Missing dependency for test-qsarcml.

Change-Id: Ia7a78b07a30ba00e0f7ef730f696f4125316dd40
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolves two long standing errors in 'cdk-extra'. The method should throw an exception when one tries to attach to an invalid atom number (e.g. 7-chlorohexane). The existing error was using the ParseException constructor incorrectly and thus would throw an error. The constructor is for generating error messages to do with syntax. As this is a semantic error the constructor did not function as intended. Simply replacing the use of this constructor with a normal error message resolves the issue.

Change-Id: I896e3a3d07322e0a98f317cb331f4ebfe66f8e15
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fail test instead of throwing an exception.

Change-Id: I68ae0081117439e6d2fca3398a02ff533582084d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Exact mass and natural abundance is not preserved on reading/writing CML. As these attributes are boxed primitives they can be null and throw an exception when unboxed by 'assertEquals'. Before checking the values the attributes are not checked for nullity.

Change-Id: If6b52cf6f22d23405b8f15045d8ca1dccf0bcd74
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
When a reaction references a molecule which is unknown - automatically create one with that Id. This happens when the set of molecules is defined after the reaction. This commit resolve the test in error 'CML2Test. testBug2697568'

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using typed list and index (so we can print a better failure message).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove stdout and catch exception to fail the test instead of returning in error.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moves assertions on non-null bond length to the same loop. Also puts the getPoint3d() null test before the bond length check. If there is a null atom the bond length check will throw an NPE - better to fail on this.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolves unit test failure (previous commits). When a double bond is found and there are no 2D coordinates (e.g. unspecified configuration) then return then return '0' for the configuration value.

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