Remove Fragment

This action removes molecule fragment(s) if the chemical structure contains more than one disconnected fragments.

There are four methods to select:

  • keep the largest fragment, remove all others (method=keeplargest) (default);

  • remove the smallest fragment, keep all others (method=removesmallest);

  • keep the smallest fragment, remove all others (method=keepsmallest);

  • remove the largest fragment, keep all others (method=removelargest).

The fragment size is determined by the number of atoms (default), the molecular mass, or by the number of heavy atoms.

  • number of atoms (measure=atomcount) (default);

  • molecule mass (measure=molmass);

  • heavy atom count (measure=heavyatomcount).

Example :

Action

Input

Output

Keep Largest Fragment by Molecule Mass
("removefragment:method=keeplargest")

images/download/attachments/1803692/removefragment-keeplargest_in.png
keep largest input

images/download/attachments/1803692/removefragment-keeplargest_out.png
keep largest output

Remove Smallest Fragment by Atomcount
("removefragment:method=removesmallest:measure=atomcount")

images/download/attachments/1803692/removefragment-keeplargest_in.png
remove smallest input

images/download/attachments/1803692/removefragment-removesmallest_out.png
remove smallest output

Note : Action "removefragment" as simple action string corresponds to the default behavior, i.e., set keepLargest and atomCount options.