John Mayfield comments

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                                            John Mayfield

breaking change in SeedGenerator?

Sounds good

Integration of sugar moiety removal functionality

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...

Integration of sugar moiety removal functionality

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 -...

Integration of sugar moiety removal functionality

Should just be to merge PR I sent you?

Integration of sugar moiety removal functionality

Then it's good to go

Integration of sugar moiety removal functionality

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

only return atoms within sphere=1 layer during generating HOSE code

Thanks please note hose codes are an outdated method and something like Signatures/CircularFingerprint is much better.

only return atoms within sphere=1 layer during generating HOSE code

You should be able to get the atom info from the circular fingerprint… but I need to check. Anyways the main point was you probably don’t want hose codes :)

IMolecularFormula remove

removeIsotope, but you need to find the isotope first. Something like this: ```java for (IIsotope iso : mf.isotopes()) { if (iso.getAtomicNumber() == IAtom.H) { mf.removeIsotope(iso); break; } } ``` You...

IMolecularFormula remove

Yes it is odd that you can't seem to explicitly set the count, any ideas @egonw? The going via an AtomContainer is overkill IMHO, perhaps a better question is why...