Remove global bond length.

Change-Id: Ibe46c3ecdbf824bd972b88c65af7f2af54d7499e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Use the average bond length of the molecule.

Change-Id: Ib059077fb100b8512017df6f6d702148cac83e22
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Overlap cutoff to 1/4th average bond length rather than 1/10th.

Change-Id: I9959152fcc9b0d840c6044de70d609dc82e8ff9e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Reusing utilities for RecursiveTests

Change-Id: I06767388a19467a3614eef7847b3d0677a08bb62
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Demonstrating that the recursive mismatch of the test is due to Daylight/CDK aromatic differences - testRecursive28.

Change-Id: I260b0c4f7853bf4c9f7a5aa6547c6b1a2b20073e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Demonstrating that the recursive mismatch of the test is due to Daylight/CDK aromatic differences - testRecursive29.

Change-Id: I941a22270a034d437ac36d6d2ad803c40ea583c6
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Demonstrating that the recursive mismatch of the test is due to Daylight/CDK aromatic differences - testRecursive26.

Change-Id: I3c45286eba829036f0a051203b1260a64e52b59e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Demonstrating that the recursive mismatch of the test is due to Daylight/CDK aromatic differences - testRecursive27.

Change-Id: I2f68e3fd23637a1a5d4c706940d62b99eec7ec36
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
There are 142 lines in 'data/smiles/drugs.smi' but only 141 non-empty lines. Technically according to the OpenSMILES specification an empty string is a valid SMILES string but the current IteratingSMILESReader skips empty molecules (a good thing).

Change-Id: Iec648a7a39d7e868620623599bc80213d3442e5d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Altering assertions for what CDK perceives as aromatic.

Change-Id: Ia5996de81114e3ded907ac620955cc6031e9a66d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test that when the aromaticity is preserve the expected number matches are found.

Change-Id: I00eb477ead115dc6057e396d0e3e10d0066ad66f
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correct assertion in atomic tsar descriptor. Assertion was likely incorrect due using the number instead of the index. Using the index '12' to access atom 13 provides the expected result. The assertions were altered to test all added hydrogens - for which two are adjacent to an aromatic system.

Change-Id: I84a15de8348cb10407e91edc0cefe9462d7e0a00
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>