s/NewDefaultChemOjectBuilder/DefaultChemObjectBuilder/g (closes #3456420)

Conflicts:

	src/main/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java
	src/main/org/openscience/cdk/reaction/type/AdductionProtonPBReaction.java
	src/main/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java
	src/main/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java
	src/main/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java
	src/main/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java
	src/main/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java
	src/main/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReaction.java
	src/main/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReaction.java
	src/main/org/openscience/cdk/reaction/type/HomolyticCleavageReaction.java
	src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java
	src/main/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java
	src/main/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java
	src/main/org/openscience/cdk/reaction/type/RearrangementAnionReaction.java
	src/main/org/openscience/cdk/reaction/type/RearrangementCationReaction.java
	src/main/org/openscience/cdk/reaction/type/RearrangementLonePairReaction.java
	src/main/org/openscience/cdk/reaction/type/RearrangementRadicalReaction.java
	src/main/org/openscience/cdk/reaction/type/SharingAnionReaction.java
	src/main/org/openscience/cdk/reaction/type/SharingChargeDBReaction.java
	src/main/org/openscience/cdk/reaction/type/SharingChargeSBReaction.java
	src/main/org/openscience/cdk/reaction/type/SharingLonePairReaction.java
	src/main/org/openscience/cdk/reaction/type/TautomerizationReaction.java
	src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptorTest.java
	src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptorTest.java
	src/test/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java
	src/test/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java
	src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java

Change-Id: I1f9be7b9f4f6871e216affa0e0e0852b62fbbe74
Updated isotope abundance values according to the IUPAC technical report 2009.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added ability to read atom parity from Mol files (inc. junit test).
Added close to unit-test resource stream

Conflicts:

	src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java

Change-Id: I00de77ab25929fb331168231053198654e2b7efa
Fixed unit test: because the implementation creates an IMolecule object, the original 'molecule' pointer does not get atoms, and the returned IMolecule object should be assigned to get a molecule with information

Change-Id: I480895ef8a0f308a279f80c869a6efb93c67cbee
Write atom parity

Writes the atom stereo parity for MDLV2000 format

Conflicts:

	src/test/org/openscience/cdk/io/MDLV2000WriterTest.java

Change-Id: I0353d15c52afb6a367669aedae24031630824526
Assertion error fix

Fixed error in new unit test assertion
Same as earlier: use the returned object, which is not the same as the passed IAtomContainer

Change-Id: I5c6424507a3bd691ce1824f64b555b643a608ff6
Resolution for Bug 3485634

Adding test molecule data/mdl/bug3585634.mol. This molecule is from the
metlin database (http://metlin.scripps.edu/)

1) MDLReader and MDLV2000Reader unit tests
   Unit test's to ensure the molecule is read.

2) MDLV2000Reader empty atom properties fix
   Fix allows MDLV2000Reader to read mol (v2000) files that are missing
   all atom properties

3) MDLReader empty atom properties fix
   Fix allows MDLReader to reader mol files with empty atom properties

4) Corrected error handling in MDLV2000Reader and MDLReader
   Handling now uses the handleError() method to respond correctly
   to format violations

Change-Id: I69f96635dd42753f4464426bd4b083417f62f74e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:

	src/main/org/openscience/cdk/io/MDLV2000Reader.java
Replaced (I)Molecule with (I)AtomContainer

Change-Id: I077605ed6ad2a4f62a7925e5b5ccdf0b30f73cf3
Fix for charge parsing in PDB files, based on the patch by Nils <nils@users.sf.net>

Change-Id: I7414228850ac87880febdebfc6e912647638f2c6
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Updated bcut descriptor to check for undefined values before getting eigenvalues. Added test file and test case. Addresses bug 3489559

Change-Id: Ic3fd58f387f8b8fb060d07accb790f27c2d8a473
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added unit test for undefined G-M partial charges

Change-Id: I71ed92eda37139a25a46f0af34555b8be4f36888
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:

	src/test/org/openscience/cdk/charges/GasteigerMarsiliPartialChargesTest.java
Fixed a wrong test for undefined values in the Burden matrix

Change-Id: I9caf4c16b236e9439b1901bb5339c369bfcd3f5c
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test to make sure the SMILES parser gets the formal neighbor counts correct

Change-Id: Ib7c4909fdeb31d1fadde46a6685b1dd20a7959f8
Added dedicated unit testing for the InChIGeneratorFactory

Change-Id: I6f77b41e950474857e953181b0f03af5fa92a4ea
Testing of the InChI generator

Change-Id: I5d67a33c596d1fadf96fef192cbd606bca710f6a
More unit tests. All methods are now at least tested once. (closes #3005889)

Change-Id: I305ed297ff335cdd20cd119c84c3968e6e7b13d6
IteratingMDLReader Skip Patch

Provides skip functionality to IteratingMDLReader. If a molecule is null the reader
can skip over it (if 'skip' boolean is set true). The skip property is set via an
mutator 'setSkip' or in the constructor. If a null molecule is read the read will
skip forward until the next record separator ($$$$). The commit include a unit test
for the patch which uses some molecules from the HMDB sdf file.

Change-Id: Ie116eb1d5119357bec049a66e2d1a0a2a3dcb620
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:

	src/main/org/openscience/cdk/io/iterator/IteratingSDFReader.java
	src/test/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java
Fixed link to the CDKMCS class, which is now in a different package

Change-Id: I357116a906d44821d2bf55c9ea406f8af73a5f3f