Fragments extracted by eMolFrag are outputed as Bricks and Linkers 



output-brick/: brick fragments after removing redundancy

  • Brick example
    • The auxiliary information included in brick SDF files : These sections are added in order to store the information of the bonds that are broken to generate the fragment and to collect data about molecules that carry similar bricks. These sections can be useful for reconnecting the fragments and to perform statistical analysis. The graph-based chemical synthesizer, eSynth in particular requires this data to generate molecules.
      • ATOMTYPES : The atom types, which is missing in the SDF format but is available in the MOL2 is appended in the order of the appearance of the atoms in the coordinate section.
      • BRANCH @atom-number eligible-atmtype-to-connect : An atom number is followed by a list of atom types. Every bond that is broken to generate a brick is stored in this section. First column is the atom number and the following columns include all the atoms that were observed to be connected to the atom in the fragment. For example, in the brick fragment shown below, the sixth atom which is an N.3 was disconnected from a C.3 atom.
      • fragments similar : After removing redundancy, only one record for each fragment is stored but the name of the molecules that contained the same fragment are recorded. Using this section, one can calculate the most and least frequent fragments or track back to find the molecules that contain a fragment of interest.

output-linker/: linker fragments after removing redundancy

  • Linker example
  • The auxiliary information included in Linker SDF files : Only one section is added to the SDF file to show the atom type and number of bonds that were dissociated to extract the linker.
    • MAX-NUMBER-Of-CONTACTS ATOMTYPES : The first column in this section shows the maximum number of observed connections at every atom following the original order of atoms in the linker's sdf file. The atom type is mentioned in the second column. For example, the second line in this section in the linker fragment shown in the figure below, "1 C.3" means that the second atom is a C.3 and it can connect 1 other atom at most.

Output format selection: eMolFrag provides three options to control the format of the output. The tables below show the different output folders/files and their corresponding descriptions.




© Michal Brylinski
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