Made QueryChemObject require a IChemObject builder when being constructed. This has a knock on effect that all the SMARTs atoms require the builder also. Although there are a lot of changes there's little front end API changes - the SMARTSQueryTool and PubChemFingerprinter now require a builder but other methods (e.g. descriptors and QueryAtomContainerCreator) could make use of the builder from other IChemObjects.

Change-Id: I64a6d7a3450ad1ad9b684d3679a11ace293e58fa
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
allow DescriptorEngine to load the two descriptors that require an IChemObjectBuilder injection. DescriptorTest was updated and generiffied to allow testing of the modified descriptors.
Added a unit test for the sorting of the multiplier

Change-Id: If572a12da7e89e80d2e986035c57acff928aeaa8
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Test to ensure that the atom type name is returned with IAtomType.toString()

Change-Id: I83ec328f025aabf0915a17ef04dcff5299690498
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
non-null atomic numbers when reading from InChi [bug:1293]

Change-Id: Ib6c5e9291913705ccb6f8ef6bd2813f3dd77745c
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added additional test that non matching symbols mismatch

Change-Id: Ia48137c987e4158db6bf801590115aa939c6ade2
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Small patch for bug 3551478

Change-Id: Ic565e6783caee915014f3d4958a243089a60ee47
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated patch d1748f93aa7810efbbdc2be7e4243f7ececc6fe4 for master

Change-Id: I179979d213d60b4346dcc4984e096a1f08846449
Fixed proton isotope perception.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added explicit atom typing and aromaticity detection to several failing fingerprinter tests.

Change-Id: I551fcf3ba3f5c77000a650c27eac3bbb51de832b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correct unit test name and added missing unit tests and annotations.

Conflicts:
	src/test/org/openscience/cdk/fingerprint/PubchemFingerprinterTest.java

Change-Id: I6af3cf7ab64e012c919f8ea37b32ad102177e61f
Corrected fingerprint call (difference due to patch from cdk-1.4.x)
Updated for a recent API change: added an IChemObjectBuilder

Change-Id: Ib70569f52cb9bd5a411bf9bf1d5af5a3dccf0191
Removed redundant import (not found in class path)

Change-Id: Ida1384817bba39a64296b4f41b1f3c54235ce166
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
throw an exception when a new instance of a non-interface is passed to a builder.

Change-Id: I719a589f81feb779981b9097393b8d1b5f1d10f7
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Minor JavaDoc cleanup

Change-Id: I88a234c655532bc69874ff4058142cdb3c7c9547
Introduced a new utility for computing the first shortest path and all shortest paths from a start to an end atom. This implementation replaces an existing static method in PathTools which has now been deprecated. Another helper class was added that simplifies the computation of all-vs-all shortest paths.

Conflicts:
	src/test/org/openscience/cdk/modulesuites/McoreTests.java

Change-Id: Ia6df8b06f3ac199be7ffe16c85c436da35656588
Improved terminology in javadoc and added @cdk.githash to production classes.
Corrected constructor visibility
Variable/method renaming and copyright update