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ChangeLog
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2008-11-22 Chris Morley
* src/mcdlutil.cpp: Small bug fixes from Sergei Trepalin
* windows-vc2005/babelconfig.h, windows-vc2005/OBDLL/OBDLL.vcproj,
windows-vc2005/OBMCDL/MCDL.vcproj,
windows-vc2005/OBUtilFormats/OBUtilFormats.vcproj: Windows
build updated to make groupRedraw() callable.
2008-11-22 Chris Morley
* src/ops/loader.cpp: do not remove comments after 4th line of
an entry in plugindefines.tx. SMARTS uses '#'!
* src/ops/optransform.cpp: revamp parsing.
* src/phmodel.cpp(OBChemTsfm::Init): correct bug in which some
kinds of transform were not taken into account when checking
whether there was anything to do.
2008-11-22 Chris Morley
* include/openbabel/text.h: NEW boring and trivial class OBText,
derived from OBBase. This was proposed last year for formats
which contained mixed content, like cdx, but has other uses.
* src/formats/xml/textformat.cpp: NEW input format for the above
* src/formats/xml/cmlreactformat.cpp: makes use of OBText class
to insert its output into boilerplate text provided in a file.
* include/openbabel/mol.h, src/mol.cpp(Has2D): add an extra
parameter to change from "has 2D or 3D" to "has 2D". Correct bug
which gave the wrong answer for some linear molecules.
* include/openbabel/obconversion.h, src/obconversion.cpp
(NumInputObjects): now adjusts for values of -f and -l options
* src/formats/xml/xml.cpp(GetDerived):correct bug which did not
update the XMLConversion object even when the base OBConversion
had changed (bug#2283422).
* src/formats/smilesformat.cpp*(SkipObjects): make work properly
for files without a new line at the end.
* src/ops/gen2D.cpp, src/ops/gen3d.cpp: set the molecule dimension.
2008-11-21 Geoff Hutchison <ghutchis@Iridium.chem.pitt.edu>
* src/data.cpp (GetAtomicNum): Fix bug with patch supplied by
Wayne Volkmuth (PR#2289021). Crashes with 3-character element.
* include/openbabel/atom.h: Patch from Wayne Volkmuth to ensure
atomic numbers are unsigned (i.e., values above 127 are
OK). PR#2289628.
* src/formats/pdbformat.cpp: Patch from Francois-Xavier Coudert to
write CRYST1 records when unit cell data is present. PR#2023510.
* src/generic.cpp (OBUnitCell::GetLatticeType): Fix bug reported
(and patched) by Jonathan Coome. PR#2100535.
* configure.in, config.* ac*.m4, Makefile.am, Makefile.in: Remove
autotools build files. Use Cmake instead.
2008-11-21 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/Makefile.am, src/ops/Makefile.am: Build mcdlutil.cpp and
gen2D.cpp plugin.
* configure.in: Update to indicate that trunk is not 2.2.0
build. (May go into a 2.3 or 3.0 build.)
2008-11-12 Chris Morley
* src/mscdlutil.cpp, data/templates.sdf: revert to previous
version with templates internal, since external templates
did not seem to be always applied.
#define nRotBondsMax 20 (from 24) which should improve performance.
2008-11-05 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/pqrformat.cpp: Apply patch from Mikael Lund to read in
partial charges and radii. The radii are added to the atoms as
OBPairData with attribute "Radius".
2008-10-31 Chris Morley
* src/formats/getinchi.cpp: prevent failure when input contains
"InChI>InChI=...", which actually occurred in an SDF file.
2008-10-27 Chris Morley
* mcdlutil.cpp: Replace all calls to fabs with abs.
Remove internal templates and template molecule sorting; all
template molecules are now in templates.sdf which has to be sorted,
largest first.
* data/templates.sdf: 147 molecules, sorted
* obconversion.cpp(Convert): make OutputAtEnd option work with
multiple input files.
2008-10-23 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/chains.cpp: Remove debug output.
* src/forcefields/forcefielduff.cpp: Check if parameters are found and
don't try to use a NULL pointer when there isn't a parameter. (Fixes:
#2187870)
2008-10-22 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefields/forcefield*.h: Fix MakeNewInstance().
2008-10-20 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/CMakeLists.txt: Add gen2D.cpp and mcdlutil.cpp
* src/mcdlutil.cpp: Replace all calls to abs(double) with fabs(double)
* src/formats/MCDLformat.cpp: Replace string.npos with string::npos
2008-10-20 Chris Morley
* include/openbabel/mcdlutil.h, src/mcdlutil.cpp: New files
which use MCDL library to generate 2D coordinates
* src/formats/MCDLformat.cpp: some code moved to the above files.
