to check that invalid SMARTS
patterns are properly rejected. Also tries buffer smashing with
random binary data.
* test/files/invalid-smarts.txt: Initial set of invalid SMARTS
which hopefully will tests certain parts of the SMARTS
parser. Crude start, but more devious patterns to come.
* test/files/random*: Random binary data for invalid format
testing and "fuzz" testing.
* test/formalcharge.cpp: New test to check formal charge
assignment. Currently does not test, simply generates results for
debugging.
* test/files/formalchargeresults.txt: Results from above.
* data/bin2hex.pl: Condense multiple spaces to one. Provides a
small amount of compression for data headers (about 3K out of
435K).
* data/*.h: Rebuild using above.
2006-06-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp (BatchFileName): Make sure to properly
strip off ".gz" extension if zlib compression is enabled. Fixes
PR#1503596.
* src/parsmart.cpp: Support for [D], [v], [X] patterns
(i.e. default values of 1), fixing part of PR#1474716. Support for
[as] as an aromatic As atom, per SMILES aromaticity for arsenic.
Support for [se] for aromatic Se atom, per SMILES aromaticity --
fixes PR#1503851.
* test/files/smartstest.txt: Add tests for [D], [v], [X], [c],
[p], [as], [s], and [se] SMARTS patterns as above.
* test/files/smartsresults.txt: Regenerate after above fixes.
* test/wrapper.sh: Make sure to pass along command-line arguments
to "prove" command. Allows "./wrapper.sh -v" for verbose output.
* src/formats/mdlformat.cpp: Make default molecular dimension to
be 2D, but check for 3D coordinates too. Many non-standard files
out there with no real dimension line (e.g. PR#1409133).
* src/formats/xyzformat.cpp: Smarter handling of
"energy" tag in title -- if present, remove it from title. If
mol.GetEnergy() is near zero, don't print it.
* scripts/openbabel.i: Update from Noel to use
vector<OBGenericData*> instead of vector<OBGenericData>.
* scripts/*.cpp: Regenerate using SWIG 1.3.29.
2006-06-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.cpp: (Init): Fix problem with parsing data --
introduced with changes on 05-24. Add null to right char*
buffer. Fixes PR#1502795.
2006-06-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/oberror.h, src/oberror.cpp (GetMessageSummary): Added
methods to track counts of messages at each level, implementing
PR#1449517.
* src/main.cpp: Use it.
* Makefile.am, Makefile.in: Make sure to eliminate .svn
directories when running "make dist"
* test/Makefile.am, test/Makefile.in: Make sure to build "smarts"
not "smartstest" on platforms without Perl.
* src/tokenst.cpp: Modified to check buffer and delimiters for
NULL strings, use default string ctor.
* src/generic.h (Clone): Change from a pure virtual function to a
virtual which returns NULL as a default. Allows building script
wrappers with vector<OBGenericData>.
* scripts/*: Regenerate to solve compilation problems, addressed
by generic.h changes above.
2006-06-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/hinformat.cpp (WriteMolecule): Make sure to escape
molecule titles in double quotes. Fixes PR#1501694.
* src/formats/xml/cmlformat.cpp (EndElement): Back out yesterday's
change after discussion with Chris -- would cause problems with
compound documents with embedded <cml></cml> blocks.
* test/roundtrip.cpp: Add check for failed OBConversion::Read()
calls suggested by Chris.
* src/base.h: Documentation updates for OBGenericData methods to
address Noel's PR#1484029.
* scripts/openbabel.i: Added template support for
vector<OBGeneric> to address iterating through generic data for
PR#1484029.
* scripts/*: Regenerate as above.
2006-06-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/rxnformat.cpp (WriteMolecule): Cast size_t to
unsigned for sprintf statement. Eliminates warning with GCC.
* src/formats/mpdformat.cpp: Eliminate unsigned/signed warning.
* src/formats/*format.cpp (more files): Remove calls to sprintf,
sscanf, strcpy.
* src/formats/xml/cmlformat.cpp (EndElement): Make sure </cml> tag
returns false (end of processing).
* src/residue.cpp: Make sure to call base class in copy
ctor. Eliminates GCC warning.
* test/cmltest/test.sh: Skip test if cml cannot be loaded.
* test/roundtrip.cpp: Fix faulty error problems with
multi-molecule CML files. Before trying a read at the end of the
file, make sure to clear molecular information.
2006-06-04 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/xml.cpp(ReadXML): Made so that returns false at
the end of the file. Solves problem with roundtrip.
* src/formats/mdlformat.cpp(ReadMolecule): Added Trim to new code
to read multiline properties, because was sometimes confused by
trailing CRs in Windows.
2006-06-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, src/config.h.in: Update to include
snprintf prototype in all files -- increased use with changing
sprintf calls to snprintf to minimize buffer overflows.
* src/math/*: Remove calls to exit(!) on faulty input -- return
errors and default values.
* src/formats/*format.cpp (more files): Remove calls to sprintf,
sscanf, strcpy.
* test/*.sh: Protect against existing environment variables when
re-defining. For test calls, we need to ensure only our binaries
load.
2006-06-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.cpp (OBElementTable::ParseLine): Change sscanf call to
use fixed length (256 chars) for name string, rather than
preprocessor #define BUFF_SIZE.
* src/formats/xml/xml.cpp, src/formats/xml/xml.h,
src/formats/*format.cpp: Remove calls to sprintf, sscanf, strcpy.
* scripts/*: Regenerate to add Craig's UnsetHash() and
UnsetWedge() calls.
2006-05-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/xml/xml.cpp (ReadXML): Fix PR#1486678 for
multi-molecule files. The libxml2 library is very unhappy reading
a file past EOF, so make sure to check the state of the istream
before reading.
* test/cmltest/*: Renamed roundtrip.sh script, which
was a confusing name, to cycleformats.sh.
* src/formats/pdbformat.cpp: Run PerceiveBondOrders regardless of
size (most PDB multiple-bonds should be picked up by residue
information). Fixes PR#1493626.
2006-05-30 Chris Morley <ob@gaseq.co.uk>
* src/formats/smilesformat.cpp (ParseSimple): Tidied up code
to handle extension lc as conjugated double bonds and radical.
Defer potential double bonds to end of ParseSmiles() when molecule
complete to ensure not applied to aromatic atoms. PR#1493148
still ok and extension works again.
2006-05-26 Craig James <cjames@emolecules.com>
* src/mol.h Added UnsetHash() and UnsetWedge() macros.
2006-05-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp (AddChemObject): Output a warning when a
format is WRITEONEONLY and more molecules are coming. Fixes
PR#1473192.
* src/formats/mdlformat.cpp (ReadMolecule): Make sure to grab all
lines of potentially multi-line properties. Fixes PR#1489209.
* src/formats/smilesformat.cpp (ParseSimple): Change behavior when
encountering a bond between two potential radical or aromatic
atoms. Previously marked bond as double, now mark as 5 -
potentially aromatic bond. Appears to fix PR#1493148.
* src/kekulize.cpp (NewPerceiveKekuleBonds): Make sure that
bestorden is reset when traversing cycle. Previous code would only
check one atom for adding extra electrons. Appears to fix
part of PR#1445453.
(expandcycle): Ensure a bond is in a ring before expanding. Fixes
part of PR#1445453 for 1-phenyl-1H-pyrrole.
* test/aromatest.cpp: Make sure to test that all ring bonds are
aromatic to confirm that above bugs do not come back.
* test/files/aromatics.smi: Add additional test cases for above
bugs.
* test/ringtest.cpp, test/smartstest.cpp: Update so that
generating results is aware of test directory.
* test/generate.sh: Shortcut to properly generate test results
under "make check" conditions.
* test/files/smartsresults.txt: Update after all of todays changes.
2006-05-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/main.cpp, tools/*.cpp, test/*.cpp: Added USING_DLL
declarations for WIN32 compiles. Thanks to Noel and Donald Curtis
for pointing out Cygwin problems.
* src/Makefile.am, src/Makefile.in: Add missing -no-undefined for
Cygwin compilation.
* src/formats/Makefile.am, src/formats/Makefile.in: Add missing
obmolecformat.cpp for Cygwin compilation.
2006-05-24 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/dlhandler_unix.cpp (findFiles): Fix PR#1493706 problem with
misplaced NULL terminator.
* README: Updated to mention 2.1 development.
* Doxyfile: Make sure to exclude src/GUI/
* src/patty.cpp, src/typer.cpp, src/rotor.cpp, src/chains.cpp,
src/parsmart.cpp, src/data.cpp, src/atom.cpp: Updates to fix calls
to strcpy, replacing some static char* with std::string.
2006-05-23 Craig James <cjames@emolecules.com>
* src/formats/smilesformat.cpp: Fixed a potential buffer
overflow when parsing SMILES.
2006-05-21 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/xml.cpp (ReadXML): Output the error
message from libxml2 when parser fails. Was previously seen
in unix builds (for some reason), but not in Windows.
2006-05-19 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/xml.cpp, xml.h (ReadStream): Simplify so that
input chunks up to '>' are taken, rather than trying to get up
to endtag. Remove gettomatch(). I hope this solves bug #1486678
and allows roundtrip test to run properly (but not tried).
2006-05-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/inchi/ : Update with InChI 1.01 pre-release.
* src/formats/inchi_api.h: Ditto.
2006-05-16 Chris Morley <ob@gaseq.co.uk>
* src/mol.cpp: Remove BeginModify and EndModify from AddAtom(),
NewAtom() and AddBond(). Doesn't seem sensible to call
EndModify() (which calls Kekulize()) before all the molecule
is there. The change should speed up conversion of large molecules.
This only change for this revison for easy reversion if
this is too drastic a change.
2006-05-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/patty.cpp, src/kekulize.cpp, src/fingerprint.cpp,
src/rotor.cpp, src/chains.cpp, src/parsmart.cpp, src/chiral.cpp,
src/bitvec.cpp, src/main.cpp, src/grid.cpp, src/mol.cpp,
src/bondtyper.cpp: Update to remove #ifdef for SSTREAM
(stringstream is ISO C++ and widely accepted). Remove other
spurious #ifdef's where possible.
2006-05-11 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/cml.sh, test/cmltest/roundtrip.sh, test/cmltest/test.sh:
Provide more fine-grained test errors and messages.
* test/roundtrip.cpp: Finding extra molecules in a file should
exit with an error.
* src/mol.cpp (GetMolWt, GetExactMass): Simplify and improve
performance by handling explicit hydrogens like any other explicit
atom. Functions identically to previous version on regression
test. Improves performance on isolated protons or bridging hydrogens.
2006-05-10 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/formula.cpp, test/files/formularesults.txt:
New test for OBMol::GetFormula(), OBMol::GetMolWt(), and
OBMol::GetExactMass().
* src/mol.cpp (GetMolWt, GetExactMass): Fix PR#1485580. Missing
parentheses in calculating # of implicit + explicit
hydrogens. Thanks to Noel for suggestion.
* src/dlhandler_unix.cpp (findFiles): If environment variable
BABEL_LIBDIR is set, ignore compiled-in default. (User setting
should always take precedence)
2006-05-09 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/files/: New subdirectory to contain test data files.
* test/Makefile.am: Update TESTDATADIR accordingly.
* test/*: Ditto.
2006-05-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, src/config.h.in: Update to include
#define's for OBERROR, OBFPTR, and OBCOMMON as below.
* scripts/*: Regenerate using SWIG.
* test/wrapper.sh: Update to include export for BABEL_DATADIR.
* test/*: Add many new unit test frameworks (atom, mol, bond,
conversion, format, etc.)
2006-05-08 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/cmlformat.cpp(WriteMolecule): since the id
must start with letter, add "id" if it doesn't and write a <name>
element.
* src/generic.h: add virtual GetValue function for OBGenericData
and also definitions in OBComment and OBPairData. Hopefully will
solve bug 1483112.
* src/oberror.h: Add default define for OBERROR as nothing
2006-05-07 Chris Morley <ob@gaseq.co.uk>
* oberror.h: Change classes from OBAPI to new OBERROR
so that can be compiled separately.
* src/mol.h, src/bitvec.cpp, oberror.cpp, obconversion.cpp:
change to OBERROR extern OBMessageHandler obErrorLog;
* src/obconversion.h: add #include "oberror.h";
* src/obconversion.cpp: now that oberror can be accessed everywhere
change all cerr messages to use obErrorLog.
* src/fingerprint.h: replace OBAPI by OBFPTR to allow fingerprint
code to be separately compiled.
* src/formats/xml.h: add OBCOMMON so that XML classes can be
separately compiled. Add implementation of SkipObjects for
XMLBaseFormat and XMLConversion::SkipXML.
* src/formats/obmolecformat.cpp: Add ReadNameIndex to speed access
in files with many molecules. I wasn't going to commit this until
it was tested a bit more, but I must have misunderstood what
Tortoise SVN was doing.
* src/GUI/OBGUI.cpp: don't crash if there are no formats.
2006-05-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/smilesformat.cpp (SmiToMol): Since SMILES sets
formal charges, turn off automatic updates. Some general cleanups
(removing commented-out code.)
2006-05-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/chains.h, src/chains.cpp: Initial work on documenting,
indentation, and general cleanup of chains.cpp.
(ConstrainBackbone): Check for valence of backbone atoms
should actually be for HvyValence() since all hydrogens are ignored.
Fixes PR#1442779.
2006-04-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* Doxyfile: Add map of included files in headers to
documentation. Need to work on removing un-necessary #includes in
headers.
* src/math/*: Minimize #include headers.
* src/generic.h: Include obutil.h for triple class -- was included
indirectly by way of vector3.h.
* test/smartstest.cpp: Changed the way tests are counted -- per
molecule instead of per pattern AND per molecule (cuts drastically
down on the test overhead). Remove endl and sync with stio to
improve buffering.
* test/smartstest.txt, test/smartsresults.txt: Add additional
SMARTS pattern tests and results.
2006-04-24 Chris Morley <ob@gaseq.co.uk>
* src/formats/xml/cmlformat.cpp: Accept coordinate2 and
coordinate3 elements for CML1.
Laxer acceptance of atomRef?? which is sometimes misused - but added
warning. Converted cerr calls to obError.
Added option to read 2D rather than 3D coordinates.
Output formula only when no bonds AND no coordinates.
Ensured atoms from formula marked as having no H.
GetMolID() gets name or number for error messages.
* src/GUI/OBGUI.cpp: uncommented standard stream redirection.
Do we need some conditional compilation?
* src/formats.smilesformat.cpp, src/mol.cpp: Recent change in
ImplictHydrogenCount broke GetMolWt,GetExactMass,GetSpacedformula
and explicit H form of output in SMILES. But it is better that
ImplictHydrogenCount means what it says. Added in appropriate form
of GetExplicitHydrogens to these routines.
* src/formats/xml/xml/cpp(gettomatch): rewrite to allow stream to
be discarded up to next match.
2006-04-21 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp: Fix broken gzip-decoding of input
(PR#1473243) introduced by 2006-04-11 change. Fix bug when writing
multi-molecule files using WriteFile() (PR#1474265).
* src/atom.cpp, src/residue.cpp: Remove inadvertant debug messages.
2006-04-20 Chris Morley <ob@gaseq.co.uk>
* src/formats.xml/xml.h, src/formats/obmolecformat.h,
windows-2005/babelconfig.h: added OBCOMMON macro to aid DLL build.
(Usually empty).
* src/obconversion.cpp(AddChemObject): prevent formats with
WRITEONEONLY from writing more than once.
2006-04-19 Chris Morley <ob@gaseq.co.uk>
* src/formats/molecformat.h: added #ifdef _WIN32 around
experimental code which cause problems in unix build.
2006-04-16 Chris Morley <ob@gaseq.co.uk>
* src/transform.cpp, src/main.cpp, src/GUI/OBGUI.cpp: To avoid
messing up help output revert to original wording of OBMol::
ClassDescription, and pick out the last word for the conversion
info message.
* src/GUI/OBGUI.cpp, src/GUI/OBGUI.h: initialize HelpFile in
current folder at program start.
* src/formats/smilesformat.cpp(CreateSmiString): ensure unbonded [H]
e.g. from formula, is output.
* src/formats/thermoformat.cpp, src/formats/xml/cmlformat.cpp:
ensure formula are read in correctly by adding ForceNoH() and
calling Assign SpinMultiplicity in the right place.
2006-04-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/Makefile.am, test/Makefile.in: Only run CML tests if XML
formats were compiled. (i.e., if libxml not available, can't test
CML)
* test/ringtest.sh, test/smartstest.sh, test/cmltest/test.sh:
Minor shell script portability fixes.
2006-04-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/perl/META.yml, scripts/python/setup.py: Packaging
changes for the scripting wrappers.
* src/formats/mdlformat.cpp: Remove inadvertent debug statement
left from yesterday.
