Substructure Query Features

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The Substructure match displays substances that contain the structure query embedded within the chemical structure. Unless specified otherwise, the substructure must appear as drawn, and any substituent is allowed at any open atom position.


You can apply substructure query features to broaden or narrow your query:

Variable Atom


You can apply the following types of variable atoms:

  • X= any halogen

  • M= any metal

  • A= any atom except H

  • Q= any atom except C or H

  • Ak= any carbon chain

  • Cy= any cycle

  • Cb= any carbocycle

  • Hy= any heterocycle

In ChemDoodle, use the X_tool.png or A_tool.png tool (found on the same palette as R_tool.png). In CAS Draw, use the VariableAtomTool.png tool.



An R-group can contain atoms, variable atoms, or shortcuts (functional groups).

In ChemDoodle, use the R_tool.png tool (found on same palette as A_tool.png and X_tool.png). In CAS Draw, use the RgroupTool.png tool.

Unspecified Bond Type


In ChemDoodle, use the Any_Bond_tool.png tool (found on the same palette as Single_Bond_tool.png). In CAS Draw, use the UnspecifiedBondTool.png tool.

Repeating Group


  • The repeating group can include atoms, shortcuts, or variables.
  • The number of repetitions can range from 0-20.
  • There must be exactly two bonds to atoms outside the repeating group.
  • These bonds cannot join directly to Ak atoms.
  • Stereo bonds cannot be included in a repeating group.
  • Repeating groups can be adjacent to each other when connected by a bond.

In ChemDoodle, use the Repeat_tool.png tool.

In CAS Draw, use the RepeatingTool.png tool.

Variable Attachment Points


In ChemDoodle, use the VAP_tool.png tool.

In CAS Draw, use the VPAtool.png tool.

Lock Atom


In ChemDoodle, use the Lock_tool.png tool. In CAS Draw, use the LockAtomTool.png tool.

Lock Ring


In ChemDoodle, use the Lock_tool.png tool. In CAS Draw, use the LockRingTool.png tool.