* src/ops/gen2D.cpp: wrapper op for --gen2d
* data/templates.sdf: New file with example template
* src/transform.cpp: help on --sort and --revsort
2008-10-20 Chris Morley
* include/openbabel/obmolecformat.h, src/obmolecformat.cpp:
New functions to sort molecules, Sort(), OutputSortedMols()
and LessThan()
* include/openbabel/descriptor.h, src/descriptor.cpp: New
virtual function LessThan() and default implementation.
Make several error messages once only.
* src/descriptors/filters.cpp: Add LessThan functions for TitleFilter
and more complex one + GetCachedValue() + Init() for InChIFilter.
* include/openbabel/plugin.h: Add virtual funtion Init()
* include/openbabel/mol.h, src/mol.cpp: extra flag to indicate
is a pattern, not a complete molecule. SetIsPatternStructure()
Previously described, but somehow not committed.
2008-10-17 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp: in OBForceField::GetGrid(), calculate grid size
before adding probe atom.
2008-10-17 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/chains.h, src/chains.cpp: some changes from
experimental branch, mainly documentation and some bug fixes.
* src/formats/atomrecord.cpp: Interpret HG11, HE11, ... as hydrogen
atoms at position gamma and epsilon. Previously these atom ids were
interpreted as Hg and He atoms. (Fixes: #2002557 & #2026265)
2008-10-16 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefields/forcefieldmmff94.cpp: Remove _logbuf[100] (Fixes
#2022120)
2008-10-16 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/builder.cpp: fix bugs with linear molecules. (Fixes #2119034 & #2013814)
2008-10-15 Chris Morley
* src/fingerprint.cpp: correct yesterdays commit which used
the wrong size to reserve for the fingerprint vector.
2008-10-15 Chris Morley
* include/openbabel/obconversion.h, src/obconversion.cpp:
New function for counting the number of molecules in an input file.
Make option to force output at end more general (for sort).
* include/openbabel/fingerprint.h, src/fingerprint.cpp:
Add extra parameter to FastSearchIndexer constructor to
allow vectors to be pre-sized.
* src/formats/fastsearchformat.cpp(ReadChemObject): change the way
the last result molecule is flagged (for sort).
(WriteChemObject) Make index updating work with GUI by detecting
a ofstream object rather than cout.
Count number of molecules in input file, report it and use it
to pre-size the fingerprint and seekposition vectors.
* src/formats/smilesformat.cpp(SkipObjects): make compatible with
previous interpretation changes. (Lines which start with non-SMILES
character are ignored.)
2008-10-15 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefields/forcefieldmmff94.cpp: Accept both forms for sulfon
and nitro groups: N(=O)O, N(=O)=O, S(O)O, S(=O)(=O) are now all valid
and typed correctly.
2008-10-11 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefields/forcefielduff.cpp: Fix minor output bug reported by
Tapani Kinnunen (Fixes: #2144142)
2008-10-11 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp, src/forcefields/forcefieldmmff94.cpp: Remove
redefinition of _logbuf[BUFF_SIZE+1] (This and Chris' previous commit
fixes: #2150390)
* src/forcefield.cpp: Fix OBForceField::GetAtomTypes() and
OBForceField::GetPartialCharges()
* src/forcefield.cpp: Check OBForceField::_validSetup flas before
doing anything that may cause a segfault. (Fixes: #2059299)
* src/forcefields/forcefield*.h: Set _validSetup to false in
constructor.
* CMakeLists.txt, src/config.h.cmake: apply patch from Christian
Ehrlicher to fix cmake MSVC compilation.
2008-10-10 Chris Morley
* src/fingerprints/finger3.cpp: rearrange
a) so that div and div-- do not appear in same statement, which
is illegal (Andrew Dalke).
b) replace ternary conditional, which did not compile in gcc
It's a pity the Microsoft compiler did not warn about either of these.
The preferred file format no longer needs a comment as first line.
* src/formats/chemkinformat.cpp(ReadReactionQualifierLines):
correct error similar to b) above flagged in bug #2150390
2008-09-26 Chris Morley
* src/formats/fastsearchformat.cpp: Improved error message when
target is SMARTS rather than SMILES. Bug #2129841
* src/formats/getinchi.cpp: small mod to avoid occasionally seeing
a "quoted" InChI when there isn't one. (There ARE none in the wild.)
2008-09-23 Chris Morley
* src/fingerprints/finger3.cpp: enhanced PatternFP which can take
extra parameters and file format.
