Added renderextra to dist-large and test-all targets

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added aromaticity-based perception: N.planar3

Added perception of PLANAR3 hyrbidization for aromatic nitrogens that are not in kekule representation (i.e. atomaticity has been read). This patch adds a unit test on pyrrole that demonstrates the functionality is working.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
There is no Se.2 atom type in the CDK; the perception seems to match Se atoms with two neighbors; I added two unit tests for the changed code, assuming one and two implicit hydrogens

Change-Id: Ia4494541ce859b952f6c994e392248e80130ced2
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added the missing S.2minus atom type for selenide

Change-Id: Ia53e8e981b471f9cb77ed022cd46581092fe01a5
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
s/Molecule/AtomContainer/

Change-Id: I5650bc75ed19e16bc2670997a18598b81c7438b0
Added meta data about commons-math jar

Change-Id: I0c3f3814e2111deb39d58a88d64a8d6c87e07d08
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixed the problem with failure if the molecule only have implicit bonds

Change-Id: I6715d098b696b0f57b5531c962e5d52ee8db3168
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixed failure when the bond order sum is not set
s/IMolecule/IAtomContainer/

Change-Id: I510443f460bf3e2eacc31c9058e6a5a3f3884045
Removed unused imports

Change-Id: Ibc279666932bab57e1a55d3beac2c2324499522f
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added an alternative aromaticity perception model, which is happy about double bonds pointing outwards from aromatic rings

Change-Id: I631ffb26431d5c80d1eb6495dbdff30e7113722e
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Because the placement of double bonds is not deterministic, we cannot be sure we always get them at the same location. Better is to just test that all carbons are perceived as C.sp2 and that they are aromatic.

Change-Id: Ifc5e41a8378de3e6b22f698c77a36fa67b88cbc8
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Testing that benzoquinone is perceived as aromatic using the alternative detection method.

Change-Id: Ia64a05d62546f6bd055043e28da68e60c67b740e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removed cdk.create dates, as suggested by the reviewer

Change-Id: I3fbef0fde1991e4c9f737450bacfefd37027c907
Removed SVN tags, as suggested by the reviewer

Change-Id: I25728722640b54d2ca3d65f6d8758ce2adf10df6
Documenting new method and extended unit test

Added documentation to method created to deal with N.planar.3 perception (S Beisken).
Added unit test to ensure that explicit hydrogens to do change the perception.
Included @cdk.inchi taglet

Change-Id: I4d43507be9357dc6fec0409e5628428202bd88cc
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added missing test annotation

Change-Id: I66318bc6a324de0ed0bb42182e99238896bf2db8
Be more informative when the test fails

Change-Id: I1603134367a41849fa24da10da943f63850f35c0
add isEmpty() to classes/interfaces ChemModel, AtomContainerSet, ReactionSet, Crystal and AtomContainer

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added unit test and @TestMehtod annotaitons for new 'isEmpty' mehtods

Change-Id: If3ab0f5797345e40596762afd4f6fc9db80b76fb
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/ChemModel.java
	src/main/org/openscience/cdk/debug/DebugChemModel.java
	src/main/org/openscience/cdk/silent/ChemModel.java