Handle annotations bound to AtomSymbols.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Some aesthetic tweaks to parameters and annotation vector calculation.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Simple method for indicating an annotation should be italic. This needs to be an attribute of the annotation and not a general rendering parameter as annotation styles may be mixed.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow the bond generator to add annotations also.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Midpoint calculation and call new annotation methods from static context. This will simplify the annotation of bonds.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Generation of bond annotations.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Make unit tests assertions relative allowing them to pass independent of the OS. Two unit tests needed to be ignored as they were testing exact values which differ between systems.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Make tests OS newline independent.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Partition extended tetrahedral elements

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
In memory identity template library.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
2D identity templates created from ChEBI 118. Tools are in 'cdk-build-util' but not committed yet (depend on this patch).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Utility to create skeleton copies of molecules. These are normalized representations when every except the element type is removed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Use the ring templates in the SDG.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow users to turn off identity templates.

Change-Id: Ic2a7ae4da788d5d491df84406e6d672dc2c99ff9
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Subtle bug, the provision of a start vector means chains were not being placed horizontal. By setting the default bond vector as static we can check if the caller has really provided a vector to use. If the default was provided we can now still place the chain horizontal.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Include hydrogens when counting degree. In practice this means carboxylic groups are always placed with the carbonyl pointing up or down when at the end of a chain.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Hydrogen count needs to be set for test.

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