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>
Atoms are not added to IQueryAtomContainer causing an index out of bounds exception downstream. Adding the atoms fixes the issue.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Avoid erroneous aromaticity due to abnormal valence.

Change-Id: I4abbb2e203c07c2dbec27dfb0090d20e06e49a64
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Beam 0.5. - resolve a bug that would randomly fail when configuring double-bond stereochemistry (found from the new random order of IStereoElement sets). - parse tetrahedral selenium and sulphur cations (okay according to inchi tech manual) - parser arbitrary labels in bracket atoms - they are never generated output but instead placed in the ‘label’ of a pseudo atom if one wants to handle them.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Arbitrary labels in SMILES bracket atoms. The label is set in the pseudo atom.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity information is lost on descriptor execution unless the 'aromaticity parameter' is set to true. Already perceived -- pre-perceived -- aromaticity information should not be lost automatically if this parameter is set to false. Perception of unset parameters only via the helper method in the AtomContainerManipulator rectifies this issue. Three test cases: 1) Benzene with pre-perceived aromaticity and no aromaticity perception in the descriptor. 2) Benzene with no pre-perceived aromaticity and no aromaticity perception in the descriptor. 3) Benzene with no pre-perceived aromaticity and perception in the descriptor.

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