Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Section
Column
width70%

Abbreviated groups are stored in a TAB-delimited text file called default.abbrevgroup. The basic format is:

    Ac	CC=O	2
    AcAc	CC(=O)CC(=O)	5
    Acet	CC=O	2
    Ade	NC1=C2N=CNC2=NC=N1	6	1
    J	C*.CCC[C@H](N)C=O |r,m:1:3.4|	7	8

 

Warning

Please make sure the words are separated by TAB characters not by spaces.

Column
width30%
Panel

Codename: abbrevgroup

Panel
titleSee also

CXSMILES and CXSMARTS

In these lines the very first word is the abbreviation, the second is the CXSMILES string representing the molecule fragment depicted by the abbreviation. These are followed by the attachment atom numbers (in the CXSMILES string). In the first line using the Ac abbreviation the second carbon is the attachment atom so if we have a connection to an other molecule part then this atom will make the connection. If there is no number following the the CXSMILES string the abbreviated group can not be connected to other atoms. (However their number is not limited too since Marvin 6.0.)

...

For developers who are developing based on the MarvinBeans library, or who are using the Marvin Applets package, it is possible to extend the abbreviated group list via files that can be defined for usage in MarvinSketch with the help of the customAbbrevGroups parameter.