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JChemPaint / jchempaint

Chemical 2D structure editor application/applet based on the Chemistry Development Kit
http://jchempaint.github.com
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Hydrogens on terminal hydroxyl groups are missing #188

Closed tmarti02 closed 6 years ago

tmarti02 commented 7 years ago

If I draw ethanol this is what I get: pic1

It didn't matter that implicit hydrogens were turned on in preferences.

If I select “View…Implicit Hydrogens…On All” it just makes all the “C” atoms visible and not the H on the oxygen:

pic2

johnmay commented 7 years ago

Dev note -> Fix with StandardGenerator

tmarti02 commented 7 years ago

A lot of the other preferences aren't working either- such as "show aromatic ring circles" and "draw atom numbers"

johnmay commented 6 years ago

Resolved primary problem - https://github.com/JChemPaint/jchempaint/commit/098615a6c7b50a65722900b67bbd22f1fc8b0e4c

image

StandardGenerator works but needs more testing

image

tmarti02 commented 6 years ago

Awesome thank you!!!

tmarti02 commented 6 years ago

Oddly now when chemicals are loaded from mol files, the valency is shown for each atom

image

johnmay commented 6 years ago

Can you open a separate issue, this is easy to fix just a conflict in how things used to be done vs are done now (mdl valence models etc).

johnmay commented 6 years ago

Fixed now https://github.com/JChemPaint/jchempaint/commit/46e05390c36748a84580e50539797d94611a6e51

tmarti02 commented 6 years ago

OK then you can close the issue I just created :).