Integration of sugar moiety removal functionality

[JonasSchaub]

Reference issue: #854

[JonasSchaub]

@johnmay and @egonw ,

I have put my Sugar Removal Utility into the extra module and there into the tools package. Again, I had to adjust the dependencies of the module a bit. Let me know what you think!

[johnmay]

Thanks for the updates, I'm quite busy this week/early next but will do an in depth check end of next week. Overall from first glance it looks good and should be OK to merge reasonably quickly - I added one comment about the IPseudoAtom - but Symbol=R is also OK.

[johnmay]

This one I am less fussy about but some bits are similar:

• required: use the CDK logging tool rather than the JDK Logger
• required: remove all cloning
• required: remove throws of runtime exceptions
• optional: terser variable names, 'anBlah', 'aBlah', 'tmpBlah' I just really don't like that as a style.

[JonasSchaub]

@johnmay sorry for dropping the ball on this here; I will make the requested changes soon! Thanks for the initial review.

[johnmay]

Should just be to merge PR I sent you?

[johnmay]

Then it's good to go

[JonasSchaub]

The PR you sent me is for the functional groups functionality. Good that you mention that because I haven't seen it before (incorrect "watch" settings on my fork, I'm very very sorry). Will get to that as well as soon as possible!

[johnmay]

Oh right sorry yes, moving house next week so things are all going 100kph ATM.

[JonasSchaub]

Good luck with that, hope it's going well!