* data/MACCS.txt; data for new MACCS fingerprint (from RDKit)
* data/plugindefines.txt; definition of MACCS fingerprint.
2008-07-19 Michael Banck <mbanck@gmx.net>
* src/formats/opendxformat.cpp: Rename theGaussianCubeFormat global
variable to theOpenDXCubeFormat.
* src/formats/CMakeLists.txt: Added opendxformat to formats.
2008-07-11 Chris Morley
* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi
Set Env Var BABEL_DATADIR to installation directory. Safer than
relying on finding the data files in the current directory.
* include/openbabel/builder.h, src/builder.cpp: check whether
fragments.txt is loaded successfully and if not return false
from Build().
2008-07-09 Noel O'Boyle <baoilleach@gmail.com>
* scripts/python/pybel.py: Bug fix for make3D for linear molecules.
Fixes bug 2014055. Minor doc fixes. Remember to close output files
in Molecule.write().
2008-07-03 Noel O'Boyle <baoilleach@gmail.com>
* windows-vc2005/OBPythonOBF/setup.py: Update setup.py to include
forcefield files when installing
2008-07-03 Michael Banck <mbanck@gmx.net>
* scripts/Makefile.am (dist-hook): Do not fail if make distclean does
not succeed in the perl and ruby directories.
* scripts/Makefile.in: Regenerated.
* data/Makefile.am (table_DATA): Added plugindefines.txt.
* data/Makefile.in: Regenerated.
* data/CMakelists.txt: Removed space-groups.xsl from to_install.
* test/cmlreadfile.cpp: Read files from TESTDATADIR, not relative to
current directory.
* test/wrapper.sh: Use ${srcdir}, not ${top_srcdir} to set
$BABEL_DATADIR.
* test/wrapper.sh: Run inchi tests from source directory if ${srcdir}
is non-empty. Set and export TESTDATADIR.
2008-07-03 Noel O'Boyle <baoilleach@gmail.com>
* scripts/ruby/README: Updated build instructions
2008-07-03 Michael Banck <mbanck@gmx.net>
* src/CMakelists.txt (LIBRARY_VERSION): New variable.
* src/CMakelists.txt (BABEL_LIBRARY): Set VERSION property to
${LIBRARY_VERSION}.
2008-07-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/Makefile.am, src/CMakeLists.txt: Update SONAME to 3 for
version 2.2.0 release.
2008-07-03 Marcus D. Hanwell <marcus@cryos.org>
* CMakeLists.txt: Relaxed the CMake requirement to 2.4.7.
* include/openbabel/griddata.h, src/griddata.cpp: Added three new
getter functions to get the x, y and z axes.
* src/CMakeLists.txt: Updated to use SONAME 3.
* include/openbabel/mol.h, src/mol.cpp: Added extra arguments to
GetMolWt, GetExactMass and GetSpacedFormula to optionally disable
implicit hydrogens. Defaults to preserve existing behaviour.
* src/grid.cpp: Fixed the Init function to apply padding correctly.
2008-07-02 Marcus D. Hanwell <marcus@cryos.org>
* include/openbabel/grid.h, src/grid.cpp: Updated the documentation
and a few fixes to the function prototypes.
* include/openbabel/griddata.h, src/griddata.cpp: Updates to the
documentation, added a GetMaxVector function and made SetLimits const
fixes for the vector3 form.
* CMakeLists.txt, src/CMakeLists.txt, src/formats/CMakeLists.txt:
Reduce the number of version variables floating around to only those
that are used...
* CMakeLists.txt, src/formats/CMakeLists.txt: Use a versioned plugin
directory as autotools does.
2008-07-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/locale.cpp: Add string.h header, from patch by Marcus
Hufgard. Allows compilation with GCC 4.3.1 on Linux:
PR#2008642.
* src/formats/gausszmatformat.cpp: Add definition of
strcasestr if not defined. Solves compile problems on Cygwin.
* configure.in, src/config.h.in, configure: Check for
rpc/xdr.h needed for xtcformat.
* src/formats/xtcformat.cpp: Use new HAVE_RPC_XDR_H #define.
* src/formats/smilesformat.cpp: Bring back FIX format, killed
during merger of canonical and standard smiles.
* src/rotamer.cpp, src/locale.cpp, src/base.cpp,
include/openbabel/atom.h, include/openbabel/locale.h,
include/openbabel/forcefield.h,
include/openbabel/pointgroup.h,
include/openbabel/fingerprint.h: Doxygen updates for 2.2.0.
2008-07-02 Chris Morley
* src/descriptor.cpp(PredictandSave): don't duplicate an existing
OBPairData. Was crashing when adding a property that was already
present.
