Added Magda Oprian to AUTHORS

Change-Id: Ibac4f2ceadbc17ced0ccdb65cf86e23936ef6b38
Removes old @cdk.depends tag from javadoc.

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

Conflicts:
	src/test/org/openscience/cdk/modulesuites/MnonotifyTests.java
Removing old @cdk.builddepends tag.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added a unit test for the double brackets SMILES bug

Change-Id: Ib956b78ba268c2ab8f452e70e4c0b619a5e774aa
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Determine earlier if the nitrogen needs an explicit implicit hydrogen (you know, like [nH], solving the double bracket problem

Change-Id: I32ab2374e403edd7c3cd5dc6656d6c94a1de0e3a
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Unit test that checks that implicit hydrogens on ring nitrogens are only added when they are negatively charged (bug #1300)

Change-Id: I2fc8c80eed751653a6d3e96b02ef0afbd60d81a5
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed generation of SMILES with non-charged nitrogen rings with an implicit hydrogen (bug #1300)

Change-Id: I92720e88b167116c01b2d049ff8af55c833f1d21
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Yeah, Ant 1.9.x is fine too

Change-Id: If058e2f839a7d8eb7937da5948d57b18957658eb
Correct addition of atoms to a list. Unlike Vector, a List does not let you use set(int, Obj) unless that index already has an item.

Change-Id: I96004873d392e572efebb94f34f040fb79112238
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
minimise scope in org.openscience.cdk.hash

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
move seed packages and minimise scope

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
moving equivalent class resolution and restricting visbility

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
move equivalent class resolution classes and minimise scope

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving hash stereo classes to a single package and minimising the scope.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
More cleanup and minimising visibility of the hash stereo classes.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
A bit matrix which will help in minimisation when constructing cycle bases

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Utility class for manipulating int[][] adjacency list graphs

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow null containers in the ShortestPaths tool

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