A module for deprecated and legacy code.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Simplified access to a new aromaticity implementation that replicates the now deprecated CDKHuekelAromaticityDetector.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Replacing usage of CDKHueckelAromaticityDetector.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move old aromaticity implementations to the legacy module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving the deprecated DoubleBondAcceptingAromaticityDetector to 'cdk-legacy'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
SwissArmyKnife is not used and is moved to cdk-legacy.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
New aromaticity perception complains on unset atom types - these tests are regressions as the atom types have not been set. That is, they were silently being ignored.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity was being silently skip for these tests - adding the correct setup in now means the expected data changed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity perception was previously being skipped on initial fragmentation. Now that aromaticity is set, some expected output has changed, note the specified single bonds in SMILES.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Treat atomic number as symbol and leave set when other properties are cleared.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
To obtain correct output in the fragmenters we need to clear all existing configurations and reperceive atom types. Could be improved.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure atom types are percevied in fragmenter tests.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Default atom type is now "X" not null. This allows us to tell when something has been typed and when it hasn't.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Regressions in reaction module to new atom type behaviour. This similar code needed updating to check for untyped atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Additional classes that were expected unset set atom types.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity can not proceed on structures that have been typed but have no 'type'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Special behaviour for atom type "X" - otherwise the default values corrupt the actual information set on the atom.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Special handling of atom type 'X', leave hydrogens alone unless the value is null and we then set it to 0. Note this conditional was only added recently to ensure pseudo atoms don't have an unset hydrogen count.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Pseudo atoms are assigned atom type 'X' (already the case) by the CDKAtomTypeMatcher. These do not need to be skipped here.

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