* src/formats/smilesformat.cpp(StandardLabels): A couple of vectors now
have 2147483647 pushed when the atom is H, to match the situation with
canonical ordering, rather than ending up with a size smaller than the
number of atoms. I assume 2147483647 = 2^31-1 is just a big number?
Fixes bug 1999348.
2008-07-01 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/kekulize.cpp (expandcycle): Add more flexible API for
expandcycle.
* scripts/perl/Makefile.PL: Update from Noel for PR#2007797.
* Makefile.*, configure.*: Update for 2.2.0 release.
2008-07-01 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/atomrecord.cpp: Fix bug where arginine hydrogen atoms
where read as dummy Xx atoms. (#2002557)
* src/formats/pdbformat.cpp: 1) Write the chain number. 2) Don't
rearrange atom ids when writing. (see chains item 2)
* src/chains.cpp: 1) Serine OG is now given the correct atom id.
2) produce correctly ordered atom ids (see pdbformat item 2)
3) fix for cyclic peptides (have no NTer)
4) water, ions and ligands are all placed in the ' ' chain now and get
unique residue numbers.
5) partially identified residues are merged with the atoms not used to
identify them and the resids is set to UNK (hetflags is also set to
true) (e.g. CSD in 1LWF = CYS with two O's on S )
2008-07-01 Noel O'Boyle <baoilleach@gmail.com>
* scripts/python/pybel.py: Make pybel use CloneData instead of SetData
2008-07-01 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-python.i: Make the BFS Iterator return two values,
the Atom and the depth
2008-07-01 Chris Morley
* data/atomtyp.txt: remove IMPVAL entry for silicon to fix
bug #1911590. (I thought I had already done this.)
* windows-vc2005/babelconfig.h: add macro which apparently
disables native tr1 in recent VC++ 2008, so that boost version
will be used. Step towards getting tit to compile on this
platform but probably not there yet. Not critical for v2.2.0
release, since Windows compilation should be done from SVN.
2008-06-30 Geoffrey Hutchison <babel@geoffhutchison.net>
* Makefile.am: Move cmake to EXTRA_DIST (4 Makefiles for one
file?)
* Makefile.in: Regenerated.
* include/openbabel/base.h, src/base.cpp: New CloneData()
method to solve PR#2004495 for scripting interfaces.
* src/Makefile.am, src/Makefile.in: Bump library version for
2.2 release.
* src/formats/smilesformat.cpp: Minor fix relating to
PR#1999348.
* src/patty.cpp, src/forcefield.cpp, src/oberror.cpp,
src/generic.cpp, src/canon.cpp, src/dlhandler_unix.cpp,
src/data.cpp, src/grid.cpp, src/mol.cpp: Minor fixes from
static code analysis. Test for empty() instead of size().
2008-06-30 Michael Banck <mbanck@gmx.net>
* src/Makefile.am (EXTRA_DIST): Added config.h.cmake.
* src/Makefile.in: Regenerated.
* Makefile.am (SUBDIRS): Added cmake.
* Makefile.in: Regenerated.
* cmake/Makefile.am: New file.
* cmake/Makefile.in: New file.
* cmake/modules/Makefile.am: Likewise.
* cmake/modules/Makefile.in: Likewise.
* configure.in (AC_OUTPUT): Added cmake/Makefile and
cmake/modules/Makefile.
* configure: Regenerated.
* acinclude (AM_PATH_XML2): New macro, copied from aclocal.m4.
2008-06-29 Marcus D. Hanwell <marcus@cryos.org>
* include/openbabel/math/vector3.h,
include/openbabel/math/matrix3x3.h: Made the destructors non-virtual,
fixes Avogadro bug 2005984.
2008-06-27 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/obiter.h, src/obiter.cpp: Fix
PR#1901348. Add support for BFS iteration from arbitrary
atoms.
* include/openbabel/math/*.h, src/math/*.cpp: Updates to fix
some GCC warnings.
* include/openbabel/bond.h, src/bond.cpp: Patch from Steven
Constable, PR#2004391. Adds SetLength() to move both atoms.
* include/openbabel/mol.h: Fix for ReserveAtoms() suggested by
Andrew Dalke.
* src/formats/mdlformat.cpp: Fix for SKP records, suggested by
Andrew.
* src/formats/pdbformat.cpp: Fix for CONECT records for atoms
with > 4 records (PR#1711154).
2008-06-26 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/parsmart.cpp: Add support for Isotopes in SMARTS. Fixes
PR#1987729.
* test/files/nci.smi: Add tests for matching isotopic
SMILES/SMARTS.
