Update troubleshooting

[mmzdouc]

Reaction SMARTS/SMILES errors

• Manually drawn tryptophans can end up without hydrogens on the indol ring, leading to "invalid SMILES" errors by RDKit
• Reactions where chiral carbons are oxidized (e.g. alpha-carbons of amino acids, specifically dehydrogenation of serin to dehydroalanine) lead to errors if the hydrogens of the alpha carbon of the product are not explicitly stated (e.g. -[#6&H0:71](=[#6:139]))