2006-04-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mdlformat.cpp (ReadMolecule): Add support for atom
stereo in v2000 format and OBChiralData. Partly addresses
PR#1463796.
* src/formats/smilesformat.cpp (GetChiralStereo): If we have a 2D
molecule and stereochemistry is unspecified, don't assume we have
a particular stereochemistry. Partly address PR#1463796.
Also fix a problem with writing chiral "H" designations with explicit
hydrogens, introduced with yesterday's fix to
OBAtom::ImplicitHydrogenCount.
2006-04-11 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.h, src/obconversion.cpp: Added a test to be
sure that we do not check gzip encoding multiple times (much less
try to gzip repeatedly). Fix PR#1465586 where ReadString() or
ReadFile() followed by Read() will fail because input streams are
closed prematurely.
* src/atom.cpp (ImplicitHydrogenCount): Fix a bug where formulas
were calculated incorrectly -- explicit hydrogens should count
against an implicit hydrogen count too. Fixes part of PR#1463787.
(i.e., SMARTS 'h' token was matching total number of hydrogens)
* src/mol.cpp (AddBond): Fix a bug exposed by PDB parsing, where
code attempts to add a bond from one atom to itself.
* src/formats/mol2format.cpp: Fix residue parsing to remove
calls to create a residue when in fact, the molecule has no residues.
* src/formats/pdbformat.cpp: Fix CONECT record parsing to read
malformed records (e.g., created by very old Open Babel versions)
via splitting by spaces. Fixes PR#1468802.
* src/parsmart.cpp: Reformat indentation for clearer code
reading. Fix bug with syntax of 'H' token -- should refer to the
*total* number of hydrogens. PR#1463787.
* test/smartsresults.txt: Regenerate after above bug-fixes.
* src/formats/crkformat.cpp (ReadCRK): Change to correctly read
multi-molecule files, where the </Structure2D> tag would appear,
but parsing would continue, uncovered using roundtrip testing.
2006-04-08 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/openbabel.i, scripts/*: Update to add Cygwin DLL headers.
* THANKS: Update with contributors to 2.0.1 release.
2006-04-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/dlhandler_unix.cpp: Upgrade to use the opendir/readdir
replacement for the non-portable scandir contributed by Mikael
Johansson.
* src/formats/Makefile.am, src/formats/Makefile.in: Fix error in
logic with building inchi, introduced yesterday. D'oh!
* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
Add --no-undefined flag to produce proper compilation on Windows
(i.e., Cygwin).
2006-04-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* NEWS: Update for 2.0.1 release notes.
* configure, configure.in, acinclude.m4: Add new configure options
for silent libtool use & compiler flags.
* scripts/Makefile.am, scripts/Makefile.in: Provide better
"distclean" target to remove python build targets and backup
files.
* src/mol.h: Update IsRotor() and NumRotors() documentation to
explain the current minimal definition of a rotatable
bond. Addresses PR#1463505.
* src/oberror.cpp: By default, retain a maximum of the 100 most
recent entries in the error log in memory. All errors will be
filtered and sent to output, but only retain some (not all). Fixes
PR#1439893.
* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
Only install the inchi_api.h header.
* src/formats/xml/Makefile.am, src/formats/xml/Makefile.in: Turn
off optimization -- appears to fix crashes on FC4 and FC5,
PR#1447233.
* src/formats/xml/xml.h: Add std:: namespace declarations, solving
compilation problems on some GCC compiler versions.
* src/formats/Makefile.am, */Makefile.in: Changes to only build
libinchi when the library is not available on the system. Fixes
PR#146451.
2006-03-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/aromatest.cpp: New test to check aromaticity. When supplied
with a test file, it checks to be sure all non-hydrogen atoms are
aromatic.
* scripts/*: Update scripting wrappers with SWIG 1.3.29.
* src/Makefile.am, src/Makefile.in : Add @LIBDL@ as
suggested by Michael Shigorin (PR#1458706). Make sure
babelconfig.h isn't included in dist tarball, as suggested by
Michael Banck.
2006-03-27 Michael Banck <mbanck@gmx.net>
* src/fingerprint.h: Fix compilation error with gcc-4.1.
Patch by <vlaaad@users.sourceforge.net>.
* src/formats/copyformat.cpp: Likewise.
* src/formats/crkformat.cpp: Likewise.
* src/formats/xml/cmlreactlformat.cpp: Likewise.
* src/formats/xml/xml.h: Likewise.
* src/formats/xml/xmlformat.cpp: Likewise.
* src/formats/fastaformat.cpp: Include babelconfig.h.
* src/rand.cpp: Include <time.h> and <sys/time.h>.
2006-03-18 Chris Morley <ob@gaseq.co.uk>
* src/obconversion.cpp, obconversion.h,
src/formats/molecformat.cpp, src/formats/rxnformat.cpp:
The ability to stop conversion on a write error has somehow
been removed. Restored this by changing the return of
AddChemObject() to a bool indicating any failure of
WriteChemObject(). I don't expect that many people are
programming at this depth for this change to matter.
* src/mol.cpp(AddHydrogens): Do not add hydrogens
when to a molecule which has no bonds and more than one atom. We
do need a review to clarify these functions, but they are generally
working ok.
* src/data.cpp, data.h: Added a global function OpenDatafile which
looks in the normal places for data files. It also starts in the
current directory. If this is acceptable, it could be used to collect
the code for this functionality in one place.
* src/formats/xml/xml.h: added std:: to a string
* src/GUI/OBGUI.cpp:Added warning when output extensions mixed.
* src/GUI/optswx.cpp: Be less restrictive with punctuation in options.
* src/formats/inchiformat.cpp: Now calculates InChI for C and CH.
* src/formats/thermoformat.cpp: minor parsing corrections
2006-03-16 Chris Morley <ob@gaseq.co.uk>
* data/atomtyp.txt: IMPVAL for halogen ions
* /src/formats/smilesformat.cpp(ParseComplex): Move hcount test
back again so that [C] is read as C not CH4
(GetSmilesElement): Restrict addition of implicit H by
resurrecting normalValence variable. Output [C], not [CH0].
2006-03-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/xml/xml.h: Fix std:: namespace decl for type_info.
* src/Makefile.am: Temporarily disable compilation of src/GUI
until compile errors are all fixed.
* scripts/* : More changes to allow building, linking, and running
(again!) with current CVS tree.
* src/generic.h (OBTorsion): Add default code for SetData(OBBond*)
-- not sure what this *should* do. Allows compilation of script
wrappers.
* src/obutil.h, src/math/matrix3x3.h, src/math/vector3.h: Add
#ifndef SWIG portions to prevent SWIG from choking on some
non-class function declarations.
* */Makefile.in: Regenerate (get rid of bogus --gnu flags).
2006-03-14 Chris Morley <ob@gaseq.co.uk>
* src/GUI/OBGUI.cpp(Expand): Mods to avoid errors when filenames
are empty, have trailing paces, semicolons, etc.
* src/formats/obmolecformat.cpp, obmolecformat.h: Deferred
molecule routines (-C -j options) rewritten to ensure no memory leaks
under normal or error conditions. (Previously rather carelessly
written, I'm afraid.)
* src/formats/smilesformat.cpp: Corrected [CH0] extension on
input and made work on output.
* src/formats/thermoformat.cpp: Added SetDimension(0). Initialise
MidT. Added tdd extension.
* src/mol.h: Comments on OBMol copy ctor and assignment saying
that OBGenericData is copied and on operator+= that it is not.
* src/base.h, kinetics.h: Mods consequent on OBGenericData changes
2006-03-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, src/Makefile.am, src/config.h.in: Add
initial support for DLL builds on Cygwin. Seems to compile a
libopenbabel.dll, but still linking problems for
babel.exe.
Also add support for detecting wx widget library to build src/GUI.
* */Makefile.in: Regenerated using automake.
* src/GUI/OBGUI.cpp: First pass at removing compilation warnings
with GCC -- make sure all functions are passed correctly.
* src/GUI/stdwx.h: Use a new babel.xpm if needed (e.g., Mac, UNIX).
* src/formats/xml/cmlreactlformat.cpp: Add back missing
reaction.h.
* src/fingerprint.h, src/formats/xml/xml.h: Change static
declarations to avoid spurious memory leak warnings with
valgrind.
* src/base.h: Add #ifdef to remove non-implemented iterators for
SWIG.
* scripts/*: Build updates for Perl and Python wrappers.
* test/roundtrip.cpp: Update to remove spurious warnings with CML
(and other) format translation.
* test/smartsresults.txt: Update to reflect recent SMARTS updates.
2006-03-13 Chris Morley <ob@gaseq.co.uk>
* src/mol.cpp(GetSpacedFormula): I like the approach added by
Craig to be independent of implicit/explicit H without
changing the OBMol. But needs some mods.
Remove call to ExplicitHydrogenCount(); they are already
included in ImplicitHydrogenCount(). Add test to correctly
handle molecules with no bonds, hydrogen isotopes. Works with
SMILES C C[2H] C[H] (=carbene) [H][H] [2H][H]
Added support for D and T.
* src/mol.cpp(GetMolWt and GetExactMass): Mods similar to above
so that implicit or explicit H is handled.
* src/atom.cpp, atom.h(ExplicitHydrogenCount): Add extra parameter
to not count D and T. (Backward compatible)
* src/mol.cpp(AssignSpinMultiplicity): Exclude D and T so that
SMILES CC[2H] is interpreted as C2H5D. Previously was CH3CH:
* src.formats/smilesformat.cpp(OBMol2Smi::GetSmilesElement):
Reduce implicit H count by number of explicit H isotopes, which
already were output explicitly. CC[2H]=> add Hs => [CH3][CH2][2H]
(ParseComplex): [CH0] means explicitly there are no hydrogens.
* src/mol.h, atom.cpp: Added flag on OBAtom to indicate there
are no hydrogens. Added get and set methods.
* src/atom.cpp(ImplicitHydrogenCount), src/mol.cpp(AddHydrogens):
Add support for SpinMultiplicity>=4. As in molecule CH - the source
of ions in a flame ionization detector.
* src/mol.cpp(AssignSpinMultiplicity): Use positively set no Hs to
allow SMILES [CH0] = C atom.
* src/rotamer.cpp(PackCoodinates,UnpackCoordinates): Make cf double
rather than float to avoid compiler warnings.
* src/transform.cpp: Added --addformula option.
* src/mol.cpp:(operator=): OBGenericData objects now copied with
OBMol.
* src/generic.cpp, generic.h: Clone function given parameter
referring to new molecule, so that OBAtom pointers can be rebased.
Added documentation that using atom and bond pointer in
OBGenericData objects is a bad idea.
* src/rotamer.cpp, rotamer.h): Moved code for copying
OBRotatmeterData into Clone(). Significant rewriting required;
not tested yet.
* src/formats/obmolecformat.cpp(MakeCombinedMolecule): simplify code
because of GetFormula changes (don't need to make copy to compare
formulae) and OBMol copying changes.
* src/GUI: Small bug when selected format begins with t now corrected.
2006-03-10 Chris Morley <ob@gaseq.co.uk>
* src/formats/smilesformat.cpp: make a default format so that
the default object is OBMol even when MOLformat (the other default
format) is not present.
* src/formats/smilesformat.cpp(ParseRingBond): prevented crash
and give error message when parse failure (e.g. a line starting
with a number) - common and of long standing.
* src/formats/obmolecformat.cpp(ReadChemObjImpl): another delete
for OBMol object when ReadMolecule returns false;
2006-03-09 Chris Morley <ob@gaseq.co.uk>
* src/reaction.h, src/format.rxnformat.cpp: revert to previous
versions, rxnformat.cpp from OB2.0.0. The boost dependent versions
were committed in error - work in progress on new some new
reaction formats.
* several formats, mainly output formats, converted to derive from
OBMoleculeFormat and their WriteChemObject functions deleted. I
don't think these were responsible for memory leaks, but it the
less code to maintain the better.
* src/formats/obmolecformat.cpp(WriteChemObjectImpl): OBMol
object not being deleted in the event of an error. Moved delete
statement so that it is.
* src/transform.cpp(DoTransformations): ensure OBMol deleted
in the event of an error.
* src/GUI/OBGUI.cpp: #include selformats.h: make lc
2006-03-09 Chris Morley <ob@gaseq.co.uk>
* src/bitvec.cpp, bond.cpp, bondtyper.cpp, chains.cpp,chiral.cpp,
generic.cpp,grid.cpp,kekulize.cpp,matrix.cpp,
mol.cpp,molchg.cpp,obiter.cpp,patty.cpp,phmodel.cpp,
rand.cpp,ring.cpp,rotamer.cpp, rotor.cpp,tokenst.cpp,transform.cpp
/src/formats/ most cpp files
/src/formats/xml/pubchem.cpp
/src/fingerprints/finger2.cpp, finger3.cpp
/src/math/matrix.cpp, vector.cpp
Add #include "babelconfig.h" at top of files. This eases my use
of pre-compiled headers and I thought (wrongly) that it would
assist memory in leak detection. Many cpp files already have this
header directly rather than relying on it through mol.h.
Not a very useful exercise, but I hope harmless.
* src/obconversion.cpp(FullConvert): Added extra test to remove an
extraneous error message under some circumatances. The bug was
introduced in when facility to use the same file for input and
output was added.
Reversed the memory leak related change of 2006-03-02 (see devel
forum discussion).
* src/formats/xml/xml.cpp(ReadXML):Add continue shortcut for nodes
that are not elements. (SetUpWriter): remove extra writer creation.
* src/dhandler_win32.cpp(findFiles): Rewritten, now handles * and *.*
Was getting confused by . and .. directories.
* src/mol.h Remove unnecessary #include "reaction.h"
Added /src/GUI for OpenbabelGUI source files. Put here because
it is now potentially cross-platform.
2006-03-02 Craig James <cjames@emolecules.com>
* src/bitvec.cpp, src/bitvec.h: Added new operator<(bv1, bv2) that
returns true if the bits in bv1 are a subset of the bits in bv2.
* src/dlhandler_unix.cpp (findFiles): Fixed a memory leak. The
code to free the memory was there but had been commented out.
* src/mol.h, src/mol.cpp: Added functions UnsetUp(), UnsetDown().
Modified SetUp() and SetDown() to also invoke UnsetUp() and
UnsetDown(), respectively, so that both up and down flags aren't
set simultaneously. Changed UnsetAromatic() to use UnsetFlag().
* src/mol.cpp (GetSpacedFormula, GetFormula): Molecular Formula
was counting only explicit hydrogens, e.g. might report C20H2.
Changed to report the total (implicit plus explicit) hydrogen
count so that Molecular Formula is correct.
* src/obconversion.cpp (OptionParamArray): Fixed memory leak.
* src/formats/mdlformat.cpp (ReadMolecule): Fixed reference to
uninitialized memory that caused random behavior. Reformatted
file to correct indenting problems.
* src/math/vector3.cpp (Comments only): Added comments to
CalcTorsionAngle() explaining how it works.
2006-03-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp (ReadFile): Fix bug PR#1435777 for crash
when calling when only the input format was set -- code mistakenly
referenced pOutFormat.
* src/parsmart.h: Add #ifndef SWIG to prevent wrapping internal
struct's used to form the Pattern type.
* src/formats/mdlformat.cpp: Use old-style Trim() syntax to
prevent backwards-incompatibility. Remove final " 0" for REGNO from
v3000 COUNTS line. Fixes PR#1439475, as susggested by Ernst-Georg.
* test/smartsresults.txt: Update to match previous atom type changes.
2006-02-22 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.cpp (AssignBonds): Make sure that OBResidueData calls
Init() before starting and some minor cleanups to atom type
assignment, exposed by comparing PDB->Mol2 files from Babel and
Sybyl. Thanks to Kevin Parkes for the example file.
* src/formats/mol2format.cpp (WriteMolecule): Add back atom names
from residues, add a residue number to each residue name (e.g.,
THR1 vs. THR). Should better match mol2 files from Sybyl.
* data/atomtyp.txt; Add an implicit valence rule for phosphates to
fix PR#1403974.
2006-02-22 Chris Morley <ob@gaseq.co.uk>
* src/formats/mdlformat.cpp: Mod to read files with no M END.
Bug found by Hassan Mamdani.
2006-02-20 Chris Morley <ob@gaseq.co.uk>
* src/obconversion.cpp(Description): Make dependent on HAVE_LIBZ.
* src/parsmart.cpp: Rename STRICT to OB_PARSMART_STRICT because of
conflict in VC8. Not used anyway.
* src.typer.cpp(OBAromaticTyper::ParseLine): Ignore blank lines
to avoid error messages.
* src/formats/mdlformat.cpp: Add Trim() after a getline() to remove
erroneous CRs when Windows binary mode used. Add m option to
Description.