2008-06-23 Chris Morley
* test/inchiwrite.cpp: add -xn option so that the tests are done without
the 'recommended' InChI options. wInChI.exe is not yet available
for InChI 1.02. Needs revisting when it is.
* src/fingerprint.cpp(FastSearchIndexer): ensure fpid is terminated
when copied to guard against theoretical problem pointed out
by Andrew Dalke.
2008-06-21 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/chains.cpp: Assign HOH and ligands to separate residues.
(#1774776)
2008-06-21 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/atomrecord.cpp: Keep original chain ID (#1760959).
2008-06-21 Carsten Niehaus <cniehaus@kde.org>
* src/obutil.cpp: Typo fixes.
* src/forcefields/[forcefielduff.cpp,forcefieldmmff94.cpp]: Typo fixes
* src/formats/[mpdformat.cpp,xtcformat.cpp]: Typo fixes
* src/forcefields/*.h: Make ctor explicit.
2008-06-20 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/obutil.cpp (CartesianToInternal): Fix PR#1923896 for
Fenske-Hall z-matrix format. When looking for non-linear
atoms, don't pick non-bonded >10.0 Angstroms, which cause
problems with FH (and other) fixed format z-matrices.
* src/mol.cpp (ConnectTheDots): Fix for PR#1813502 for
existing bonds getting deleted by ConnectTheDots. Make sure to
preserve all original connections from PDB.
* src/formats/pdbformat.cpp (ReadMolecule): Fix for PR#1985681
with virtual bonds still built into a PDB file.
2008-06-20 Chris Morley
* include/openbabel/locale.h, src/locale.cpp: extra #includes
* windows-vc2005/babelconfig.h: define strdup. Version to 2.2.0
* include/openbabel/obiter.h: trivial change to avoid compiler warning
* src/fingerprints/finger3.cpp: do singel SMARTS match, as suggested by
Ernst-Georg Schmid
* windows-vc2005/OBError/OBError.vcproj: add locale.cpp
2008-06-20 Noel O'Boyle <baoilleach@gmail.com>
* Revert of r2347: I had set eol:native instead of eol-style native.
2008-06-19 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/fingerprint.cpp: Contribution from Andrew Dalke for
improved speed using GCC.
2008-06-18 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/locale.h, src/locale.cpp: New OBLocale class
to centralize calls to setlocale/uselocale. Should solve strange
segfault on Linux with freelocale.
* include/openbabel/obiter.h, src/obiter.cpp: Add depth tracking
for DFS and BFS iterators. Addresses PR#1901348.
2008-06-18 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/*.cpp: Checked all files for their use of tokenize().
All added lines are like:
if (vs.size() < 1) return false; // timvdm 18/06/2008
* include/openbabel/obiter.h, src/obiter.cpp: Reimplement
FOR_PAIRS_OF_MOL. Do not build a list of all pairs in the constructor,
but find the pairs while iterating. This is faster and requires less
memory.
* include/openbabel/forcefield.cpp: Add SetParameterFile().
* src/forcefields/forcefieldmmff94.*: Use the new SetParameterFile().
Add a global definition for MMFF94s.
* data/*: Add MMFF94s parameters.
MMFF94s: Same functional form, only torsion and oop parameters are
different. To see the difference, you can try to minimize alanine with
both force fields, MMFF94s will give a planar nitrogen while MMFF94
will not.
2008-06-17 Noel O'Boyle <baoilleach@gmail.com>
* Reverted r2535 except for changes to scripts/perl/Makefile.PL
* scripts/openbabel-python.i: Updated SWIG interface file to ignore 21
methods of each std::vector created. This should substantially reduce
the size of the wrapper code.
2008-06-16 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/xtcformat.cpp: make confs a std::vector too. Was double
*confs = new double[natoms * 3].
2008-06-16 Chris Morley
* include/openbabel/oberror.h, src/oberror.cpp:
add a parameter to ThrowError to allow error messages to be
output only once (although they are all logged.). The default
behaviour is as at present.
* src/formats/inchiformat.cpp: default output uses the "recommended"
set of InChi options. -xn option uses no options as at present.
Add -xl option to output the InChI log - only once for multiple
molecules.
* include/openbabel/fingerprint.h, src/formats/fingerprintformat.cpp:
Make DescribeBits error message appear only once.
* src/mol.cpp(GetTitle): make variable title static to avoid returning
a pointer to a temporary variable. But this might cause problems with
multiple molecules unless the title is captured in the calling code
before getting the next. Until this is done properly, add a
test so that the problem can only occur with multi-line titles.
* src/formats/smilesformat.cpp: add option to output explicit hydrogen
form like [CH3][CH3].
