Clean 2D

    Action performs automatic two-dimensional atom coordinate calculation. The following clean options can be specified:

    • Partial: Calculates coordinates for new/changed atoms and preserves original atom coordinates where possible. (clean2d) (default)

    • Full: Recalculates all atom coordinates. (clean2d:full)

    • Remove Z-Coordinate: Sets the z-coordinate of the molecule to zero. (clean2d:removezcoordinate)

    • Template based: It recalculates atom coordinates according to a set template file. Template file is specified in the TemplateFile attribute. If the template molecules are not in 2D, they are cleaned in 2D upon startup. Template based clean is performed in the following way: templates are searched in the target molecule in the order as they are given in the template file. The first matching is processed: template atom coordinates are copied to the corresponding target atoms and the remaining atoms are cleaned with partial clean. See some complex structures processed with template based cleaning below. (clean2d:<template file>)

      Example :

      Action Input Output
      Partial Clean (clean2d) images/download/attachments/1803690/cleanpartial_in.png Partial clean input images/download/thumbnails/1803690/cleanpartial_out.png Partial cleaned molecule
      Full Clean (clean2d:full) images/download/attachments/1803690/cleanpartial_in.png Partial clean input images/download/attachments/1803690/cleanfull_out.png Full cleaned molecule
      Remove Z-Coordinate Clean (clean2d:removezcoordinate) images/download/attachments/1803690/cleanflatten_in.png Remove Z Coordinate input images/download/attachments/1803690/cleanflatten_out.png Remove Z Coordinate input
      Template Based Clean (clean2d:<template file>) images/download/attachments/1803690/CrownEtherTemplate.png template 1 images/download/attachments/1803690/CrownEther.png crown ether images/download/attachments/1803690/CrownEtherCleaned.png crown ether cleaned
      Template Based Clean (clean2d:<template file>) images/download/attachments/1803690/PorphyrineTemplate.png template 2 images/download/attachments/1803690/Porphyrine.png Porphyrine images/download/attachments/1803690/PorphyrineCleaned.png Porphyrine cleaned
      Template Based Clean (clean2d:<template file>) images/download/attachments/1803690/BicycleTemplate.png template 3 images/download/attachments/1803690/Bicycle.png Bicycle images/download/attachments/1803690/BicycleCleaned.png Bicycle cleaned

      Note :

    • If the input is in 3D, output will be in 2D.

    • In case of SMILES input, only full clean or template based clean is available since the input has no atom coordinates originally; however, action "clean2d" is also accepted, but full clean will be performed.

    • Full clean converts all unspecified double bonds to "wiggly" representation as the IUPAC recommended representation. See also the description of Convert Double Bonds action.