* src/xml/cmlformat.cpp(WriteFormula): Pass copy of OBMol so that
can add implicit hydrogen when molecule is an atom.
As suggested by Tappani Kinnunen:
Added test for NULL pointer in reading Nasa_OldThermo;
deleted erroneous xmlTextWriterStartElementNS(); but
have not yet added empty dictRef attribute to property
(needs more consideration).
* src/format/xml/xml.cpp(ReadXML):Skip over non-elements.
2006-02-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/parsmart.cpp (ParseComplexAtomPrimitive): Fix PR#1364604 for
no default value for "X" primative (should default to one
connection if no number is specified).
* ChangeLog.1.x: New file, contains changes for 1.x releases.
* Doxyfile: Update to allow 2.1 documentation generation.
* configure, configure.in, Makefile.*: Update to test for Perl and
"prove" used for new test harness.
* test/*: New test "harness" using Perl, if available to provide
summary output. Yields much better summary information and sets
BABEL_LIBDIR as needed to prevent user problems with the 2.0.0 release.
2006-02-19 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/pdbformat.cpp: Fix PR#1368851 for PDB export with
large coordinates. Optionally shifts coordinates if needed.
* src/mol.h: Fix PR#1373650 -- return NULL if no coordinate array
is available. Prevents segfault.
* src/atom.cpp (GetResidue): Make sure to return NULL if chains
perception fails.
* src/chains.cpp: If only one residue is found, and it's UNK, it's
probably not a residue, so nuke it.
* src/formats/mol2format.cpp: Combined with two above fixes,
ensure atom labels are printed correctly for mol2 files. All three
fix PR#1371789.
* src/obconversion.cpp: Update documentation to point out
workaround for PR#1368969 with static members of OBConversion --
declare dummy variable to make sure LoadFormatFiles() has been called.
* tools/obxyz.cpp: New program to allow cartesian transformations
(translations, rotations).
2006-02-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* residue.h, residue.cpp: Move residue property definitions into
new header to support biomolecule formats.
* src/formats/fastaformat.cpp: New format, contributed by Sangwoo
Shim. Resolves format request PR#902406.
* src/formats/mdlformat.cpp: Fix possible memory leak
with comment data and ensure comment is stored properly.
* src/math/matrix3x3.cpp, src/math/matrix3x3.h,
src/math/vector3.cpp: Fix documentation errors.
* src/obconversion.h, src/obconversion.cpp: Add option to
WriteString to omit any trailing whitespace. Resolves PR#1396953.
2006-01-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/zipstreamimpl.h (overflow): Patch calls to setp as
suggested by Rathann Mierzejewski.
* scripts/perl/* : Added more unit tests, fixed bug with
case-sensitive filesystems, and problems with dynamic loading on
Linux.
* scripts/python/*: Updated to fix problem with dynamic loading on
Linux.
* aclocal.m4, configure, configure.in, ltmain.sh, */Makefile.in
*/Makefile.am: Update to libtool-1.5.22 and ensure libxml2 is only
used if v2.6.5 or later.
* src/kinetics.h: Move from src/formats/xml/ for general utility.
* src/formats/xml/xcmlformat.cpp: Remove deprecated file.
2005-12-22 Chris Morley <ob@gaseq.co.uk>
* src/main.cpp (main): removed unsigned from pos to correct bug
found by Mikael Johansson.
* src/formats/turbomole.cpp: Updates by Mikael Johansson.
2005-12-19 Chris Morley <ob@gaseq.co.uk>
* src/molecformat.h, molecformat.cpp: Put most of code into static
functions which can be called from elsewhere.
Changed implementation of the -j option so that combining is done by
+= of OBMol so that useable with any format.
* src/formats/xml/xml.h(XMLMoleculeFormat): Reduced code duplication
by calling static OBMoleculeFormat functions.
* src/mol.cpp(operator+=): Combined molecule has a dimension equal
to the smallest of its constituents.
* src/chiral.h: added missing std:: and #include <vector>
2005-12-18 Chris Morley <ob@gaseq.co.uk>
* src/obconversion.h, obconversion.cpp (IsFirstInput())mod.
(OneObjectOnly) Added inverse call.
(Convert) Call WriteChemObject only at end with C option
(FullConvert) Can now have input and output files the same
#define ZEROATOMSOK
* src/generic.h, src/mol.h, tokenst.cpp(Trim): Now returns a reference
to the string to make it easier to use, esp in function parameters.
* src/generic.h: OBGenericData and derived classes: OBCommentData,
OBExternalBond, OBPairData,OBVirtualBond,OBRingData,OBUnitCell,
OBConformerData,OBSymmetryData,OBTorsionData,OBAngleData,OBChiralData,
OBSerialNums added virtual Clone() method to allow copying given a
polymorphic OBGenericData pointer.
* src/rotameter.h: ditto OBRotameterData
* src/residue.cpp: Commented out OBGenericData methods in OBResidue
and deletion of objects in destructor - now in base class.
* src/mol.h: OBResidue now derived from OBBase; comment out its
OBGenericData methods and _vdata. ditto OBAtom, OBBond, OBMol,
* src/mol.h, mol.cpp: I kept needing a more easily parsed
GetFormula(). Added GetSpacedFormula()and changed the implementation
(but not interface) of GetFormula().
Initialized and copied _dimension in constructors.
* src/parsmart.cpp: changed error message handling.
* src/transform.cpp: Added --title and --property options. Improved
handling or error conditions while doing options.
* src/main.cpp: Ensure that long options can take more than one
following text parameter. (Used for --property).
Make clog message describe the type of object converted, e.g.
"2 reactions converted" (when reaction.h is updated) Small
consequent change in help().
* src/formats/APIInterface.cpp, main.cpp: All long options are now
GENOPTIONS
* src/obmolecformat.h: Split out implementation into a new
src/formats/obmolecformat.cpp. Added code for -C option to defer
output of molecules so that molecular properties, defined in several
files can be combined. Move obmolecformat.h to src/formats/
* src/formats.mdlformat.cpp: Corrected bug #1370212 with code along
the lines suggested.
Attempt to reconcile bug #1368849 and earlier suggestions:
As before $$$$ is written between molecules but is now written at the
end only if any properties have been written (sdf) but not if they haven't
(mol). Add option -xm to not output any properties.
* src/formats/fastsearchformat.cpp: Added -u option for updating index.
* src/formats/: add thermoformat.cpp and titleformat.cpp.
* src/formats/xml/xml.h: remove SetFormatting; add missing std::
* src/formats/xml/xml.cpp: add option to have no xml formating
* src/formats/xml/xcmlformat.cpp: add option to output properties.
Read and write properties, read and write Nasa thermo data.
GetSpacedFormula() simplifies cml output!
Renamed to src/formats/xml/cmlformat.cpp
* src/formats/smilesformat.cpp: reads * as radical centre, as NIST is doing.
* src/formats/titleformat.cpp added.
* src/formats/xml/kinetics.h added, containing OBRateData and
OBNasaThermoData classes derived from OBGenericData.
2005-11-25 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/mdlformat.cpp, rxnformat.cpp: Yesterdays change
broke rxnformat. Add option to supress $$$$.
* windows/obabel/OBabel.dsp: This config sees fingerprints ok.
* windows/OBRunTime.dsw: rename to OpenBabel.dsw
2005-11-24 Chris Morley <c.morley@gaseq.co.uk>
* windows-vc2005: upadtae files but struggling with wrong tags
on some files. Renamed as OpenBabel.sln
* src/INSTALL.WINDOWS: removed. (First draft 2004 by PMR)
* src/README: removed. (about 2003 oblib)
2005-11-23 Chris Morley <c.morley@gaseq.co.uk>
* src/fingerprint.h, fingerprint.cpp: rearrange so that FptIndex
has member functions.
* src/formats/fastsearchformat.cpp: Add -xu option to update
index.
* src/parsmart.cpp(SMARTSError): Error messages were being
writen by fprintf(stderr... and stdout. This made no difference
on console output but was not being picked up by the Windows GUI.
Changed to obErrorLog style.
* src/chains.cpp(GenerateByteCodes): Changed error messages to
obErrorLog style.
* zipstreamimpl.h(flush):Added test for NULL ostream, which had
been causing crashes (in Windows).
* kekulize.cpp: L152 bestorden was not being initialized (my new
debugger tells me) and the code was testing it. Moved the line
bestorden=99 to before the while loop. Not extensively tested but
seems to give the same as before for a few molecules.
* src/obconversion.cpp(Write): Added conditional compilation to
remove zipstream call in Windows. Started crashing with
---errorlevel. A kludge until we sort out the Windows compression
problems. Two other similar calls in obconversion are still there...
* src/obconversion.cpp(FullConvert): Added SetInStream and changed
the names of pInStream and pOutStream which were stupidly
given names which are also member variables! It's a bit late to
be altering core code like this but splitting, aggregation,
batch and normal all seem ok on Windows.
* src/finger3.cpp: Change name of FP3 file.
* data/SMARTS_InteLigand_051110.txt: replaced by
SMARTS_InteLigand.txt
*src/formats/mdlformat.cpp: Writes $$$$ for every molecule to
resolve bug #1362781
* INSTALL.windows: rewritten
windows-vc2005: Add DLL projects and update.
2005-11-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mdlformat.cpp: Correctly handle unspecified chiral
centers (CFG=3), fixes PR#1324929.
2005-11-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* Makefile.am, Makefile.in: Make sure INSTALL.Windows is included
in dist.
* doc/babel.1: Update with recent format additions.
* src/formats/amberformat.cpp, src/formats/balstformat.cpp,
src/formats/smilesformat.cpp, src/formats/turbomoleformat.cpp:
Update specification URLs.
2005-11-16 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp(Convert): m_IsLast set more definitely
as part of solution to bug #1357957.
(FullConvert) Extra gzip code to solve bug #1357705.
[Windows builds are now reading gzip ok but not always writing it
properly.]
src/formats/fastsearchformat.cpp: Extra lines withconditional
SetMoreFilesToCome to solve bug #1357957. [There may possibly be
a gzip incompatibility here as well].
* src/fingerprint.h, src/fingerprint.cpp,
src/fingerprints/finger2.cpp, src/fingerprints/finger3.cpp:
Make bitsperint a private variable and provide a Get(). Not
worth doing - the bug was a missing USING_DYNAMIC_LIBS in
the settings for OBExtraFormats project.
Windows build files.
2005-11-15 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp: remove #include <dflcn.h>
* windows/OBGUIDlg.cpp (OnInitDialog): add dummy OBConversion
object to load format files.
2005-11-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* Makefile.am, Makefile.in: Remove non-functional b32.mak file
from distribution.
* NEWS, THANKS: Further updates for 2.0 release.
* data/types.h, data/types.txt: Added PCM atom types.
* doc/Makefile.am, doc/Makefile.in: Removed defunct Migration.html
(from OELib).
* doc/FAQ.html, doc/OBTwoMigration.html, scripts/python/Examples.html:
Updated documentation (from the new website).
* src/formats/pcmodelformat.cpp: Initial support for PCModel
files. Possibly does not include all atom types, but does read all
the initial files I threw at it.
* src/formats/Makefile.am, src/formats/Makefile.in: Compile it.
* src/formats/freefracformat.cpp: Add support for reading files
with atomic symbol in 4th column, rather than first (i.e.,
PCModel-style "free form fractional").
2005-11-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/atomtyp.h: Updated with Chris's recent changes.
* data/Makefile.am, data/Makefile.in: Add Christian's data file.
* scripts/perl/Makefile.PL, scripts/python/setup.py: Bump version
number for 1.0 release.
* src/obconversion.cpp: Patch from Jean Brefort to ensure dynamic
loading of modules occurs correctly on UNIX.
* src/fingerprints/finger3.cpp: Update to also check versioned
directories. Fixes bug reported by Chris Swain.
* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
Fix capitalization errors pointed out by Jean Brefort.
* src/formats/xyzformat.cpp, src/formats/freefractformat.cpp: Add
specification URLs to point to Open Babel website. New format
database will give information on what OB reads/writes.
* src/formats/gaussformat.cpp: Fix error uncovered in roundtrip
test with graphite & 2D translation vectors. TV are reported as
atomic number -2.
* test/Makefile.am, test/Makefile.in: Clean-up of Makefile.am.
* tools/obdoc.cpp: Fix HTML -- there was a trailing </h2> tag.
2005-11-12 Chris Morley <c.morley@gaseq.co.uk>
* src/finger3.cpp: reads two formats of patterns file. Added FP4
with patterns in...
* data/SMARTS_InteLigand_051110.txt: from Christian Laggner with
extra LGPL line.
* data/patterns.txt: Added extra firstline to identify format.
* data/atomtyp.txt: Added additional IMPVAL lines for
atoms of F Cl Br I P S to allow implicit hydrogens(e.g.in SMILES)
and improve the reversibility of add/remove hydrogens. Needs to be
put into equiv .h file.
* src/formats/xml/xcmlformat.cpp: Now writes correct namespace uri
for CML1. Test for no bonds (for outputting a formula instead)
now made before removing hydrogens.
* src/formats/xml/xcmlformat.cpp, xml.h: Mods to allow nested
molecules.
* src/formats/xml/xml.cpp: XML programming notes added.
* src/formats/xml/xmlformat.cpp, xml.cpp, xml.h: files can now
contain objects of different types, e.g. molecules in cml and pubchem
* test-set/others/: added some cml files
* src/obconversion.cpp: minor changes to comments
Update Windows build files
2005-11-10 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/bgfformat.cpp (ReadMolecule): Fix problem with atom
type translation uncovered during roundtrip testing -- atom type
was "cleaned" before assignment.
* src/formats/Makefile.am, src/formats/Makefile.in: Make sure
libinchi is correctly linked to inchiformat module.
* src/formats/PQSformat.cpp, src/formats/fastsearchformat.cpp,
src/formats/fingerprintformat.cpp, src/formats/inchiformat.cpp,
src/formats/rxnformat.cpp: Found a few remaining calls to
cerr. Updated to use OBMessageHandler framework, fixing PR#1281758.
2005-11-09 Geoffrey Hutchison <babel@geoffhutchison.net>
* Doxyfile: Update version number for 2.0 release.
* NEWS, THANKS: Updates for 2.0 release.
* data/patterns.txt: Updated with new version from Chris Morley
with corrected SMARTS patterns.
* doc/Makefile.am: Remove man.1 pages from target list for now -- new
versions are much better than doxygen generated versions.
* doc/api-header.html, doc/api-footer.html: Updated for new
website template.
* doc/*.1: Updated man pages by hand.
* configure, configure.in, src/config.h.in, */Makefile.in: Updated
to always build InChI now that the IUPAC code is distributed under
the GNU LGPL.
* src/formats/Makefile.am, src/formats/Makefile.in,
src/formats/inchi/*: Ditto.
* scripts/perl/Makefile.PL: Make sure to include libz in
compilation.
* src/bitvec.cpp, src/bondtyper.cpp, src/chains.cpp,
src/chiral.cpp, src/fingerprint.cpp, src/generic.cpp,
src/obconversion.cpp, src/patty.cpp, src/resdiue.cpp,
src/rotor.cpp: src/formats/mdlformat.cpp,
src/formats/mol2format.cpp, src/formats/smilesformat.cpp:
Updated to use OBMessageHandler framework for errors rather than
old ThrowError or cerr directly. Solves PR#1281758.
* src/parsmart.cpp: Actually implement up & down bond
primitives. Solves PR#1219329.
* src/formats/PQSformat.cpp: Remove calls to exit() which should
never be used in production code.
* src/formats/balstformat.cpp: Add specification URL.
* tools/Makefile.am, tools/obdoc.cpp: Add hint for "obdoc" tool
which creates the file format documentation.
* tools/obchiral.cpp, tools/obprop.cpp: Add Doxygen man page.
2005-11-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/hinformat.cpp: Make sure to mark all aromatic bonds
as "a" in output. Fixes bug reported by Rajarshi Guha.
2005-10-21 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/atomtyp.txt, data/atomtyp.h, data/types.txt, data/types.h:
Updated Dreiding atom types, contributed by Menno Deij.
2005-10-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* Makefile.am, Makefile.in: Make sure both windows and
windows-vc2005 directories are included.
* src/data.cpp (OBTypeTableTranslate): Fix possible crashes when
translating atom types and one or both columns are out of range.
* src/freefractformat.cpp: Add TrimErrors routine to trim trailing
standard error notations in numbers. Now properly reads 1.234(56)
as input.
* test/ringresults.txt, test/smartsresults.txt: Updated to reflect
atom typing changes.
2005-10-19 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/xcmlformat.cpp: Added reading and writing
of <crystal> xFract etc.