**** The SMILES output currently crashes with Nc1nc(O)c2nc[nH]c2n1
but I haven't tracked this down.****
* src/ops/addpolarh.cpp: add simple op for Feature Request #1995162
* windows-vc2005/gen3D/gen3D.vcproj,
windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj: update
2008-06-15 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/cssrformat.cpp, src/formats/MCDLformat.cpp,
src/formats/mmcifformat.cpp, src/formats/balstformat.cpp,
src/formats/chemdrawcdx.cpp, src/formats/boxformat.cpp,
src/formats/unichemformat.cpp, src/formats/yasaraformat.cpp,
src/formats/zindoformat.cpp, src/formats/gromos96format.cpp,
src/formats/xedformat.cpp: sprintf --> snprintf
* src/chains.cpp, src/pointgroup.cpp, src/rotor.cpp: Some more sprintf
-> snprintf (I don't expect any problems here, but just in case...)
* include/openbabel/forcefield.cpp, src/forcefield.cpp,
src/forcefields/*: Replace sprintf(_logbuf, ...) with
snprintf(_logbuf, BUFF_SIZE).
2008-06-14 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/chain.h, src/chain.cpp: Replace:
1) malloc/free with new/delete
2) new T[n] with std::vector (where possible)
Original code still there as comments, can be removed once reviewed.
* src/parsmarts.cpp: Replace malloc/free with new/delete.
Replace realloc(array, size) with:
T *tmp = new T[size];
copy(array, array + old_size, tmp);
delete [] array;
array = tmp;
2005-06-14 Marcus D. Hanwell <marcus@cryos.org>
* src/formats/xtcformat.cpp: Some modifications to the xtc format to
use C++ structures.
* CMakeLists.txt, src/formats/CMakeLists.txt: Some build system
updates to build format plugins as modules.
* src/ops/loader.cpp: GCC 4.3 fix - cstdlib needed for free calls.
2008-06-14 Geoffrey Hutchison <babel@geoffhutchison.net>
* include/openbabel/atom.h, src/atom.cpp: Add OBAtom::Duplcate()
which will copy everything except the internal index.
* include/openbabel/generic.h, src/generic.cpp: Add
OBUnitCell::FillUnitCell() method to create space-group-defined
atoms. Uses OBAtom::Duplicate.
2008-06-13 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/forcefield.cpp: Change GetGradient(..., int terms
= ...) to GetGradient(..., int /*terms*/ = ...). (comiler warning:
unused parameter).
* src/forcefields/*.cpp: Change i->Compute<gradients>() to i->template
Compute<gradients>().
* include/openbabel/builder.h, src/builder.cpp: Make most functions
static.
* src/mol.cpp: Use OBBuilder::GetNewBondVector() in AddHydrogens().
2005-06-13 Marcus D. Hanwell <marcus@cryos.org>
* src/formats/mdlformat.cpp: Use static_cast in the min function.
2008-06-13 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/typer.cpp: Add a special case for guanidinium carbon
atoms. (We may need additional special cases.)
* data/atomtyp.txt, data/atomtyp.h: Change pattern for N3+ to
match any 4-valent N, regardless of whether the formal charge has
been set.
* src/kekulize.cpp (NewPerceiveKekulizeBonds): Give up on
kekulization when we find "cycles" with < 3 atoms. Sybyl mol2
labels some atoms as aromatic that aren't in rings. Fixes
PR#1965566 and PR#1784204.
* include/openbabel/mol.h, src/mol.cpp (GetTitle): Add a parameter
to replace newlines with spaces. Fixes PR#1984742.
* configure.in: Check for xlocale.h, locale.h, and uselocale functions.
* src/data.cpp, src/ops/loader.cpp, src/ops/optransform.cpp,
src/descriptors/groupcontrib.cpp, src/builder.cpp,
src/forcefields/forcefieldmm2.cpp,
src/forcefields/forcefielduff.cpp,
src/forcefields/forcefieldmmff94.cpp,
src/forcefields/forcefieldghemical.cpp, src/obconversion.cpp:
Change locale using uselocale if available and reset it to the
afterwards. Update of previous change, suggested by Benoit.
* include/openbabel/bond.h, include/openbabel/atom.h,
src/bond.cpp: Fixes for "const" correctness. It's now possible to
get the bond length of a const OBBond.
2008-06-10 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/data.cpp, src/ops/loader.cpp, src/ops/optransform.cpp,
src/descriptors/groupcontrib.cpp, src/builder.cpp,
src/forcefields/forcefieldmm2.cpp,
src/forcefields/forcefielduff.cpp,
src/forcefields/forcefieldmmff94.cpp,
src/forcefields/forcefieldghemical.cpp, src/obconversion.cpp:
Change locale before parsing files to use "C" numeric locale and
reset it to the original state afterwards. Should solve PR#1785463.
