Adding guava library

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using guava for the cycle perception code - note some tests changed as the initial cycles are now always returned in lexicography order.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing non-module from dependencies

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moved ILoggingTool to cdk-interfaces and AbstractLoggingToolTest to cdk-test. This allows us to remove dependency of cdk-log4j on cdk-core.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moved qsar atom descriptor PartialTChargeMMFF94Descriptor from 'cdk-builder3d' to 'cdk-qsaratomic' module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Copied MoleculeFactory (cdk-extra) to TestMolecularFactory (cdk-test-data), this will allow test-modules which depend on cdk-extra for the molecule creation to no longer depend on 'cdk-extra'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Seperated fingerprint and signature tests of tanimoto distance.

Conflicts:
	src/META-INF/test-fingerprint.libdepends

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing cdk-test-formula's dependence on cdk-extra.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allowing IOFormats to be created with a public constructor. This allows us to use the inbuilt service loader (next commit) and there is little benefit from these being singletons.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Equality testing of IChemFormatMatchers, now different instances can be created they should implement hashcode and equals.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using ServiceLoader in FormatFactory, formats is now non-static (and thread safe)

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moved PDBWriter and it's test class from cdk-io to cdk-pdb to mirror PDBReader.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Separating cdk-test-libiocml and cdk-test-io tests

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Separating out reader factory tests

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moved all tests with smiles from cdk-test-io to cdk-test-smiles

Conflicts:
	src/META-INF/test-io.devellibdepends

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moved the tests for readers in 'cdk-extra' from 'cdk-test-io' to 'cdk-test-extra'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Separated cdk-pdbcml from cdk-libiocml and created module suite for cdk-test-pdbcml.

Conflicts:
	src/main/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving tests for MDCustomizer from libiocml to the existing MDMoleculeTest.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Separating out cdk-extra from the cdk-io modules

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