* src/formats/freefracformat.cpp: added kludge for
getline() in Windows(binary mode) possibly returning 0x0d
from a blank line.
Removed two unreferenced variables
* doc/OBTwoMigration.html: Replace example of Reaction SMILES
(sadly not yet done) by CMLReact. Couple of typos.
2005-10-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* Doxyfile: Updated for new doxygen release (1.4.5).
* NEWS: Updated with initial release notes for 2.0.
* configure, configure.in: Fix problems with libz detection.
* doc/OBTwoMigration.html: Add a draft migration guide, touching
on four key code updates.
* doc/*.1: Updated manpages.
* scripts/*: New versions (1.0.0b5) using SWIG 1.3.27.
* src/atom.cpp, src/mol.cpp, src/molchrg.cpp: Documentation
updates (switching to new iterators).
* src/chains.h, src/chains.cpp: Updates from last OELib GPL
version, which were not previously incorporated.
2005-10-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* COPYING: Updated FSF address.
* src/formats/Makefile.*: Add new copyformat code.
* src/atom.cpp, src/base.cpp, src/ring.cpp, src/patty.cpp,
src/mol.h, src/molchrg.cpp, src/oberror.h, src/oberror.cpp,
src/obiter.cpp: Documentation updates.
* src/obconversion.h, src/obmolecformat.h : Revert change of
std::type_info -- GCC requires the namespace declaration.
2005-10-17 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/xml/xcmlformat.cpp: Added CML1 writing.
Corrected bug in writing "x","y" instead of "x2","y3" etc.
Corrected bug in x and z 3D coords in array mode.
2005-10-17 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.h:Replaced std::type_info by type_info
in preparation for mods to ensure STL/VC6 compatibility.
I hope it will still compile in unix.
* src/obconversion.cpp,obconversion.h: Added GetInLen(), wInlen,
rInlen to provide the length of the object being written.
This simple operation is irritatingly complex because of object
queue.
* src/copyformat.cpp: simple new format which allows chemical
filtering from a multi-object file with no possibility of losing
content by OB's conversion, e.g. sdf or xml files.
* src/formats/exampleformat.cpp: Now a heavily commented
format template. Maybe should be put in another folder.
* src/formats/inchiformt.cpp(WriteMolecule): correct bug sometimes
causing crash when no 0Dstereo info.
* windows-vc2005: Added project files for Visual C++ 2005
2005-10-14 Geoffrey Hutchison <ghutchis@Alumina.local>
* Source-code documentation updates. Ensure all classes and struct
definitions have at least a brief description.
2005-10-14 Chris Morley <c.morley@gaseq.co.uk>
Update Windows build files and documentation. Remove unused files.
2005-10-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* acinclude.m4: Fix bug in CHECK_ZLIB macro to correctly disable
zlib support if --without-zlib option is selected.
* src/data.h, src/typer.h, src/bondtyper.h, src/phmodel.h,
src/rotor.h: Add a GetSize() method to all OBGlobalDatabase
classes. Ensures a data table is not empty after calling Init().
* configure.in, configure, src/config.h.in: Update for a 2005-10-15
snapshot. Require libxml2 >= 2.6.0 (which adds the xmlwriter API).
* doc/api-header.html, doc/api-style.css: Update with new Doxygen
version (which adds "tabs" to organize sections).
* src/Makefile.am, src/Makefile.in: Update to zipstreamimpl.h
instead of zipstream.cpp.
* src/zipstream.h: Switch basic_zip_ostream and
basic_unzip_istream to using public base classes, which works
around a bug in some versions of GCC.
* src/formats/xml/Makefile.am, src/formats/xml/Makefile.in: Switch
from defining LDFLAGS to correct AM_LDFLAGS (which allows the user
to customize LDFLAGS as desired).
2005-10-11 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp(FormatFromExt): correct mistake
in last mod.
src/obconversion.h Add explicit copy constructor for
OBConversion (just so pAuxConv is set to NULL).
* src/generic.cpp, src/chiral.cpp: added return statements
etc to avoid compiler warnings.
* src/data.h: Added OBAPI to class OBResidueData (for DLL builds)
* src/mol.h, src/formats/pdbformat.h, src/data.cpp: Moved
global variable OBResidueData resdat to data.cpp and
treat it like other global variables. (This makes DLL builds
easier.) If its use is specific to pdb format, perhaps it
should be a a static variable in PDBFormat?
* windows/babelconfig.h: removed HAVE_LIBZ because in DLL
builds unzipping code was preventing input of any file. OK
in OBGUIs where is now defined in Settings.
Updated Windows build files.
2005-10-09 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp(FormatFromExt): test failure of
string::find, etc by return of string::npos
* src/obconversion.cpp(SetStartAndEnd):
If EndNumber < StartNumber output only one object
* src/mdlformat.cpp(SkipObjects): inverted test for "$$$"
which was causing -f and -l errors reported by Chris Swain.
* src/formats/inchiformat.cpp: Added 'test' format for
doing round trip, testing before and after with InChI
* src/zipstreamimpl.h: Name changed from zipstream.cpp
* src/zipsteam.h: consequent name change of #include
2005-10-07 Chris Morley <c.morley@gaseq.co.uk>
Update Windows build files.
* src/chiral.cpp(CalcSignedVolume): change name of second
loop variable from i to j (VC6 deficiency)
* src/data.cpp(OBElementTable::ParseLine); make symbol[5]
[3] wasn't enough. (Better debugger!)
* src/fingerprint.cpp: remove #if HAVE_CONFIG
2005-10-05 Chris Morley <c.morley@gaseq.co.uk>
* src/zipstream.cpp(add_footer): changed 2nd var n to m to
accomodate VC6 compiler. (But still not writing properly in VC6)
* src/obconversion.cpp: moved compression code from Convert()
to Convert((std::istream* is, std::ostream* os) and restored
pOutStream after conversion. Also in write();
* src/obconversion.cpp (FullConvert): moved call to
OneObjectOnly() inside loop in splitting section to cure bug
#1313201.
* src/formats/fastsearchformat.cpp: Changed Convert() to
Convert(NULL,NULL) (two places) so that compression code will
be called.
* src/formats/smilesformat.cpp (SmiToMol): removed call to
AddHydrogens().
2005-10-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/obgrep.cpp: Fix PR#1286797. Count of matching molecules
was stored as a char??. Corrected code to store as unsigned int
and output correctly. Thanks to Chris Swain for the bug report.
* src/zipstream.h, src/zipstream.cpp: Update to (hopefully) fix
syntax problems with VC++ experienced by Chris Morley.
* src/atom.cpp (GetType): Make sure to save and restore
OBTypeTable patterns -- otherwise higher-level code will see
unexpected type translations.
* src/data.h src/data.cpp (OBTypeTable): Set const on parameters
where needed, add error checking for GetToType and GetFromType()
methods.
* src/formats/*.cpp: Add code to move to ifs.eof() after reading
to ensure the multiple-molecule parsing doesn't attempt to add an
invalid empty molecule.
* src/formats/smilesformat.cpp: Add defensive code around chiral
search code -- ensure all pointers are valid before dereferencing.
* test/roundtrip.cpp: Ensure the filestream is not at EOF before
attempting to read another molecule (and complain that a format
has translated an incorrect number of molecules).
* tools/README: Remove comments about deprecated obtanimoto program.
2005-10-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure, configure.in: Fix BUILD_SHARED condition to only
build dynamic file format modules when shared libraries are also
enabled.
* scripts/*: Update SWIG modules using SWIG 1.3.26rc1.
* src/formats/smilesformat.cpp: By default, add implicit hydrogens
when reading SMILES files.
* tools/obprop.cpp: No need to add hydrogens to SMILES files, as
above.
* src/formats/carformat.cpp: Modifications to better handle
multiple-molecule CAR files, as suggested by Jean Dessolin.
* test/roundtrip.cpp: Refined error messages to report molecule
number and file number (1 vs. 2).
2005-09-29 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/types.h: Updated (as below).
* src/zipstream.h, src/zipstream.cpp: Updated with cleaned-up
versions from OpenSG project. Added method to add gzip header
after creating stream.
* src/obconversion.cpp: Clean up WriteString() and WriteFile()
methods to use Write() -- eliminates duplicated code. (Maybe
Convert should use Read() and Write() similarly.) Now works
correctly with gzip output.
* src/dlhandler_unix.cpp: Update to fix crashing bugs with global
loading of OBConversion::LoadFormatFiles().
* configure, configure.in, */Makefile.am, */Makefile.in: Update
for new snapshot, minor fixes for distribution.
* Doxyfile, src/base.cpp: Update for eventual 2.0.0 release.
2005-09-17 Chris Morley <c.morley@gaseq.co.uk>
* src/formats.mpdformat.cpp: Nick England's format for printing
atom types added (Slightly modifed option handling.)
* data/types.txt: Extended. types.h not yet updated.
2005-09-14 Chris Morley <c.morley@gaseq.co.uk>
* src/main.cpp(main): line 322 Mods to place * correctly
when file name has *.gz
* src/obconversion.cpp, obconversion.h: Removed dummy
instance which was causing trouble and called LoadFileFormats()
from the initialisation of a static variable. Removed call to
LoadFileFormats in constructor.
* src/obconversion.cpp: Added -z option and code for zipstream
output in Convert() and Write(). But ozipstream seems not to be
working properly at present.
Messed around with ReadString() and ReadFile().
2005-09-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp: Only use dummy instance on WIN32 or when
not using dynamic modules (e.g., CygWin).
* src/zipstream.cpp, src/zipstream.h: Changes to compile on
GCC. (Hopefully it will *still* compile on VC6.)
2005-09-14 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.h, obconversion.cpp(Read): Make non-templated
and move to .cpp; Add zipstream code to Read and Convert,
* src/OBConversion.cpp: Add global dummy instance, so that format
files are loaded. (A better way to do this needs to be found.)
* src/zipstream h, zipstream.cpp: changed to compile on VC6!
2005-09-12 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/zipstream.h, src/zipstream.cpp: Modified classes (updated to
compile in GCC) to support gzip/zlib compression streams.
* configure.in, configure, src/Makefile.am, */Makefile.in: Add
support for conditional compilation of code depending on zlib. (i.e.,
zipstream.cpp).
* src/obconversion.cpp (FormatFromExt): Change to detect .gz
extension and look for previous extension.
2005-09-11 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, src/config.h.in, Makefile.in,
*/Makefile.in: Update to detect libxml2 headers and libraries
using AM_PATH_XML2 and compile src/formats/xml directory.
* src/formats/Makefile.am: Remove cml.cpp and cmlformat.cpp old
code.
* data/bondtyp.txt, data/bondtyp.h: Updated porphyrin /
phthaloc. patterns with hand-written SMARTS and bond
orders. Ensures correct bond order assignment.
* src/data.h, src/data.cpp: Move OBResidueData from pdbformat.cpp,
so that other code can use residue data.
* src/generic.h: Move OBSerialNums from pdbformat.cpp.
* src/formats/pdbformat.cpp: Remove OBResidueData and OBSerialNums
as above.
* src/formats/smilesformat.cpp (OBSmilesParser): Make sure _mapcd
is cleared before reading a molecule -- would crash when
reading/writing multiple SMILES files.
* src/formats/yasaraformat.cpp: New format, contributed by Elmar.
* src/formats/xml/pubchem.cpp, src/formats/xml/xcmlformat.cpp:
Change OBMol::SetTitle() calls to be ISO C++ compilant.
* src/dlhandler_unix.cpp: Add support for multiple search paths
for shared format modules. Uses environmental variable
BABEL_LIBDIR which can be a colon separated list of paths
(e.g. /usr/lib/openbabel:/usr/local/lib/openbabel ...)
* test/ringresults.txt, test/smartsresults.txt: Regenerate after
recent SMARTS and atom typing changes.
2005-09-10 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/libxml: Added libxml2 header files. I have
used a Windows DLL for libxml2 and haven't used the
source files, but I guess they should be added.
* src/formats/xml: Added classes for CML, CMLReact,
PubChem and a general XMLFormat which chooses based on
xmlnamespace.
xml.cpp amd xml.h contain an extended OBConversion
with libxml2xmlreader and xmlwriter, XMLBaseFormat and
XMLMoleculeFormat abstract classes.
This subfolder may not be the best place for
the format cpp files but are here for the moment because of
possible conflict with the existing cml.cpp and cmlformat.cpp
which they are intended to replace when their bugs have been
reduced.
2005-09-09 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/chiral.h, src/chiral.cpp: Updates from Nick England to
compute chiral volume and track the atoms used.
* tools/obchiral.cpp: New tool from Nick England to print
chirality information on molecules.
* src/formats/mdlformat.cpp, src/formats/smilesformat.cpp: Fixes
from Nick to properly interconvert MDL and SMILES chirality
flags. Solves PR#1257494.
* src/generic.h, src/generic.cpp: New class OBChiralData
contributed by Nick for above.
Removed obDataType enum, replacing with namespace
OBGenericDataType. Allows significantly larger range of "slots"
with room for future expansion without breaking
backwards-compatibility.
* src/atom.cpp, src/bond.cpp, src/mol.cpp, src/mol.h,
src/residue.cpp, src/ring.cpp, src/rotamer.h,
src/formats/cacaoformat.cpp, src/formats/cml.cpp,
src/formats/cssrformat.cpp, src/formats/dmolformat.cpp,
src/formats/freefracformat.cpp, src/format/mdlformat.cpp,
src/format/mol2format.cpp, src/formats/pdbformat.cpp,
src/formats/reportformat.cpp, src/formats/smilesformat.cpp:
Update to use new OBGenericDataType:: declarations.
* src/formats/Makefile.am, src/formats/Makefile.in: Remove
mm3format bits. Not correctly implemented.
2005-09-09 Chris Morley <c.morley@gaseq.co.uk>
* atom.cpp (operator=): _spinmultiplicity now copied
* obconversion.cpp (SetOneObjectOnly): Set _IsLast
* obmolecformat.h: Small comment change
2005-09-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* Makefile.am: Add dist-hook to remove CVS directories from
included windows/ subdir.
* configure.in: Add test for libinchi -- compile InChI format if
libinchi is already available. (Acceptable under both GPL and
InChI terms.)
* src/formats/Makefile.am: Compile InChI format *ONLY* if libinchi
is available already.
* doc/Makefile.am: Build man pages for all obtools, only if
--enable-maintainer-mode was passed to configure.
* scripts/Makefile.am: Build SWIG wrappers only if
--enable-maintainer-mode was passed to configure.
* src/Makefile.am: Ensure headers are installed into
openbabel-2.0/openbabel directory and #include decl are re-written
on install.
* src/math/Makefile.am: Ditto.
* aclocal.m4, configure, config.guess, install-sh, ltmain.sh,
missing, mkinstalldirs, config.sub, */Makefile.in,
src/config.h.in: Updated with libtool-1.5.20 and automake-1.9.6
after above updates.
* openbabel-2.0.pc.in: Update to reflect new include path.
* scripts/openbabel.i: Wrap classes in data.h (OBElementTable,
etc.) too.
* scripts/*: Ditto. Renumber versions from 1.0 to separate from OB
release version numbers. (Scripting wrappers will likely change
more quickly.)
* src/data.h, src/main.cpp, tools/obgrep.cpp, tools/obrotate.cpp,
tools/obfit.cpp, tools/obprop.cpp: Documentation updates.
* src/rand.cpp (OBRandom::TimeSeed): If sranddev() is available
(i.e., BSD and Macintosh), use it -- higher quality results.
2005-09-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.cpp: Update documentation, perform more error checking
for ParseLine() methods -- report to obErrorLog if needed. Fixes
PR#1252607.
* src/phmodel.cpp, src/typer.cpp (ParseLine): Ditto.
* src/generic.h: Added additional types to enum obDataType, plus
documentation.
* src/bond.cpp: Switch IsDoubleBondGeometry to OBBond method.
* src/mol.cpp, src/mol.h: Update OBMol documentation for OBConversion
class. Add new PerceiveBondOrders() check for
IsDoubleBondGeometry, using patch PR#1275166, contributed by Elmar.
* src/residue.cpp: Update documentation on property namespaces.
* src/parsmart.cpp: Fix matching explicit hydrogen count 'H'
PR#1275176, contributed by Elmar.
2005-09-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/cacaoformat.cpp (SetHilderbrandt): Mark a todo to
ensure this method is completely bulletproof -- still appears to
dereference atoms without checking for NULLs.
* src/fingerprint.h, src/fingerprint.cpp (SetBit): Change to take an
unsigned int to prevent crash caused by "negative" parameter.
* src/fingerprints/finger2.cpp (CalcHash): Ditto.
2005-09-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure: Bump version to 2.0b4-20050901 for
snapshot. Add support for conditional compilation of source based
on libxml2.
* */Makefile.in: Ditto.