* src/obiter.cpp: Fixes from Izhar for DFS and BFS iterators.
* src/mol.cpp, include/openbabel/mol.h: Added iterative
GetFragment method to augment Separate(), contributed by Izhar.
2008-06-07 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/phmodel.cpp (OBPhModel::CorrectForPH): Fix PR#1835204. Allow
SMILES to have pH-correction. (i.e., only check for automatic
formal charges for molecules with dimension > 0).
* src/formats/mdlformat.cpp: Add a check for EOF before reading,
as suggested by Izhar.
* src/formats/smilesformat.cpp: Add initial pass at "standard"
SMILES labels.
* Doxygen, include/*.h, src/*.cpp: Update doxygen documentation.
2008-06-07 Chris Morley
* src/formats/fingerprintformat.cpp: correct folding error message
and prevent description of bits when fingerprint is folded.
* src/formats/smilesformat.cpp: change -xc to -xa (for atomclass)
* windows-vc2005/OBFS/OBFS.vcproj,windows-vc2005/OpenBabelOBF.sln
add dependency of OBCommon to Fastsearch project
2008-06-06 Chris Morley
* src/formats/smilesformat.cpp: SMIFormat was being hidden because
its constructor was being called again when its derived class
CANSMIFormat was made. Now both derived from a base class with most
of the functionality.
Modified Description() and made same for both.
Removed DEFAULTFORMAT flag (MolFormat already is).
* include/openbabel/mol.h: add back #include <float.h> which was
somehow removed in the last commit and is need for Windows build.
* windows-vc2005/OBCommonFormats/OBCommonFormats.vcproj: remove
cansmilesformat.cpp
2008-06-06 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* include/openbabel/phmodel.h, src/phmodel.cpp: Changes to OBPhModel,
use the Henderson-Hasselbalch formula to determine protonation states.
Updated doxygen documentation to give some info about the method.
* include/openbabel/mol.h, src/mol.cpp: Use it.
OBMol::AddHydrogens(bool polar=false, bool correctForPH=true, double
pH=7.4)
* data/phmodel.txt: Add extra column with pKa values.
* test/phmodel.cpp: Unit test for the new phmodel. The two errors are
Glutamate (4.0 used, should be 4.3) and Lysine (10.0 used, should be
10.1). I'll probably have to add a visited list so we can only
transform an atom once, transformations would then have to be ordered
by decreasing complexity. But the errors are very small and this is a
major improvement compared to what we had.
2008-06-05 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/openbabel-python*, scripts/python/*: Split the python
bindings into three pieces for improved compilation. Should solve
PR#1905826.
* src/obconversion.cpp: Add stdlib.h to hopefully solve
PR#1985717.
* configure.in, configure: Update to build libinchi by default.
* src/formats/smilesformat.cpp: Incorporate cansmilesformat
code. Now all SMILES export goes through Craig's cleaner,
less-buggy code. Currently all SMILES are canonically
ordered. Need to add code to provide non-canonical ordering for "regular."
* src/formats/Makefile.* src/formats/CMakeLists.txt: Update for above.
2008-06-05 Chris Morley
* src/obconversion.cpp(Convert): test for Cntl Z to terminate
commandline input rather than \n (a blank line).
Fixes bug 1984660: piping with titleless mol files.
Commandline data input always was clunky and is even clunkier now.
Being able to pipe is more important.
* src/forcefield.cpp:In line 2535 replace 'dafault:' by 'default:'
This may have a real effect and needs to be checked.
* include/openbabel/bitvec.h, src/canon.cpp,src/dlhandler_win32.cpp,
src/forcefield.cpp, src/formats/cansmilesformat.cpp,
src/formats/gamessformat.cpp, src/formats/gaussformat.cpp,
src/formats/KFReader.c,src/formats/mol2format.cpp,
src/formats/msmsformat.cpp, src/pointgroup.cpp,
src/tokenst.cpp:
Tidy to reduce compiler warnings: remove or comment out unreferenced
variables; size_t decalation replaces some int or unsigned;
!=NULL added to avoid implict const char* to bool conversion
* windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj: change to
project build order as pointed out by peterennis bug #1985163
2008-06-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/formats/mopacformat.cpp: Fix for PR#1978982 with reading
Mopac 2007 force calculations.
* src/formats/atomrecord.cpp: Fix SetAtomID as reported in
PR#1838095. Thanks to Marc Lasson for bug report and fix.
