Remove net.sf.* classes - now in ‘cdk-build-utils’

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Incuding the utils in the classpath allows project to build correctly.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Custom taglets all work correctly including the IOOptions - the ‘cheminf.bibx’ is now duplicated in the ‘cdk-build-util’ project.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Open JavaDoc Checker now working with the doc tests in cdk-build-utils. We can also remove the compilation taglets / docchecks.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Can’t run devel.xml but this should be working correctly.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Also initialise descriptors loaded by name.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correct filtering of unique atom and bond matches. The filter now uses a new predicate for each successive iterations.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Implicit hydrogen count should always be 0 or greater.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure an exception is not thrown when a tetrahedral centre has an implicit hydrogen by the target does not. We want matching to be consistent whether the query as implicit/explicit hydrogens and so we say this is not a substructure match (with stereochemistry).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove deprecation warning - this will likely be the best way to set the parameters for SMARTS for a while.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Point to correct usage in error message

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Find all cycles up to (and including) a specified length.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Simplified creation of a custom 'fall-back' cycle finder.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removed redundant System.out statement.

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