* Doxyfile: Bump version to 2.0b4-20050901.
* src/base.cpp: Remove reference to fixed version number in
documentation.
* src/obconversion.h: Remove extraneous OBConversion:: on
OptionParamArray() decl, which confused doxygen.
* src/formats/CSRformat.cpp: Attempt to fix crash encountered
during roundtrip testing from writing audit message.
* src/formats/cacaoformat.cpp (SetHilderbrandt): Prevent crashes
caused by attempting to derference NULL pointers (i.e., small
molecules without a full z-matrix).
* src/formats/mmodformat.cpp: Test to be sure # atoms > 0. Fixes
crash encountered with roundtrip testing on binary data.
* src/formats/mdlformat.cpp: Test to be sure bond record refers to
existing atoms (i.e., 0 < start <= NumAtoms()). Prevents crash
encountered with intentionally invalid MDL files.
* src/formats/zindoformat.cpp: Remove debugging string for
non-standard elements.
* src/chains.cpp (MatchConstraint): Ensure OBAtom parameters are
non-NULL before proceeding. Fixes a bug encountered when
roundtripping H2O.
* src/generic.cpp, src/obutil.cpp, src/ring.cpp src/mol.cpp: Add
identifiers for Blue Obelisk algorithm dictionary.
2005-08-31 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/element.txt, data/element.h: Updated with new data from the
Blue Obelisk shared repository. Should be more consistent with
other values (particularly covalent radii).
* src/data.h, src/data.cpp (OBElement, OBElementTable): Add
support for new data, including ionization potential, electron
affinity, name, and visualization colors.
* data/bondtyp.txt, data/bondtyp.txt: Changes contributed by Elmar
for PR#1275146.
* src/mol.h, src/mol.cpp: Add new method IsDoubleBondGeometry to
assist with bond order assignment (PR#1275170). Fix bugs in
PerceiveBondOrders with conjugated single/double bonds and biotin
PR#1275151, PR#1275160.
* scripts/*: Updated with current API changes. Added more
examples, particularly for Python.
* Doxyfile: Bump for 2.0b4 snapshot.
2005-08-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/bondtyp.txt, data/bondtyp.h: Add initial porphyrin / heme
patterns. Probably still a bit buggy. Addresses PR#1259757.
* src/bond.cpp (SetBO): Add calls to SetKSingle(), SetKDouble(),
and SetKTriple() as appropriate. This mirrors expected behavior,
IMHO.
* src/bondtyper.cpp: Remove calls to SetKSingle() etc. since these
are now covered above. All SetBO() calls are handled
correctly. Thanks to Elmar Krieger for noticing this.
* src/formats/freefracformat.cpp: New format for free-form
fractional input (title, unit cell parameters, coordinates).
* src/formats/Makefile.am, src/formats/Makefile.in: Compile it.
* src/formats/xyzformat.cpp: Fix bug with setting title line.
2005-08-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/parsmart.cpp: Fix AL_CONST case (currently in non-compiled
code) as suggested by Elmar Krieger. Fixes PR#1261285.
* src/obutil.cpp (InternalToCartesian): Add a check to make sure
pointers are valid before dereferencing. Fixes crash caused by
Amber PREP reading random binary data in a roundtrip test.
* src/formats/amberformat.cpp (ReadMolecule): Add a check to only
call InternalToCartesian when some coordinates have been read,
as above.
* src/formats/viewmolformat.cpp: Prevent an infinite loop when
reading random binary data. Even if no correct records are read,
continue to read a new line to look for a new record.
* src/formats/Makefile.am, src/formats/Makefile.in: For now,
disable compilation of mm3format.cpp since it is incomplete and
incorrect. Related to PR#125604, 1252510.
* src/math/matrix3x3.h, src/math/matrix3x3.cpp:
Add some basic error checking to methods marked TODO.
(FillOrth) Change to matrix specified in PDB documentation:
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_75.html
* src/generic.cpp, src/generic.h (OBUnitCell): Simplify code and
re-use matrix3x3::FillOrth() rather than duplicate code.
(OBUnitCell::GetFractionalMatrix): New method to convert from
Cartesian to fractional coordinates.
2005-08-17 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.h, obconversion.cpp, main.cpp: Added code
to register how many parameters an option takes(currently 0 or 1).
Gives extra flexibility to command line options, like position
independence, parameter can start immediately or after a space.
Cures bug #1260540 see bug report.
* src/formats/fingerprintformat.cpp, fastsearchformats.cpp,
APIInterface.cpp, smilesformat.cpp, mdlformat.cpp:
Option parameter registrations consequent on above.
* src/obmolecformat.h: Added GetType() (returns typeid for OBMol).
Option parameter registrations for -b -s input options and
for API general options which relate to OBMol.
* src/obconversion.h, obconversion.cpp: Added hook to extend
OBConversion (initially for an XML reader). AuxConv is a pointer
to an object derived from OBConversion which is deleted in
the destructor.
2005-08-16 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/mol.h: Add obiter.h to standard included headers to allow
STL-compatible iterators.
* data/torlib.txt, data/torlib.h: Add nitro rotation pattern
contributed via JOELib2.
* data/phmodel.txt: Update comment on imidazole charge, transform
patterns.
* data/aromatic.txt, data/aromatic.h: Add "default" aromatic rules
for carbon and nitrogen with a range of possible electrons
(depending on specific bonds, formal charges, etc.) Solves
PR#1257827.
* test/smartsresults.txt: Regenerate after recent typing changes.
2005-08-15 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/bondtyp.txt, data/bondtyp.h: Add fix for carbonic acid bond
typing bug (a.k.a. "multimatch") and carbon dioxide, both
contributed by Elmar Krieger. Fixes PR#1253307 and #1257588.
* src/parsmart.cpp (EvalAtomExpr): Add fixes for PR#1253301,
contributed by Elmar Krieger. Solves problems with phosphates and
phosphorous acid.
* src/typer.cpp (CheckAromaticity): Add fix for multi-ring
compounds like heme / porphyrins, where not all rings are properly
typed as aromatic, contributed by Elmar. Fixes PR#1259786.
* src/formats/mol2format.cpp: Updated Tripos Mol2 format
specfication URL, as contributed by Nick England (PR#1257712).
* src/formats/mdlformat.cpp: Ensure no "4" aromatic bond orders
are used when writing MDL files. If a bond is detected to have
BO == 5, re-run Kekulize() on the molecule. Fixes problems
mentioned in e-mail discussions initiated by Rich Apodaca.
2005-08-12 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/mdlformat.cpp: Following Nick England's discussion,
reversed clockwise/anticlockwise in V300 read.
Re-added IsUp() IsDown() in V3000 write. These were removed for some
reason on 31stJan 2005, but are needed for double bond isomers.
2005-08-11 Chris Morley <c.morley@gaseq.co.uk>
* src/molecformat.h: Move test for NULL pmol.
* src/format/smilesformat.cpp: Molecules with zero atoms now accepted.
2005-08-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* doc/Makefile.am, doc/Makefile.in: Fix bug with rename of
Doxyfile to Doxyfile-man. Handle man page updates.
* doc/babel.1: Updated man page with doxygen (still needs many
updates).
* src/base.cpp: Documentation update.
* src/kekulize.cpp: Fix compilation error under GCC caused by
Chris' previous change.
* src/mol.cpp: Remove cerr calls.
* src/obconversion.cpp (OBconversion::Description): Remove space
at end to properly balance spacing in main.cpp.
* src/formats/*.cpp: Add audit entries for formats not derived
from OBMoleculeFormat.
* src/formats/Makefile.am, src/formats/Makefile.in: Add
cmlppformat.cpp as an example.
2005-07-29 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/obmolecformat.h: Changed to allowed molecules with
zero atoms to be written, since they can have meaning CML.
Replaced with a obInfo message. I hope this
doesn't cause problems with other formats.
* src/formats/cmlppformat.cpp: cmlpp version of cmlformat
For general interest only.
* src/util.cpp, kekulize.cpp: Make some loop variables VC6 compatible.
Maybe it is the only compiler in the universe which uses the old
scope rules for loop variables, but it would be better if they
were done like:
unsigned i;
for(i=0;....{}
for(i=0;... {} another loop
to avoid "re-initialisation" errors in VC6.
2005-07-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, */Makefile.in: Add
--disable-dynamic-modules configure option for building static
file formats library. Should solve temporary Cygwin build problems
-- not sure why/how formats aren't installed properly.
Partially fixes PR#1246761.
* src/config.h.in, src/dlhandler_unix.cpp:
Properly handle environments where .so isn't the extension
for modules.
* src/formats/mol2format.cpp: Fix typo PR#1246836.
2005-07-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/fingerprints/*: New directory for finger2.cpp and
finger3.cpp. Place new fingerprint formats here.
* src/Makefile.am, src/Makefile.in: Ditto.
* Doxyfile, doc/Doxyfile-man: Updated for new snapshot.
* configure.in, configure, Makefile.am, Makefile.in: Generate the
scripts interfaces automatically if SWIG is installed.
* scripts/Makefile.am, scripts/Makefile.in: Ditto.
* src/config.h.in: Add check for libxml2.
* scripts/perl/*: More documentation.
* data/Makefile.am, data/Makefile.in: Add patterns.txt fingerprint
data to ensure it's installed properly.
* data/atomtyp.txt, data/atomtyp.h: Add + formal charges on carbon
to IMPVAL rules, matching Chris's change below.
* data/patterns.txt: Add descriptive header, explaining format and
purpose of this file.
* src/fingerprint.cpp, src/fingerprint.h, src/kekulize.cpp,
src/obutil.cpp, src/patty.cpp, src/formats/fastsearchformat.cpp:
Fix signed/unsigned integer warnings.
* src/generic.cpp: Fix copy ctor compiler warnings (call base
class ctor).
* src/oberror.h, src/oberror.cpp: Move "level" into OBError class
out of OBMessageHandler. Allows OBError to format the message
output based on the type of message.
* src/formats/Makefile.am, src/formats/Makefile.in: Add
APIInterface to build list. Fixes problems passing flags via
command-line.
* src/formats/bgfformat.cpp: Fix bug discovered during
roundtripping -- need to move istream to the end of the file, not
the END record.
* src/formats/cml.cpp: Temporarily demote CML errors to info
messages -- currently too verbose.
* test/unitcell.cpp: Fix compilation warning with vector3
assignment.
* test/roundtrip.cpp: Remove debug message left inadvertantly.
* test/smartsresults.txt: Regenerate after atom typing changes.
2005-07-27 Chris Morley <c.morley@gaseq.co.uk>
* data/atomtyp.txt: Add line for C in isocyanide to correct
bug 1226846
* src/atom.cpp (ImplicitHydrogenCount): undo the last correction
which was making other case go wrong.
* src/main.cpp: renamed the variable which has the result of
OBConversion::FindFormat("obapi") because an existing variable was
being used.
2005-07-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/atom.cpp (ImplicitHydrogenCount): Add a fix for PR#1226846
-- in methyl isocyanide, the carbanion is marked as an implicit
valence of 1, but a multiplicity of 0. Now handles this case correctly.
* src/obconversion.h, src/obconversion.cpp: Switch ReadString and
ReadFile to non-template OBBase* arguments to facilitate scripting
access. (Handling C++ templates in SWIG is touchy.)
* scripts/* Updates to add OBConversion framework to scripting
interfaces. Includes new perl tests.
* src/formats/smilesformat.cpp: Add a tab delimiter between SMILES
string and title rather than a space as suggested in
PR#1241609. Seem to work OK on Daylight's DEPICT online form with
tabs or spaces.
* src/mol.h: Up BUFF_SIZE to 32768 from 1024 to handle larger line
lengths in input.
* src/data.cpp: Remove duplicate BUFF_SIZE declaration.
* src/kekulize.cpp: Migrate to use OBMessageHandler error
reporting.
* src/fingerprint.h: Rewrite "<nCandidates>" bit, which was
assumed to be an HTML tag by doxygen.
2005-07-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* test/roundtrip.cpp: Migrate OBMol::Clear() statements to more
logical place -- right before a read.
* src/formats/turbomoleformat.cpp, src/formats/hinformat.cpp,
src/formats/dmolformat.cpp: Fix bugs found during roundtripping --
ReadMolecule() would go into an infinite loop looking for the
"next" molecule in a single-molecule file.
* src/formats/cml.cpp: Migrate to OBMessageHandler framework and
make sure to clear the molPtr when a <molecule> beginning record
is encountered.
* src/obmolecformat.h (ReadChemObject): Before attempting to read
from the istream, check to see the status -- are we at the end of
the stream?
* src/obconversion.h src/obconversion.cpp: New methods ReadString,
ReadFile, WriteString, and WriteFile for convenience access
through scripting languages which do not have "stream" support.
2005-07-22 Geoffrey Hutchison <babel@geoffhutchison.net>
* openbabel-2.0.pc.in: Rename pkg-config data to prevent conflicts
with 1.x releases.
* configure.in, configure, */Makefile.in: Ditto.
* data/torlib.txt: Update documentation on torsion rules using
SMARTS patterns.
* src/Makefile.am, src/Makefile.in: Add finger3.cpp to compilation
list, remove fastsearch.cpp.
* src/dlhandler.h, src/fingerprint.h: Add OB_ prefix to
#define/ifdef guards.
* src/oberror.h, src/oberror.cpp: Add methods to turn off error
logging and limit the size of the message queue.
* src/fingerprint.cpp: Add temporary string to eliminate
compilation errors with GCC.
* src/formats/chem3dformat.cpp, src/formats/ghemicalformat.cpp,
src/formats/viewmolformat.cpp: Fix translation errors -- formats
are supposed to be subclasses of OBMoleculeFormat.
* tools/Makefile.am, tools/Makefile.in: Temporarily disable
compilation of obtanimoto -- fingerprint API has changed and this
is not updated yet.
2005-07-19 Chris Morley <c.morley@gaseq.co.uk>
* src/main.cpp src/formats/APIInterface.cpp: API options are now
like ---errorlevel (this was -w) and the name now appears
only in APIInterface.cpp. Added a description and called it in
help().
* src/obmolecformat.h: Changed auditMsg in WriteChemObject to
"...Write...);
* src/fingerprint.h, fingerprint.cpp: Changed parameters of
FastSearchIndexer ctor. Replaced #include "config.h" by
#include "babelconfig.h"
This may solve David Hoekman's compilation difficulties.
* src/transform.cpp: Made type conversion more explicit in
addtotitle handler. ditto
* src.finger3.cpp: looks for data file first in env var and
BABEL_DATADIR
2005-07-13 Chris Morley <c.morley@gaseq.co.uk>
* src/fingerprint.cpp, /srcfingerprint.h, src/finger2.cpp:
modified so that fingerprints are dynamic.
Incorporated fastsearch into fingerprint.h and .cpp.
* src/finger3.cpp: Added a SMARTS pattern matching fingerprint.
Also an incomplete src/patterns.txt. Should probably be moved to
data folder although code to allow this not yet included.
* src/fastsearch.cpp, src/fastsearch.h: Deleted
* src/main.cpp: changed -w handling to pseudo-format, obapi,
to avoid having to #include oberror.h.
Added two lines to exclude its display in format lists.
Added -F option to display available fingerprints.
* src/obconversion.h: small changes in documentation.
* src/transform.cpp; added empty test for options and addtotitle
option (mainly for use in fastsearch)
* src/formats/APIInterface.cpp: Added pseudo format to transfer
data from user interface to API.
* src/formats/fingerprintformat.cpp, src/formats/fastsearchformat.cpp
Modified to make fingerprints dynamic.
* src/formats/mdlformat.cpp, src/formats/smilesformat.cpp Added
extra lines in Description to improve GUI display.
2005-07-11 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/atom.cpp, src/bond.cpp, src/chiral.cpp, src,molchrg.cpp,
src/obmolecformat.h, src/patty.cpp, src/phmodel.cpp, src/ring.cpp,
src/rotor.cpp: Add obAuditMsg "audit log" messages for perception
and "assignment" methods, including methods with "chemical
intelligence" (e.g., OBAtom::HtoMethyl or OBAtom::SetHybAndGeom).
* src/formats/pdbformat.cpp: Transition CONECT warnings to
obErrorLog::ThrowError calls.
* src/oberror.cpp: Turn off default "error wrapping" of cerr to
OBError messages.
2005-07-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/atomtyp.txt, data/atomtyp.h: Change implicit valence rules
to fix PR#1226444. N=C(N)C is properly interpreted.
* tools/obprop.cpp: Add hydrogens for SMILES input (checked by
.smi extension). Fixes PR#1222443.
* test/roundtrip.cpp: Fix checks for BOX and SMILES extensions.
2005-07-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.h (OBElement): Reorder initialization to remove
compiler warning. Documentation updates.
* src/data.cpp (OBElementTable::ParseLine): Format declarations
should be ignored for red, blue, green columns in sscanf call.
* src/main.cpp: Add error log filtering back -- not handled in
OBConversion.
* src/chains.cpp, src/mol.cpp, src/obutil.cpp, src/ring.cpp,
src/typer.cpp:
Add obAuditMsg messages for methods substantially altering an OBMol.
* src/matrix.cpp (convert_matrix_f): Partly unroll loop to
increase performance.
* src/rotor.h, src/rotamer.cpp, src/obconversion.h: Documentation
updates.
* test/roundtrip.cpp: Loop over all molecules in files, checking
to see if one file has more molecules than another.
* src/formats/Makefile.am, src/formats/Makefile.in:
Rename grosmos96format to gromos (correct name of program).
* src/formats/*format.cpp: Add BeginModify() / EndModify() calls
as appropriate (i.e. before and after major changes to OBMol,
including ConnectTheDots or PerceiveBondOrders).
2005-07-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.h: Move include "babelconfig.h" to the top of
all #includes to ensure proper conditional compilation. Suggested
by Jean Brefort.
* src/mol.h: Ensure std:: is used on Trim() declaration.
* src/generic.h: Call Trim() for OBCommentData().
* src/formats/Makefile.in, src/formats/Makefile.am: Merge cml.cpp
and cmlformat.cpp into a combined library for proper loading -- as
reported by Jean.
2005-07-04 Chris Morley <c.morley@gaseq.co.uk>
Some of Jean Brefort's suggested patches.
*src/obconversion.h, src/obconversion.cpp:
The base class OBFormat needs a virtual destructor,but then
derived format classes don't need their own; the compiler
will generate one if needed.
I've realized that OBConversion does not need an explicit
copy constructor and have removed it.
*src/formats/bgfformat.cpp, cacaoformat.cpp, ccformat.cpp.
chem3dformat.cpp, ckrformat.cpp, featformat.cpp, shelxformat.cpp:
assigned the filename to OBMol title when reading.
*src/formats/mdlformat.cpp, src/formats/rxnformat.cpp,
src/formats/smilesformat.cpp:
2005-07-02 Chris Morley <c.morley@gaseq.co.uk>
*src/tokenst.cpp: Added Trim(), decl in mol.h
*src/mol.h, src/mol.cpp (OBMol::SetTitle): Moved definitions
to mol.cpp and added trim(). Tidier, but also overcomes
Windows(VC++6) problem with CR left at end after getline on
stream in binary mode, which is need for unix file compatibilty.
For consistency should also be done for OBCommentData::SetData()
Would this be safe?
*src/dat.h, src/data.cpp (OBElementTable::GetNumberOfElements):
Added initialization and moved definition to to cpp file.
MOL2Format was getting uninitialized data. Lazy loading was
too lazy.
2005-07-01 Geoffrey Hutchison <ghutchis@Alumina.local>
* src/formats/chemdrawformat.cpp, src/formats/crkformat.cpp,
src/formats/fastsearchformat.cpp, src/formats/mdlformat.cpp,
src/bondtyper.cpp, src/oberror.cpp:
Fix comparisons between signed and unsigned int.
* src/base.h (OBBase): Update DoTransformations for new format.
(OBGraphBase): Call base class from copy ctor.
* Doxyfile, doc/api-footer.html, doc/api-header.html: Update for
generating website SHTML documentation. Still looks good as a
local copy.
* src/Makefile.am, src/Makefile.in, src/formats/Makefile.am,
src/formats/Makefile.in: Update to fix errors from "make dist" for
snapshot.
* scripts/perl/openbabel_perl.cpp,
scripts/python/openbabel_python.cpp: Updated for 2005-07-01 snapshot.
2005-06-30 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/smilesformat.cpp(OBSmilesParser::ParseComplex():
Change size of symbol[] in to 7. Was failing on iodine
isotope [123I]. Another deficiency found by David Hoekman.
2005-06-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure: Add a check for swig to allow scripting
language wrappers to be rebuilt.
* Makefile.am: Make sure scripts directory will be added to dist.
* src/Makefile.am: Add back matrix.cpp, which was inadvertantly
removed.
* src/matrix.h: Remove unnecessary forward declaration of class Vector.
* */Makefile.in: Rebuilt.
2005-06-30 Chris Morley <c.morley@gaseq.co.uk>
Major change to how options handled. Many files in
/src, /src/formats, /windows altered. (Sorry I don't have a
tool to list them all.)
The options now stored internally in three std::maps for
input, output and general options. These are set on the
command line like -a? -x? and -? respectively.
b and s formats recently added to many formats are now input
options.
Derived most remaining formats from OBMoleculeFormat.
2005-06-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/ New directory for perl and python scripting wrappers
(and associated setup.py and Makefile.PL build scripts).
* src/openbabel.i, src/openbabel_python.cpp,
src/openbabel_perl.cpp, src/openbabel.py src/openbabel.pm:
Moved, as above.
* src/main.cpp: Add -w# flag for filtering different error/warning
levels with OBMessageHandler.
2005-06-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/torlib.txt, src/torlib.h: New files to implement torsional
rules from rotor.cpp::OBRotorRules. Does not (yet) describe all
features in OBRotorRules::ParseLine() code.
* src/rotor.cpp: Use it (rather than declaring the data here).
* data/Makefile.am, data/Makefile.in: Add rules for torlib.
* src/phmodel.cpp, src/mol.h, src/oberror.h, src/bondtyper.cpp:
Add documentation for global variables.
* src/oberror.h, src/oberror.cpp: Add new class obLogBuf, a
streambuf class to filter output going to cerr. Add new methods
OBMessageHandler::StartErrorWrap and ::StopErrorWrap to turn on
(default) and off wrapping of cerr.
2005-06-25 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/amberformat.cpp, src/formats/cacaoformat.cpp,
src/formats/carformat.cpp, src/formats/cmlformat.cpp,
src/formats/dmolformat.cpp, src/formats/gamessformat.cpp,
src/formats/gaussformat.cpp, src/formats/grosmos96format.cpp,
src/formats/jaguarformat.cpp, src/formats/mopacformat.cpp,
src/formats/mpqcformat.cpp, src/formats/nwchemformat.cpp,
src/formats/pdbformat.cpp, src/formats/qchemformat.cpp,
src/formats/shelxformat.cpp, src/formats/turbomoleformat.cpp,
src/formats/unichemformat.cpp, src/formats/viewmolformat.cpp,
src/formats/xyzformat.cpp:
Add command-line options -xs to prevent PerceiveBondOrders from
running (i.e., single bonds only) and -xb to prevent bonding via
ConnectTheDots entirely.
* src/formats/PQSformat.cpp, src/formats/alchemyformat.cpp,
src/formats/balstformat.cpp, src/formats/bgfformat.cpp,
src/formats/boxformat.cpp, src/formats/chem3dformat.cpp,
src/formats/chemdrawformat.cpp, src/formats/crkformat.cpp,
src/formats/featformat.cpp, src/formats/ghemicalformat.cpp,
src/formats/hinformat.cpp, src/formats/mmodformat.cpp:
Update to use OBMoleculeFormat, eliminate redundant code.
2005-06-25 Chris Morley <c.morley@gaseq.co.uk>
* src/mol.cpp, src/mol.h, src/transform.cpp: Added
OBMol::ConvertDativeBonds() (e.g. [N+]([O-])=O to N(=O)=O )
and -b option to invoke it.
* src/formats/fastsearchformat.cpp,
src/formats/fingerprintformat.cpp:
Used ConvertDativeBonds and -b option so that searches are
the same with and with dative bond form in data or target.
* src/finger2.cpp (getFragments): Removed code which only
partially does the above.
2005-06-24 Chris Morley <c.morley@gaseq.co.uk>
* src/finger2.cpp (DoRings) Add the non-ring form of all ring
rotations to remedy some of faults found by David Hoekman.
2005-06-24 Geoffrey Hutchison <babel@geoffhutchison.net>
* Doxyfile, doc/api-header.html, doc/api-footer.html,
doc/api-style.css: Add custom documentation header, footer, and
stylesheet.
* src/generic.h, src/generic.cpp (OBConformerData): Initial
framework for custom per-conformer data. Still need to add access
to individual conformer "frames" and code to add/delete frames
when adding new conformers to an OBMol.
2005-06-23 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/configure.in, src/configure: Generate babelconfig.h from
config.h using AC_CONFIG_COMMANDS as recommended by Jean Brefort.
* src/*.h src/*.cpp, src/openbabel.i: Convert back from config.h
(which still conflicts with other packages on UNIX-ish systems) to
babelconfig.h, as above.
* src/formats/viewmolformat.cpp: Switch to OBMoleculeFormat.
(Testing the difference in compiled code size. Not much.)
* src/formats/smilesformat.cpp: Remove asserts. (Asserts should
not be included in "production" code, IMHO.)
* Doxyfile, */*.h */*.cpp: Documentation updates.
2005-06-23 Chris Morley <c.morley@gaseq.co.uk>
* src/math/vector3.h, src/math/vector3.cpp: Moved the initiallization
of global variables VZero etc from vector3.h to vector3.cpp.
This is recorded for 2005-04-15 but I must have forgotten to
commit it. Added OBAPIs for DLL build compatibility.
* src/math/matrix3x3.h: Added OBAPIs.
2005-06-22 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/kekulize.cpp: Update with Fabien's latest version, fixing
PR#1214545 and adding doxygen documentation.
* src/bondtyper.cpp (AssignFunctionalGroupBonds): Mark assigned
bonds with KSingle, KDouble, KTriple for OBMol::Kekulize()
routine. Fixes PR#1219611.
* src/obmolecformat.h, src/Makefile.am, src/Makefile.in,
src/formats/Makefile.am, src/formats/Makefile.in: Move
obmolecformat.h to src/ from src/formats.
* src/obifstream.h: Removed. Completely unused.
* src/rotamer.h: Remove Read/WriteBinary declarations and
OBBinaryDBase -- unused. We cannot ensure compatibility with
OEBinary (which is now a proprietary format).
2005-06-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mol2format.cpp (ReadMolecule, WriteMolecule):
Contributions from Zhiguo Liu, notably to clean up bonding table,
and to mark O.co2 bonds as "aromatic."
* src/mol.h, src/atom.cpp: Add new methods IsHbondDonor(),
IsHbondAcceptor(), IsHbondDonorH(), contributed by Zhiguo Liu.
* src/vector3.h, src/vector3.cpp: Add new method Point2Plane() for
calculating the distance between a point (vector3) and a point
defined by three points (vector3), contributed by Zhiguo Liu.
2005-06-17 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.h, src/data.cpp (OBTypeTable): New methods GetToType
and GetFromType -- primarily for debugging purposes.
* src/formats/mol2format.cpp (WriteMolecule): Make sure
OBTypeTable is always set to translate to SYB format -- would
sometimes be reset to other formats. Fixes PR#1221324.
2005-06-16 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/generic.h, src/generic.cpp (OBSymmetryData): New class for
storing point group and space group symmetry information.
(OBUnitCell): Add support for storing translation vectors for
cleaner roundtrip support from v1,v2,v3 ->a,b,c...->v1,v2,v3 and
for origin offsets.
* src/Makefile.am, src/Makefile.in: Add hints for perl module
compilation.
* src/openbabel.pm, src/openbabel_perl.cpp: Change Perl wrapper
namespace to Chemistry::OpenBabel on advice of other perl users.
2005-06-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/mol.h: Remove (temporarily) un-implemented BeginConformer,
NextConformer, and AssignResidueBonds methods. These block use of
the SWIG python wrappers.
* src/openbabel.py, src/openbabel_python.cpp: Regenerate. SWIG
wrapper will now compile and import cleanly into Python.
* src/bondtyper.cpp (AssignFunctionalGroupBonds): Make sure
OBBondTyper data is initialized -- and ensure loop termination is
handled correctly. Resolves part of PR#1219611.
* src/openbabel.pm, src/openbabel_perl.cpp: New files from SWIG --
wrappers for Perl.
2005-06-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure: Update scandir test with fix from Jean
Brefort.
* Makefile.am, Makefile.in: Make sure windows/ directory is
included in distribution.
* src/Makefile.am, src/Makefile.in: Include hints for SWIG wrapper
generation. Make sure openbabel.i is included in dist.
* src/mol.h, src/atom.cpp, src/data.cpp, src/main.cpp,
src/obconversion.cpp, src/formats/alchemyformat.cpp,
src/formats/balstformat.cpp, src/formats/pdbformat.cpp,
test/roundtrip.cpp: Move declarations of rint, snprintf,
strncasecmp (for platforms that require replacement functions) out
of mol.h header and into source files that particularly use these
functions. (Pointed out by Jean Brefort.)
* src/openbabel.i, src/openbabel.py, src/openbabel_python.cpp:
Updated SWIG development wrappers.
* src/kekulize.cpp: Update with Fabien's latest version, should
fix recent bug reports (no assigned PR for these). Bug fixed
when huckel rule not satisfied + path search.
2005-06-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* tools/obgrep.cpp: Fixed mistake(?) in #elif define to compile
cleanly on GCC.
2005-06-04 Chris Morley <c.morley@gaseq.co.uk>
* tools/obgrep.cpp: Correct bug 1213806 and modify to allow
Windows build
* windows/: Add obgrep/ build files and XGetOpt.cpp and XGetOpt.h
for Windows getopt port.
2005-06-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, src/config.h.in: Define SCANDIR_CONST
for the matchFiles scandir() filter function. Should solve problem
between BSD (which doesn't need const) and Linux (which does).
* src/dlhandler_unix.cpp: Use it.
2005-06-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/dlhandler_unix.cpp: Fix cast bug reported and fixed by Jean
Brefort.
* configure.in, configure, src/Makefile.am, tools/Makefile.am,
test/Makefile.am, src/config.h.in, Makefile.in, src/Makefile.in,
data/Makefile.in, doc/Makefile.in, src/Makefile.in,
src/formats/Makefile.in, src/math/Makefile.in, test/Makefile.in,
test/cmltest/Makefile.in, tools/Makefile.in:
Add test for scandir cast above. Add test for dlopen in libdl and
add it to LDFLAGS if needed. Should fix bug reported by Jean
Brefort.
2005-06-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* configure.in, configure, src/config.h.in: Bump version for
2005-06-01 snapshot.
* test/attype.00.smi: Add label for last test molecule.
* test/smartsresults.txt: Regenerate using current atom type
patterns.
* test/smartstest.cpp: Make sure to set input and output formats
-- otherwise dynamic loading does not find SMILES importer on UNIX.
* test/unitcell.txt: Switch to ZnO unit cell for new unit cell
tests.
* test/unitcell.cpp: Added some debugging statements to test unit
cell translation vectors. (Currently do not seem to "roundtrip"
properly.)
* tools/obgrep.cpp: Allow input from STDIN to address feature
request PR# 1116202.
2005-05-27 Fabien Fontaine <fabfont@users.sourceforge.net>
* src/kekulize.cpp: Fix bugs reported by Chris Morley and David
Hoekman.
2005-05-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* acinclude.m4: Add CHECK_ZLIB macro for detection of zlib
compression library.
* configure.in, configure, src/config.h.in: Use it.
* aclocal.m4, config.guess, config.sub, ltmain.sh: Update for libtool
1.5.18.
* src/Makefile.am, src/Makefile.in: Ignore kekulize.cpp and
libinchi. Mark library as 1:0:0 version so that libopenbabel from
1.100.x series can coexist.
* src/formats/Makefile.am, src/formats/Makefile.in: Ignore InChI
code until license issues can be resolved. Do not compile
inchiformat.cpp.
* src/bond.cpp: Use PerceiveKekuleBonds() instead of
NewPerceiveKekuleBonds().
* src/bondtyper.cpp, src/fastsearch.cpp, src/finger2.cpp,
src/fingerprint.cpp, src/kekulize.cpp, src/obconversion.cpp,
src/transform.cpp, tools/obfit.cpp, tools/obrotate.cpp:
Standardize top comments.
* src/openbabel.i: Initial SWIG file for scripting language
wrappers. Modules currently build, but experiencing linking
problems on Mac OS X.
* src/mol.h: Declare replacement C library functions rint(),
snprintf(), and strncasecmp() as namespace std:: to fix compile
problems with SWIG.
2005-05-22 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.h, src/obconversion.cpp: Added IsFirstInput().
* src/formats/obmolecformat.h: Implemented -j format to aggregate
into a single output molecule.
* src/transform.cpp (OBMol::ClassDescription): added -j option
* src/formats/mdlformat.cpp (ReadMolecule): Added offset
reading in a mdl sdf/mol file to a OBMol object which already has
atoms will now add a disconnected fragment.
2005-05-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/Makefile.am data/Makefile.in: Make sure that data files are
included in a "make dist".