* src/formats/adfformat.cpp, src/formats/Makefile.am: Add KFReader
and ArrayList code contributed under LGPL by SCM, Inc. for
improved ADF binary support.
2008-06-04 Chris Morley
* include/openbabel/mol.h: include float.h so that isinfinite
is handled properly in Windows
Deficiencies raised by Andrew Dalke
* src/fingerprint.cpp: Error message if attempting to fold to
less than size of unsigned int.
* src/formats/fingerprintformat.cpp(WriteMolecule) Error message
when parameter of -xN option (fold) is negative.
* src/formats/fastsearchformat.cpp(WriteChem Object):
Error message if more than one input file.
Delete the outputstream after deleting the index, which is when
it is written. Sometimes a fs file made without a specified name
was empty.
* tools/babel.cpp: change indentation on help text
* windows-vc2005/OpenBabelOBF.sln: another go at getting debug and
release configurations right. The scripting interfaces need to be
explicitly enabled before building if they are required. (I get
tired of waiting for them.)
2008-06-04 Geoffrey Hutchison <babel@geoffhutchison.net>
* src/residue.cpp (GetResidueNumber): Fix bug reported by Izhar
Wallach.
* src/forcefields/forcefielduff.cpp: Fix error reported by Chris
Morley with Microsoft compiler -- don't duplicate loop variable names.
2008-06-03 Geoffrey Hutchison <babel@geoffhutchison.net>
* data/atomtyp.txt, data/atomtyp.h: Add hybridization rules for
Si, Al, Ge, As, Se, and Te. (Atom typing and valence rules need to
be generalized.) Fixes problems with adding hydrogens to Si
uncovered in Avogadro.
2005-06-02 Marcus D. Hanwell <marcus@cryos.org>
* src/atom.cpp, src/mol.cpp: Added extra checks in AddHydrogens for
finite hydrogen coordinates. Also added some extra checks in the
GetNewBondVector function to check for sane numbers.
2008-06-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* Makefile.am, Makefile.in: Correct small automake typo with
"autoconf" libtool macro directory.
* configure: Regenerated using autogen.sh.
* include/openbabel/grid.h: Fix compiler warning -- make sure to
return values in all methods.
* src/forcefield.cpp: Fix compiler warning "default" not "dafault"
in switch statements.
* src/formats/qchemformat.cpp, src/formats/gamessformat.cpp,
src/formats/gaussformat.cpp, src/formats/fchkformat.cpp: Add
support for reading dipole moments using OBVectorData.
2008-06-01 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/formats/atomrecord.cpp: Call OBAtom::ForceImplH() for all atoms.
Loading a pdb file and calling OBMol::AddHydrogens() added only on
hydrogen.
2005-05-31 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-csharp.i: Fixed two of the three remaining
std::vectors based on examples found in Krugle code search
2005-05-30 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-csharp.i: Fixed most of the std::vectors by using
weird macro described in std_vector.i in the SWIG distribution
2005-05-30 Marcus D. Hanwell <marcus@cryos.org>
* configure, configure.in: Stop the wx-config test being called when
the wx-gui is not enabled - bug 1979603.
2005-05-30 Noel O'Boyle <baoilleach@gmail.com>
* scripts/openbabel-csharp.i: Added header file to SWIG wrapper. Also
removed several of the vector templates. These don't seem to be
handled correctly by SWIG (should report bug to them).
2008-05-30 Tim Vandermeersch <tim.vandermeersch@gmail.com>
* src/forcefield.cpp: OBFFConstraints::Clear(), clear all the bitvecs.
ConjugateGradientsTakeNSteps(), set _grad1[] to (0,0,0) when atom is
fixed and not _gradientPtr (_grad1 is used for linesearch).
Setup() & SetConstraints, check if SetupCalculations needs to be
called. This is the case when the ignored bitvecs of both
OBFFConstraints are different.
* include/openbabel/forcefield.h: OBFFConstraints::GetIgnoredBitVec().
Used in Setup() & SetConstraints().
2008-05-28 Chris Morley
* windows-vc2005/OBCSharp/OBCSharp.vcproj,
* windows-vc2005/OBJava/OBJava.vcproj,
* windows-vc2005/OpenBabelOBF.sln
Build release versions even in Debug mode.
Use env var JAVABASE, e.g."C:\Program Files\Java\jdk1.6.0_03"
so that there is no dependence in the code on the installed
Java version. (Is there a standard variable for this?)
* windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj:add adfformat
2008-05-28 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/openbabel-perl.i, scripts/perl/Makefile.PL: