Variable Aerobic Likelihood
Some rules handle a wide range of compounds, and a single aerobic likelihood is not appropriate for all of them.
Thus structure-based variable aerobic likelihood has been added to the PPS.
For aerobically likely aromatic ring monooxygenation, ring dioxygenation, ring cleavage, and ring decarboxylation rules, when the substrate contains one or more halogens, the aerobic likelihood for the transformation is changed to "neutral".
This is the first step toward better handling of aerobic likelihood.
Compare the previous predicted pathway for benzyl alcohol, with the pathway below for p-chlorobenzyl alcohol.
The aerobic likelihood for the first three transformations are likely, as above. However when the ring is oxygenated and cleaved, the aerobic likelihoods are neutral for the chlorinated compound, rather than the likely found for the non-halogen.

Drawing Structures
The PPS uses Chemaxon's MarvinSketch for drawing compounds. To draw Benzyl Alchol in the MarvinSketch
window, select the "Benzene Ring" from the lower tool bar menu. Drag the structure to the desired location in
the window and click to paste. Next select the "single bond" button from the left tool bar (for more options e.g. double bond, single
bond up, etc., click and hold the "single bond" button). With the "single bond" selected, click a corner of
the bezene ring, drag the bond in the desired direction and release to paste. With the "single bond" still
selected, click the methyl group, drag in the desired direction, and release to create a two carbon chain.
To make the compound an alcohol, select the atomic symbol for oxygen, "O", from the right menu bar. Click on the
methyl group to replace it with a hydroxide. For further information, a tutorial for using Marvin Sketch is
available at http://www.chemaxon.com/jchem/marvin/chemaxon/marvin/help/about-sketch.html.

After creating an image image in the Marvin Sketch window, a user must generate the SMILES string for that
specific compound. To generate the SMILES string, click the "Write SMILES" button located beneath the
MarvinSketch window.

The SMILES string will appear in the window directly underneath your structure.

Click on the "Continue" button to proceed to the