* src/Makefile.am, src/Makefile.in: Build dlhandler_unix.cpp. Use
dynamic OBFormat loading.
* src/dlhandler_unix.cpp: Add initial support for dynamic loading
file format modules using $(libdir)/openbabel/*.so
paths. Currently this can cause problems when building/debugging
before installation. I have a symlink from
/usr/local/lib/openbabel -> $(top_builddir)/src/formats/.libs as a
workaround.
* src/formats/Makefile.am, src/formats/Makefile.in: Build each
format as an independent shared-module.
* src/*.h: Minor updates. Make sure to only #include config.h once
per header. Add standard top comments (with description of each
file and Open Babel URL, etc.) to all headers.
* src/dlhandler_win32.cpp: Add file description to top comments.
2005-05-14 Chris Morley <c.morley@gaseq.co.uk>
* src/fingerprint.h, src/finger2.cpp: Yet more bug fixes following
comments by David Hoekman.
* fingerprintformat.cpp: Added IsPossibleSubstructure() and the
display of its result.
2005-05-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/base.cpp, src/base.h, src/bitvec.h, src/data.cpp,
src/data.h, src/dlhandler.h, src/fastsearch.cpp, src/grid.h,
src/kekulize.cpp, src/main.cpp, src/matrix.h, src/mol.h,
src/obconversion.h, src/oberror.cpp, src/obifstream.h,
src/obutil.cpp, src/obutil.h, src/patty.cpp, src/phmodel.cpp,
src/residue.cpp, src/rotor.cpp, src/tokenst.cpp, src/typer.cpp,
src/formats/PQSformat.cpp, src/formats/pdbformat.cpp,
src/formats/povrayformat.cpp, test/matrixtest.cpp,
test/ringtest.cpp, test/roundtrip.cpp, test/smartstest.cpp:
Rename babelconfig.h to config.h and conditionally #include it
based on the HAVE_CONFIG_H define (which on UNIX is passed by the
Makefile). This solves PR#885828 in terms on installation and
including the build-dependent babelconfig/config headers.
* configure.in, configure, Makefile.in, doc/Makefile.in,
src/Makefile.am, src/Makefile.in, src/math/Makefile.in,
test/Makefile.in, test/cmltest/Makefile.in, tools/Makefile.in: Ditto.
* data/Makefile.am, data/Makefile.in: Update for version-dependent
data installation (e.g. /usr/local/share/openbabel/2.0.0/*).
* src/formats/Makefile.am, src/formats/Makefile.in: Don't directly
include libinchi (which is now installed separately). Set for
installation of libobformats, which should be dynamically linked
with libopenbabel.
* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in:
Fix problems with case-sensitive filenames. (i.e., filenames
changed case in InChI 1.0 release, but were already in CVS tree
with lowercase.) Set for shared-library installation of libinchi.
2005-05-08 Chris Morley <c.morley@gaseq.co.uk>
* src/formats.inchiformat.cpp: remove incomplete code for reading
InChi. Add URL. Post libinchi.lb abd libinchi.dll. More options have
been documented, but are not yet implemented in OB.
*src/base.h, src/base.cpp: The latest MS compiler is more picky, and
(correctly) objects to an iterator being returned as NULL in
OBGraphBase::BgnMatch() and EndMatch(). To work round this the whole
of the code for "substructure search functions" has been commented
out. These are virtual placeholder functions anyway and are not used
internally in the real substructure routines. In the unlikely event
of them being found to be used in an external program we'll have to
find another fix.
* Removed OBConversion::GetDimension(),SetDimension(),SetTitle(),
Redefined SetTitle() to return InFileName as a c_str.
Made return type of strrchr() const char* (picky compiler).
* src/formats/CSRformat.cpp,PQSformat.cpp,alchemyformat.cpp,balstformat.cpp,
bgfformat.cpp,boxformat.cpp,acaoformat.cpp,acheformat.cpp,
chem3dformat.cpp,chemdrawformat.cpp,chemtoolformat.cpp,
crkformat.cpp,cssrformat.cpp,dmolformat.cpp,featformat.cpp,
fhformat.cpp,amessformat.cpp,gaussformat.cpp,ghemicalformat.cpp,
grosmos96format.cpp,hinformat.cpp,jaguarformat.cpp,mm3format.cpp,
mmodformat.cpp,mol2format.cpp,mopacformat.cpp,mpqcformat.cpp,
nwchemformat.cpp,pdbformat.cpp,povrayformat.cpp,qchemformat.cpp,
smilesformat.cpp,tinkerformat.cpp,unichemformat.cpp,viewmolformat.cpp,
xedformat.cpp,xyzformat.cpp,zindoformat.cpp:
Removed
const char *dimension = pConv->GetDimension();
* src/formats/cmlformat.cpp, mdlformat.cpp, pqsformat.cpp:
changes to dimension handling (now an int not a string).
* src/bitvec.h: replace EXTERN by OBAPI extern and tidied.
* src/obiter.h: added several OBAPI.
* src/dlhandler.h, dlhandler_win32.h; Sleep() added.
* src/main.cpp: Space after -i and -o now allowed (but not yet
other options with text). I'm told it is more unix.
Made return type of strchr() const char* (picky compiler).
Commented out debug code to pause at end (better compiler).
Some other files tidied - removal of unused variables.
Somewhere else(?) changed a new loop variable name from i to j
(rubbish old compiler).
2005-05-06 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/inchi: Updated with InChI v1.0 release code.
* src/formats/inchiformat.cpp, src/formats/inchi_api.h: Ditto.
* src/formats/inchi/Makefile.am, src/formats/inchi/Makefile.in,
src/formats/Makefile.am, configure.in, configure:
Update Makefiles for InChI code.
* src/fingerprint.cpp, src/kekulize.cpp, src/obutil.cpp,
src/patty.cpp, src/rotor.cpp: Change error reports
to go to cerr instead of cout. OBMessageHandler will soon grab
cerr, but shouldn't block cout (since it's used for output through
pipes).
* src/main.cpp: Send conversion message to clog instead of cerr,
avoiding problems with OBMessageHandler rerouting cerr.
* src/mol.h, src/mol.cpp: New methods GetFormula() and
SetFormula() to handle stoichiometric formulas.
* src/formats/reportformat.cpp: Use it.
* src/data.h: New method GetNumberOfElements() to return the
number of elements in an OBElementTable.
* src/generic.h: Change SetAttribute to take "const" string
arguments. Ditto for SetData for OBCommentData and SetValue for
OBPairData.
2005-04-24 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp, src/obconversion.h:
Change implementation of inputfile seek position, to prevent
it being affected by newlines at the end of the file.
Changed option to ignore errors to -e from -c which was already
used for centre coordinates. Removed -z option.
Remove some obsolete commented out code.
* src/main.cpp: Removed -z option for using previously stored
options. This was conflicting with use with Apache, and was
never of enormous benefit anyway.
* src/finger2.cpp, src/fingerprint.h: fingerprint2 revised
to properly use canonical hash values. Molecules were being missed.
* src/formats/fastsearchformat.cpp: Ensure datafile file
properly read when it is the specified input file.
* windows/*.*: Updated Windows build files
2005-04-19 Geoffrey Hutchison <babel@geoffhutchison.net>
* NEWS: Add notes for formats that were changed/deleted.
* configure.in, configure, src/babelconfig.h.in: Update to #define
OBAPI.
* test/matrixtest.cpp: Include babelconfig.h.
* src/bitvec.h: Make sure to define EXTERN if not otherwise
defined.
* src/obiter.cpp, src/obiter.h: STL-style iterators (and #define'd
shorthand) for OBAtom, OBMol, OBBond and OBResidue.
* src/Makefile.am, src/Makefile.in: Add fastsearch.cpp,
finger2.cpp, obiter.cpp, fastsearch.h, obiter.h.
* src/formats/Makefile.am, src/formats/Makefile.in: Add
fastsearchformat.cpp.
* src/finger2.cpp (RemoveDuplicates): Enforce "const"
declaration.
* src/fingerprint.h (fingerprint2): Enforce std:: namespace.
* src/formats/smilesformat.cpp (SpecificationURL): Add pointer to
Daylight webpage.
* src/formats/mpqcformat.cpp: Add MPQC input format.
* src/formats/qchemformat.cpp, src/formats/povrayformat.cpp,
src/formats/nwchemformat.cpp, src/formats/CSRformat.cpp,
src/formats/bgfformat.cpp, src/formats/cacaoformat.cpp,
src/formats/cacheformat.cpp, src/formats/chemtoolformat.cpp,
src/formats/hinformat.cpp: Minor fixes to descriptions.
2005-04-17 Chris Morley <c.morley@gaseq.co.uk>
* src/fastsearch.h, src/fastsearch.cpp,
src//formats/fastsearchformat.cpp:
Mod to keep fastsearch index in memory after it has
been loaded, to shorten subsequent queries.
2005-04-15 Chris Morley <c.morley@gaseq.co.uk>
* src/*.h, src/vector3.cpp, windows/OBDLL/OBDLL.dsp
windows/OBDLL/OBDLL.mak :
To assist DLL builds, added OBAPI macro to class declarations,
global functions and variables in API files. OBAPI needs to
be set to nothing in babelconfig.h for non-DLL builds.
Had to moved the initiallization global variables VZero etc
from vector3.h to vector3.cpp, where it should have been anyway.
OBDLL can now be built in a conventional way. The whole API
should be exported but I may have missed some items.
2005-04-13 Chris Morley <c.morley@gaseq.co.uk>
*src/fastsearch.cpp, src/formats/fastsearchformat.cpp:
Separated format from API code.
Default fingerprint length is now 32 words.
2005-04-12 Chris Morley <c.morley@gaseq.co.uk>
* src/finger2.cpp src/fastsearch.h src/fastsearch.cpp:
Added. (Fastsearch format really needs to be separated and put
into src/formats.)
* src/formats/fingerprintformat.cpp: Extensive revision to
allow choice of fingerprint type and Tanimoto calculation.
* src/obconversion.h, src/obconversion.cpp (Convert):
Changed implementation of OneObjectOnly
Added capability for the write format to retrieve the seek position
of the object in the input file: wInpos, GetInPos().
Added READBINARY and WRITEBINARY options in format flags
which are implemented when files are opened. Applicable for
binary formats (which there are currently none?) in non-unix systems.
(FullConvert), (OpenAndSetFormat)For VC++6 in Windows,
opening all files in binary mode seems to allow unix text files
to be read. But in case this messes up Macs or other Windows
implementations it is dependent on a macro ALL_READS_BINARY
being set in babelconfig.h.
* src/fingerprint.h, src/fingerprint.cpp (HashFragments):
Changed h and mod from long int to unsigned int to avoid
memory corruption with molecules with heavy atoms. Added
the declarations for fingerprint2 class and global
GetFingerprint().
* src/bitvec.h: Comments to highlight resizing behaviour.
* src/format/smilesformat.cpp (OBSmilesParser::ParseSmiles):
Mod to prevent unpaired ) causing program to hang.
* windows: Updated build files
2005-04-06 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/inchi: added InChI 1.0 files from NIST.
2005-04-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obconversion.cpp: Change "Readonly" and "Writeonly" to
"Read-only" and "Write-only" to match more typical computer
documentation (e.g., Windows, UNIX and Mac generally use hyphens.)
* src/formats/viewmolformat.cpp (ReadMolecule): Fix
multiple-molecule support. Read loop would never hit an $end
record and break, thus reading all molecules in a multi-molecule
file as one.
* src/formats/PQSformat.cpp (ReadMolecule): Replace rindex ->
strrchr for ISO C/C++ compliance. (Fixes problems with compiling
on MinGW/gcc.)
* src/formats/inchiformat.cpp: Change for loop to while loop to
fix compile problems with gcc (and make slightly more readable
IMHO), change comment to remove "??/" interpreted as a Unicode
trigraph by gcc, and fix mol.SetTitle() call to fix compilation
problems with gcc/g++.
* src/formats/gamessformat.cpp, src/formats/gaussformat.cpp,
src/formats/nwchemformat.cpp, src/formats/qchemformat.cpp: Break
read and write support into separate formats since output formats
are read-only and input formats are write-only.
2005-04-01 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/inchiformat.cpp, src/formats.inchi_api.h,
windows/InChI_DLL.dll and windows/InChI_DLL.lib
my build of version 1.0RC from NIST : writes InChI; format
is writeonly because reading code, although included is
incomplete. I haven't put the source code for the DLL up,
although it is cross-platform, because I want to check with
NIST first.
* src/data.cpp, src/data.h: OBElementTable::GetAtomicNum
Changed unsigned short int& to int&. More consistent with other
ints since have to use the exact int type when calling.
Now used in mdlformat.cpp.
* src/formats/mdlformat.cpp: V2000 writes and reads isotope info
(M ISO line), V2000 V3000 reads D and T. Changes in V2000
writing M RAD and header. Is #include <iomanip> a problem?
2005-03-25 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp, src/main.cpp, src/obconversion.h:
Multiple input files can now be different formats
* src/onconversion.h: Added virtual function
OBFormat::MakeNewInstance to meet possible future need for
formats with member functions. (InChIFormat will.)
* src/formats/smilesformat.cpp: Can now output isotope info and
input and output H and H2. Pharma might be able to do without
these but Combustion can't.
* windows/OBGUI/ Several files: Mods to ease use with multiple
input files, but interface could still do with some work.
2005-03-23 Geoffrey Hutchison <babel@geoffhutchison.net>
* AUTHORS, NEWS, README: Begin updating for a 2.0 release.
* data/extable.txt: Mark as deprecated. (Should this be deleted?)
* src/*.h, src/*.cpp, src/math/*.cpp, src/math/*.h,
src/formats/*.cpp, tools/*.cpp, test/*.cpp: Update copyright
statements to include 2005 and standardize text.
* data/Makefile.am: Make sure to include *.h files in a distribution.
* src/Makefile.am: Make sure to include dlhandler.h,
obconversion.h, and reaction.h in a distribution.
* src/formats/Makefile.am: Make sure to install obmolecformat.h
and include in distribution.
* data/Makefile.in, src/Makefile.in, src/formats/Makefile.in:
Regenerated.
* src/generic.h: Expand obDataType to include more typical
chemical data and offer 16 custom data slots obData0 through
obData15. In particular, adds obConformerData and obSymmetryData
for future enhancements.
* src/obutil.cpp, src/tokenst.cpp, src/typer.h: Added more doxygen
documentation.
* tools/obfit.cpp: Further improvements from Konrad -- now loops
through multiple matches to fit the match with the smallest RMSD.
2005-03-07 Geoff Hutchison <babel@geoffhutchison.net>
* src/formats/cml.cpp (endMolecule): Only call InternalToCartesian
if required (i.e., only internal coords available, all cartesian
coords are zero) and only call bonding methods (ConnectTheDots and
PerceiveBondOrders) if needed. Provides a huge performance
increase on most files.
* tools/obfit.cpp: Modified to output an RMSD of the fit as
contributed by Konrad Koehler. Addresses PR#1157440.
2005-03-02 Geoff Hutchison <babel@geoffhutchison.net>
* src/parsmart.cpp (OBSSMatch::Match): Added check to prevent
accessing atoms that do not exist -- appears in PR#1119970.
2005-03-02 Chris Morley <c.morley@gaseq.co.uk>
* src/mol.h, babelconfig.h Move some DLL-related #defines
to babelconfig.h
* src/oberror.h Declare global obErrorLog here to aid DLL builds.
Update Windows build files
2005-02-27 Geoff Hutchison <babel@geoffhutchison.net>
* src/atom.cpp (GetType): Call global OBTypeTable ttab rather than
declaring a local version.
* src/mol.cpp (RenumberAtoms): Add documentation and return
without action if supplied vector is the wrong size.
2005-02-27 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.cpp: Removed ThrowError and #include mol.h
Added -c option for continuing with next molecule after an error
2005-02-17 Geoff Hutchison <babel@geoffhutchison.net>
* src/formats/ghemicalformat.cpp (ReadMolecule): Add some initial
support for ghemical 1.5x files. Reported by Avell Diroll.
* src/formats/mdlformat.cpp (ReadMolecule): Improve flexibility in
handling non-standard SDFiles. Now handles "VAMP" output, thanks
to an example file from Dr. James Smith, Erlangen.
* src/data.h, src/data.cpp (OBElementTable::GetAtomicNum): Fix bug
with isotope support as pointed out by Chris Morley -- need to
pass a reference back to the isotope value. Added a
backwards-compatible one-argument function which throws away the
isotope value.
* src/obconversion.cpp (Convert): Throw a debugging error if the
ReadChemObject method returns false.
* aclocal.m4, config.guess, config.sub, install-sh, ltmain.sh,
missing, mkinstalldirs: Update with latest GNU versions from
Automake 1.9.5 and libtool 1.5.14.
