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
s/Molecule/AtomContainer/

Change-Id: I854763947af96b956c948967a131dfc32b7a53c6
Added the now requires isEmpty() method, copying the implementation from AtomContainer

Change-Id: I5007b9e1438b83951d7b07d1a0d02f7e842db797
Removed redundant code - we don't need to check whether the bond is already in the container as we create a new instance. We also don't need to check the array size as this is done by addBond(IBond)

Change-Id: I9b7ddfa356874aee18995e766513cdfca9e6acd2
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removed print to standard out from ChemObjectBuilders

Change-Id: I6e69e8bab5781f67346fc9a33240c357d55ef01e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added check to ensure a DoubleBondStereochemistry is never created with more then 2 bonds - this would cause errors with some methods.

Change-Id: Icbfb1902560d1588dec7b95aac3a775053728450
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added removal of stereo elements in 'removeAllElements()' - documentation has been updated

Change-Id: I02bd4d114e918c5aaabd881546c29afae55d6800
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removed redundant code from ChemObj clone - the existing code did exactly what the copy constructor of HashMap does and thus provides a cleaner implementation

Change-Id: I3815bd122d8e1dd943076da434dcda4f40bee35c
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/ChemObject.java
	src/main/org/openscience/cdk/silent/ChemObject.java
Added cdk-silent dependency for test-renderextra

Change-Id: Ie5c9aba77e946a669e173c0cfb6e5079399b0c83
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixed closing <ul> (fixes #1265)

Change-Id: Ib903e924bcbc730ec2df1f39b640860f77a7aceb
Renamed constructer parameter out to writer (Writer) and change default constructor to use the ByteArrayOutputStream. Added Writer -> OutputStream conversion in setWriter() similar to constructor and modified both to print a warning message. I'm aware the OutputStream doesn't handle encodings… but I'm not sure if this is an issue as the CML serializers take an encoding as a parameters. Added null check on 'close()'

Change-Id: I44a5d361a9b3e6c321e47cde93d5c578cdf4221d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>