Graph View - Step-by-Step and Automatic Analyses

Graph View displays all pathways proposed for your target in one common graph. This can be very useful for quickly assessing the overall diversity of your pathways, or for checking if certain reactions or molecules appear in multiple pathways.You can access Graph View by clicking on the ‘Graph’ tab on the top right of your screen.

In Graph View, molecules and reactions are represented by color-coded, round and diamond nodes, respectively. See the “Graph View Legend” section below for more details. 

There are three distinct ways to view the graph: Force, Dagre, and Polar.

Force

Dagre

Polar

You can move the graph using your mouse to drag it in any direction. Zoom in and out using the controls at the lower right of the screen or your mouse wheel. Click the ‘Reset’ icon to return the view to center.

Hover over or click any molecule or reaction node to highlight the pathway it belongs to and open a pop-up window showing the molecule structure or reaction scheme, respectively. The pop-up window allows you to access the reaction or molecule card. (See “Molecule Cards” or “Reaction Cards” for more details.)

>> Molecule Cards
>> Reaction Cards

Hover over any colored reaction arrow to see a label indicating whether the reaction is nonselective or diasteroselective only (red arrows), or whether it is suggested as part of a Strategy or Power Search option (green arrows). 

Graph View Legend

Click the ‘Legend’ icon to open a panel which shows the color-coding of molecule and reaction nodes.

Accessibility and Availability

Accessibility and Availability icons can be turned on/off by opening the Graph View Settings panel and checking/un-checking the accessibility and availability options.

Accessibility icons label target, commercial, published, and unknown compounds for increased visibility.

Availability icons label molecules that are commercially available on SigmaAldrich.com

Graph View Settings

In the Settings panel, you can add diverse labels to molecule and reaction nodes, resize molecule nodes according to the value of one of their properties, or color reaction nodes and arrows.

Molecule Node Labels

Select labels for molecule nodes.

Options

• None
• CAS number
• Name
• Formula
• Molecular weight
• Compound price
• Popularity measure
• Mass per gram of target
• Cost or popularity 

Molecule Node Sizing

Select parameter for molecule node size.

Options

• Default (selected by default)
• Molecular weight
• Compound price
• Popularity measure
• Mass per gram of target

Reaction Arrow Color

Select parameter for reaction arrow color. 

Options

• None
• Non-selective and diastereoselective-only
• Power search, strategies
• Non-selective and diastereoselective-only, power search, strategies (selected by default)

Note: For the last option, non-selectivity is displayed over tunnels or strategies in case of overlap.

Reaction Node Labels

Select label for reaction nodes. 

Options

• None (selected by default)
• Retrosynthesis ID

Accessibility

Molecule nodes are labelled as target, commercially available, known, or unknown.

Availability

Molecule nodes available through sigmaaldrich.com are marked with a green tick.