Additional reaction arrow types.

[johnmay]

Here we add in some extra arrow types which are controlled by the "direction" attribution on the reaction. I was considering a separate enum (ArrowDisplay?) but it fits more or less into the existing direction attribute.

To paraphrase Oprah, "You get an arrow, you get an arrow, you get an arrow!"

Note the RETERO_SYNTHETIC arrow swaps the sense of reactant/product. I think that makes sense but happy to discuss.

SVG

NO_GO

RETRO_SYNTHETIC

BIDIRECTIONAL (restyled)

RESONANCE

PNG

NO_GO

RETRO_SYNTHETIC

BIDIRECTIONAL (restyled)

RESONANCE

Demo Code

SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IReaction reaction = smipar.parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]");

Abbreviations abbreviations = new Abbreviations();
abbreviations.add("[Al+3].[Cl-].[Cl-].[Cl-] AlCl3");
abbreviations.add("ClCCl DCM");
abbreviations.setContractToSingleLabel(true);
for (IAtomContainer mol : ReactionManipulator.getAllAtomContainers(reaction))
    abbreviations.apply(mol);

reaction.setDirection(IReaction.Direction.NO_GO);
new DepictionGenerator().depict(reaction)
                        .writeTo("/tmp/nogo.svg");

reaction = smipar.parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]");
reaction.setDirection(IReaction.Direction.RETRO_SYNTHETIC);
new DepictionGenerator().depict(reaction)
                        .writeTo("/tmp/retro.svg");

reaction.setDirection(IReaction.Direction.BIDIRECTIONAL);
new DepictionGenerator().depict(reaction)
                        .writeTo("/tmp/bidirectional.svg");

reaction = smipar.parseReactionSmiles("c1c(Cl)cccc1[N-][N+]#N>>c1c(Cl)cccc1N=[N+]=[N-]");
reaction.setDirection(IReaction.Direction.RESONANCE);
new DepictionGenerator().depict(reaction)
                        .writeTo("/tmp/resonance.svg");

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