Yes, it is possible to align molecules in StarDrop. To do this, select Align 2D Diagrams from the Data Set menu and sketch a substructure in the desired orientation.

Alternatively, you can right-click and select paste SMARTS or select the molecule you want to use to define the desired orientation in the data set table.

When you click the Align button, any molecules in the data set with a matching substructure will be aligned into the same orientation by performing a rigid rotation.

It is possible to define multiple substructures to use for matching by defying Atom, Bond or Bond Path Constraints by selecting the Constraints menu.

For more information visit 2D structure alignment.

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