* configure, */Makefile.in: Updated automatically from above.
2005-02-15 Geoff Hutchison <babel@geoffhutchison.net>
* src/formats/mdlformat.cpp (ReadMolecule): Fix bug where long
property lines would set ifs.fail() and consequently file appeared
to be at EOF. Since property lines can be >1024 bytes, read
using std::getline(ifs,string). Fixes PR#1120738, thanks to
Dr. Christian Laggner for the bug report.
* doc/Makefile.am: Fix bug in doxygen rule.
* configure, configure.in, */Makefile.in: Regnerated.
* src/data.cpp, src/data.h (CorrectedBondRad): Change to use
covalent radii -- this is used internally in many places and
cannot easily be removed. Add more doxygen documentation.
2005-02-10 Geoff Hutchison <babel@geoffhutchison.net>
* src/mol.cpp (operator+): Fix PR#119352 to copy bond flag
information when adding bonds. Thanks to Daen de Leon for the bug
report and fix.
2005-02-09 Geoff Hutchison <babel@geoffhutchison.net>
* data/atomtyp.txt: Change implicit valence rules for acidic
oxygens -- ensure default AddHydrogen() response is to add acidic
protons, but correctForPH will not. Fixes PR # 1106706.
* data/atomtyp.h: Update using bin2hex.pl.
* doc/babel.1: Update for new options.
* src/mol.h: Add oberror.h and update documentation and
indentation. Add OB_POS_CHIRAL_ATOM and OB_NEG_CHIRAL_ATOM flags for
marking + and - chiral volume and accessor methods.
* src/chiral.cpp(GetChirality): Set + and - chiral volume for
atoms using these methods.
* src/main.cpp: Update to handle -imime and -omime flags to set
format by supplied MIME type.
* src/obconversion.cpp, src/obconversion.h: Update to handle MIME
types with an additional format map with RegisterFormat(), rather
than "polluting" the extension map.
* src/formats/alchemyformat.cpp, src/formats/cmlformat.cpp,
src/formats/crkformat.cpp, src/formats/mdlformat.cpp,
src/formats/mmodformat.cpp, src/formats/mol2format.cpp,
src/formats/mopacformat.cpp, src/pdbformat.cpp,
src/smilesformat.cpp: Register MIME types with the new MIME map as
above.
* src/oberror.cpp: Add a global OBMessageHandler obErrorLog.
* src/obutil.cpp (ThrowError): Update to use obErrorLog -- to
migrate code to the new error logging OBMessageHandler class.
* src/bitvec.cpp, src/mol.cpp, src/phmodel.cpp, src/rotor.cpp,
src/formats/chem3dformat.cpp, src/xyzformat.cpp: Update
ThrowError() calls to use obErrorLog as above.
* configure.in: Add support to conditionally build documentation
if doxygen is availale. Not currently used.
* */Makefile.in: Update using automake for above.
2005-02-09 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.h, src/obconversion.h.cpp: Added
OBFormat::SkipObjects and its use in Convert and SetStartAndEnd
* src/formats/mdlformat.cpp: Changed wording in option
description. "Default" means something in Windows GUI!
Added SkipObjects()
Added output of wedge and hash in V2000 as suggested previously
in a discuusion(?). But stereochemistry needs revisiting!
* src/formats/smilesformat.cpp: ReadMolecule erroneously always
returned true, now corrected. Removed SMIFormat::SmiToMol()
Added SkipObjects()
Added support for input of radicals like[O.]
2005-01-31 Chris Morley <c.morley@gaseq.co.uk>
* src/obconversion.h, src/obconversion.h.cpp: rationalized
SetInFormat, etc; Added GetInFile; corrected bug in IsOption
* src/main.cpp: added -? option as synonym of -H
Check for empty FileList;
In Windows moved saved options file from current folder to TEMP
2005-01-30 Geoff Hutchison <babel@geoffhutchison.net>
* src/bondtyper.cpp (ParseLine): Make sure loop variable "i" is
initialized, pointed out by Chris Morley.
* data/element.txt: Add note about deprecated "bond order" radii.
* src/base.h: Remove \defgroup documentation bits.
* src/data.h (OBElementTable): Mark bond order radii methods as
deprecated.
* src/chiral.cpp: Add std:: namespace to match headers for
documentation. Convert comments to doxygen docs.
* src/data.cpp (OBGlobalDataBase): When searching for data files,
check the environment variable directories, then the compiled-in
directory path -- starting with a subdirectory for BABEL_VERSION,
followed by the parent directory. Allows for versioning the data
files.
* src/main.cpp: Output "molecules converted" to cerr and use
"molecule" converted if only one molecule was found.
* src/mol.h: Add documentation about "up" and "down" bond flags
vs. wedge and hash types.
* src/obconversion.h, src/obconversion.cpp: Allow MIME types to be
registered to match particular extensions/IDs.
* src/oberror.h, src/oberror.cpp: New class OBMessageHandler to
organize errors/messages and allow errors to go to cerr or another
output stream. Allows filtering of error levels.
* src/formats/carformat.cpp: Correct a variety of problems with
reading multiple molecules in a CAR file and read in 3D unit cell
information if supplied. Bugs reported by Jean Dessolin. Fixes PR#
1060110.
* src/smilesformat.cpp: Set OBMol dimension to 0.
* src/mdlformat.cpp: Output v3000 files for >999 atoms or >999
bonds, as suggested by MDL standard specification. Set OBMol
dimension as needed.
* src/crkformat.cpp (CRK2DFormat::ReadCRK): Fix bugs with
wedge/hash and up/down bonds. Assign OBMol dimension to 2.
* src/cml.cpp: Ditto.
* src/chemdrawformat.cpp (ReadMolecule): Set OBMol dimension to 2.
* src/formats/*.cpp: Ensure consistency of format description
naming, particularly to match Open Babel 1.100.x and Babel 1.6.
2005-01-20 Geoff Hutchison <babel@geoffhutchison.net>
* src/main.cpp: For non-Win32 platforms, use $HOME/.openbabel to
store recent options -- keeping with standard UNIX practices.
* src/rotamer.cpp, src/rotamer.h: Move OBRotamerList from
now-defunct binary.* files to specific rotamer files -- binary
format is now obsolete.
* src/Makefile.am: Remove binary.* and rename to rotamer.*.
* tools/obrotate.cpp: Rename binary.h to rotamer.h
* src/data.cpp, src/data.h: Excise io_type and OBExtensionTable.
* data/extable.h, data/extable.txt: Ditto.
* data/Makefile.am: Ditto.
* tools/*.cpp: Ditto.
* src/formats/cml.cpp: Remove reference to GetInputType and
GetOutputType.
* src/mol.h, src/mol.cpp: Add OBMol:_dimension, along with
accessor methods GetDimension() and SetDimension() for specifying
the dimension of the OBMol coordinates. Default is 3 for now --
conversion or user code must specify this! Among other PRs, fixed
PR# 110671.
2005-01-19 Geoff Hutchison <babel@geoffhutchison.net>
* src/bondtyper.h src/bondtyper.cpp: New method
AssignFunctionalGroupBonds() to replace code in
mol.cpp::PerceiveBondOrders() -- assigns generic SMARTS patterns
and then angle/distance constrained SMARTS patterns (like
carbonyl).
* src/mol.cpp: Use the new OBBondTyper method above.
* configure, aclocal.m4, config.guess, config.sub, ltmain.sh,
*/Makefile.in: Update with latest automake/libtool/autoconf
versions (automake-1.9.4, libtool-1.5.10 autoconf 2.59).
2005-01-13 Chris Morley <c.morley@gaseq.co.uk>
* src/formats/obmoleculeformat.h: Added. Class to reduce code duplication.
* src/formats/mdlformat.cpp: added V3000 support
* src/formats/smilesformat.cpp: added option for radical output as lc
* src/formats/fingerprintformat.cpp Added.
2005-01-13 Chris Morley <c.morley@gaseq.co.uk>
Correct number of implicit hydrogens in radicals
Previously used decremented implicit valency which sometimes was reset;
now correct with _spinmultiplicity.
* src/atom.cpp (ImplicitHydrogenCount): add code
* src/mol.cpp (AddHydrogens): (2 routines) add code
* src/mol.cpp (AssignSpinMultiplicity): remove code
2005-01-12 Chris Morley <c.morley@gaseq.co.uk>
* src/dlhandler.h: Add findFiles decl needed for Windows builds
2005-01-09 Chris Morley <c.morley@gaseq.co.uk>
* windows/*.dsp, *.mak: Synchronize Windows build files to handle
changed file locations and extra source files
* windows/OBDLL/map2def2.exe added
* windows/babelconfig.h updated
2005-01-07 Geoff Hutchison <babel@geoffhutchison.net>
* src/obconversion.h (GetMIMEType): New method for chemical MIME
support.
* src/formats/*.cpp: Update file extensions for formats for
lower-case and previous Babel standards. Added MIME types where
appropriate.
2005-01-06 Geoff Hutchison <babel@geoffhutchison.net>
* src/main.cpp, src/obconversion.cpp, src/obconversion.h: Updated
files from Chris Morley.
2005-01-01 Geoff Hutchison <babel@geoffhutchison.net>
* tools/obfit.cpp, tools/obgrep.cpp, tools/obprop.cpp,
tools/obrotate.cpp, tools/obtanimoto.cpp: Update to use the
OBConversion framework.
* src/formats/*.cpp: Clean out formats which don't currently have
format specification URLs.
2004-12-23 Geoff Hutchison <babel@geoffhutchison.net>
* *.cpp, *.h: Reformat using astyle --style=ansi.
* src/mol.cpp(PerceiveBondOrders): Fix thinko with abs() calls.
* src/formats/Makefile.am: Fix typos preventing all format files
from being compiled.
* src/formats/cml.cpp: Pull iterator variables out of for()
declarations to fix compilation problems.
* src/formats/turbomoleformat.cpp: Remove call to strlwr() which
is a non-ANSI (non-ISO) function call.
* test/ringtest.cpp, test/smartstest.cpp, test/rountrip.cpp:
Convert to using OBConversion from OBFileFormat.
2004-10-19 Geoff Hutchison <babel@geoffhutchison.net>
* Initial merging of Chris Morley's new file translation framework.
Compiles and runs through "babel -H".
* data/* : Move data files and headers to this directory to
segregate from source code.
* configure.in, Makefile.am, */Makefile.am: Build updates.
* src/: Removed all file translation files. (Now in formats directory.)
* src/formats/*: New files.
* src/windows/*: Removed.
* windows/*: New files.
2004-10-04 Michael Banck <mbanck@gmx.net>
* src/crk.cpp: Use sstream if present and strstream if not.
2004-28-30 Fabien Fontaine <ffontaine@imim.es>
* tools/obtanimoto.cpp : new tool
* tools/README: update
* tools/makefile.am update
2004-27-30 Fabien Fontaine <ffontaine@imim.es>
* src/fingerprint.cpp: New output format
* src/fingerprint.h
* src/Makefile.am (libopenbabel_la_SOURCES): Added fingerprint.cpp.
* src/data.cpp (TextToType): Added FINGERPRINT typestring.
* src/data.h (io_type): Added FINGERPRINT.
* src/extable.txt: Added fingerprint entry for writing.
* src/extable.h: Regenerated.
* src/fileformat.cpp (ReadMolecule): Added fingerprint handler.
(WriteMolecule): Likewise.
* src/fileformat.h (WriteFingerprint): Declare it.
2004-09-10 Michael Banck <mbanck@gmx.net>
* src/turbomole.cpp: New file.
* src/Makefile.am (libopenbabel_la_SOURCES): Added turbomole.cpp.
* src/data.cpp (TextToType): Added TURBOMOLE typestring.
* src/data.h (io_type): Added TURBOMOLE.
* src/extable.txt: Added turbomole entry for reading and writing.
* src/extable.h: Regenerated.
* src/fileformat.cpp (ReadMolecule): Added Turbomole handler.
(WriteMolecule): Likewise.
* src/fileformat.h (ReadTurbomole): Declare it.
(WriteTurbomole): Likewise.
2004-08-30 Fabien Fontaine <ffontaine@imim.es>
* src/mol.cpp bond.cpp kekulize.cpp: Kekulize function changed to
what it was before. PerceiveBondOrders replaced by
NewPerceiveBondOrders. SetK* functions added to NewPerceiveBondOrders
2004-08-27 Michael Banck <mbanck@gmx.net>
* mol.h (tokenize): Initialize *delimstr to " \t\n" for the
version of the function using strings as well.
2004-08-25 Fabien Fontaine <ffontaine@imim.es>
* src/mol.cpp: Kekulize is replaced by a new kekulize function
situated in kekulize.cpp
* src/mol.cpp (PerceiveBondOrders): New SMART pattern added
some decision are taken according to the geometry of the bonds
2004-08-24 Fabien Fontaine <ffontaine@imim.es>
* src/mol.cpp (PerceiveBondOrders): Bug in calculation of
average torsion angles of cycles fixed.
* src/atom.cpp: function AverageBondAngle added.
2004-08-19 Michael Banck <mbanck@gmx.net>
* src/data.cpp: Include mol.h.
(tokenize): Removed declaration, already declared in mol.h.
* src/mol.h [OBDLL_EXPORTS, USING_OBDLL]: redefine extern as
'__declspec(dllexport) extern'. Update global definitions
accordingly.
2004-08-17 Geoff Hutchison <ghutchis@wso.williams.edu>
* configure.in: Make the check for doxygen to be a typical
AC_PATH_PROG -- it's not a critical dependency.
* configure, aclocal.m4, config.guess, config.sub, ltmain.sh,
*/Makefile.in: Update with latest automake/libtool/autoconf
versions (automake-1.9.1, libtool-1.5.8 autoconf 2.59).
* src/isotope-small.txt, src/isotope.txt: Update with latest data
from 2003 canonical data.
2004-07-20 Geoff Hutchison <ghutchis@wso.williams.edu>
* src/ghemical.cpp: Ignore multiple coordinate sets -- only read
the first one currently, but don't bail if more than one exists.
* src/cssr.cpp: Update with unit cell information and fixing bugs
reported by Mathias Weigt when dealing with SOMFA package.
2004-07-02 Michael Banck <mbanck@gmx.net>
* src/obutil.cpp (InternalToCartesian): avec, bvec, cvec, dst, ang,
tor: New short circuit variables. Start index at zero again. Fix
torsion angle of the fourth atom. Thanks to Gerd Menche.
2004-03-13 Michael Banck <mbanck@gmx.net>
* test/unitcell.cpp (TestUnitCell): Use %lf instead of %f to read
in the values from unitcell.txt.
2004-03-07 Geoff Hutchison <ghutchis@wso.williams.edu>
* src/chdrw.cpp (ReadChemDraw): Add support for reading ChemDraw
CT files.
* src/data.h, src/data.cpp: Change GAUSSIANZMAT to GAUSSIANOUT to
allow support for reading G98 and G03 output.
* src/extable.txt: Add ChemDraw reading and Gaussian 98/03 output
to list.
* src/fileformat.h, src/fileformat.cpp: Ditto.
* src/extable.h: Regenerate.
* src/gaussian.cpp: Add support for reading G98/G03 output and
writing isotopes where applicable.
* src/hin.cpp: Fix bug with more recent HIN formats with basis set
information.
* configure, Makefile.in, */Makefile.in: Update with latest
autotools.
* src/mol.cpp, src/mol.h: Backpedal slightly with Fabien's
2003-12-17 changes. Use OB_TSPIN_MOL as used by 1.100.2 and
revised AssignSpinMultiplicty to assign OBMol::_tspin.
2004-03-03 Michael Banck <mbanck@gmx.net>
Fixes to make InternalToCartesian() and ReadQChem() consistent
with CartesianToInternal(), so that round-tripping between
InternalToCartesian() and CartesianToInternal() is
possible. Thanks to Gerd Menche for the fix.
* src/obutil.cpp (InternalToCartesian): Initialize index as
atom->GetIdx() rather than atom->GetIdx() - 1. Subsequently,
increase the index checks for the first three atoms by one.
Convert angles to radians before computing cartesian
coordinates.
* src/qchem.cpp (ReadQChem): Uncommented the z-matrix reading
code. Generate one empty internal coordinate in advance.
Replaced loop until end of block in input file with a for loop
over the existing atoms. Do not generate new atoms in the loop,
as they are already present. Do not convert angles to radians
any more, this is now done in InternalToCartesian().
2004-02-29 Michael Banck <mbanck@gmx.net>
Merged changes from openbabel-1-100-x branch back into HEAD.
* src/pqs.cpp: New file.
* NEWS: Updated from 1.100.2 release.
* ChangeLog: Fixed some tabs.
