Set atomic numbers when creating an element from a symbol

Change-Id: Ibc96f55efb6922113e652b9ea7177390ec421199
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Tests for ChemObject compare() methods.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Object equality null-safe testing.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Required decency which is inherited from builder3d.

Change-Id: I025e14891170b9249f34a4bbf6d5323dfd4aa5d5
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromatic selenium can be parsed from SMILES. The current aromaticity perception doesn't consider Se but thats not related to SMILES parsing.

Change-Id: I88f6848775912e88f1a7f1d60634dca88970039e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Use model builder to place the test alkanes - the AtomPlacer3D is only for placing chains.

Change-Id: I554dda109a5ed5fbd6a4b015e610eb6027b08437
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Throw an exception when a non-chain is provided. Documentation was also updated.

Change-Id: I59d802abb924d328516f06f9216759bdea30dd25
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test that providing a non-chain as a chain throws an exception.

Change-Id: I4eaf8883bc7f8da7a743091b65006fdb4eea852e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Expect exception for a symbol we can't calculate the charge for - e.g. 'As' in this case.

Change-Id: Ie45700c65312c8ef2a48d3cf818a1e5f373a97b1
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Throw an exception if the symbol isn't supported.

Change-Id: Iab010551e605457f1b1120a253a7f5dcbaa500c4
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
JavaDoc error

Change-Id: I78f6b6b017a221291af9345a372e6a5c8ccda30a
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Change in exception message.

Change-Id: If71dd20d3e543657959e72f2eee9ffa865f42b54
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using the bootstrap seems to cause regressions.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Avoid set the atomic number twice. Previously invoking 'new Element("H", null)' would still set the atomic number to '1'. Chaining the constructors so that all fields are assigned in the same places avoids this problem.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated PMD from 5.0.1 to 5.0.4

Change-Id: I82bc18998f0044fdf478bad90b2529265d3adbf5