Part 2 - mainly tweaks to depiction classes (now immutable), reaction layout, and some long overdue patches to the SDG (allow it to handle fragments).

Rendering code hard to test as usual but added some for the layout updates.

Reaction Layout

Testing the removal of parts, here's the original...

CNC1=C(OCCC#N)C=CC=C1.CCCC[Sn](CCCC)(CCCC)N=[N+]=[N-].CC[Al]CC)CC>CC1=CC=CC=C1.CCOC(C)=O.O>CNC1=C(OCCC2=NN=NN2)C=CC=C1

No Agents...

Products Only...

Reactants Only...

Empty Reaction - (failed reaction)...

Agents only... it doesn't depict the arrow, actually I think that makes sense!

Atom Maps and Highlight

In the generator we turn on withAtomMapNumbers() or withAtomMapHighlight() to show the atom-mapping between reactants and products (supplied in the input SMILES).

CC1(C)CCCC(C)(C)N1.C([Li])CCC.[s:16]1[cH:20][cH:19][cH:18][c:17]1-[c:21]1[c:29]2[c:25]([n:26][s:27][n:28]2)[c:24](-[c:30]2[s:31][cH:32][cH:33][cH:34]2)[cH:23][cH:22]1.[CH3:35][Sn:36](Cl)([CH3:38])[CH3:37]>C1OCCC1.C(OCC)C.O>[CH3:35][Sn:36]([CH3:38])([CH3:37])[c:32]1[s:31][c:30](-[c:24]2[c:25]3[c:29]([n:28][s:27][n:26]3)[c:21](-[c:17]3[s:16][c:20]([Sn:36]([CH3:38])([CH3:37])[CH3:35])[cH:19][cH:18]3)[cH:22][cH:23]2)[cH:34][cH:33]1

Cl[c:2]1[c:11]2[c:6]([c:7]3[cH:15][cH:14][cH:13][cH:12][c:8]3[cH:9][cH:10]2)[n:5][cH:4][n:3]1.O1CCCC1.[Br-].[CH2:22]([Mg+])[CH:23]([CH3:25])[CH3:24].Cl>CN1CCCC1=O>[CH2:22]([c:2]1[c:11]2[c:6]([c:7]3[cH:15][cH:14][cH:13][cH:12][c:8]3[cH:9][cH:10]2)[n:5][cH:4][n:3]1)[CH:23]([CH3:25])[CH3:24]

Salt Layout

By default, the SDG now lays out fragments of a molecule in a grid. If possible it tries to (re)bond ionic fragments before doing so with temporary bonds. Here's some results:

Sodium Benzoate

AlCl3
[Al+3].[Cl-].[Cl-].[Cl-]

K2CO3
[K+].[O-]C=O[O-][K+]

CHEMBL11933 - avoids the nitro