white-listing for export properties

Only properties explicitly inputed into SdfWriter should be
exported. This new behavior could be added with an extra constructor
that takes a Set of properties. Using existing constructors keeps
the old behavior.

Change-Id: I04d42b0d245f5b7479436396efecbcb6daf13669

Conflicts:
	src/main/org/openscience/cdk/io/SDFWriter.java
Unit tests for optional property writing.

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

Conflicts:
	src/test/org/openscience/cdk/io/SDFWriterTest.java
Removing output from unit tests.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixed the group for Ds (fixes #1282)

Change-Id: I8fdbb50f171697371090bc8c4615a1af4aa6d8e3
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Basic unit test for bug 1305: null should not match AnyOrderQueryBond

Change-Id: Ia5f6b0e297d6ba571af690b534dc5fb3f2d1a5c0
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a positive unit test too

Change-Id: Ica5ed8c3f3ab944da83e3c3bdfbd05fcc13e2826
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Any bond order is fine, but the IBond must exist (fixes #1305)

Change-Id: Ida9971b5326c4e33e2c1513419b7ad8cb6ac9861
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed the import, matching the cdkdeps and adapting for master

Change-Id: Ia1de7eea08c8b4ce0fb4b3e131d482634b14635f
Added Lv and Fl names and two missing elements (Uup and Uut) used in Elements.java

Change-Id: I16cfb6e31a5eead58cef870ac5a4d25416870c59
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

Conflicts:
	src/main/org/openscience/cdk/config/Elements.java
Two convenience methods to make dealing with BODR data a lot easier

Change-Id: I1c29e2d1b412a898bf01ecc2a4d0bb3a145249cd
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Providing required delta for comparing floating points.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using 'hamcrest-all' for additional matchers.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
hamcrest-all for eclipse users

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Adding assertions to non-test and removing stdout.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Adding back in test which were moved to SignatureTanimotoTest during module rearrangement.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
The input header 'Marvin 07140515482D' is 2 characters longer than the output header 'CDK 0803131301'. This shifts the index by two characters.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Revert "Fixing test regression that depended on the molecule having the same kekule form - i.e. order dependant. When the ring perception changed the order may not be exactly the same but nothing should rely on that fact. Setting the aromaticity fixes the test failure.". This was actually a true failure, the pi-bonding movement tests for different kekule forms and the failure was correct.

This reverts commit fdfbf5e8e092161eadd373f319482b2b76af90e6.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Convenience method for matching in test

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving assertion to make it clearer what is going to change.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correcting test assertion. This reaction type generates two products (as there are two rings in the conjugated ring system). The new ring perception code perceives the two six member rings (used by the reaction) in a different order and so the output order of the products was switched. To avoid this happening again the matching was modified to check both combinations.

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