printing the full ligand structure from deepfrag

Computer-Aided Drug Design at the Durrant Lab Forums DeepFrag printing the full ligand structure from deepfrag

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    • #48296 Reply
      Jong Hui Hong
      Guest

      Hi

      I’m testing deepfrag for our drug design purpose.
      It seems really useful for very fist step in drug design process

      while I’m using it as a result it produce only added fragment like below

      1 0.658789 *c1ccnc2c1C(=O)N(C)C2
      2 0.649510 *c1ncnc2c1C(C)CC2O
      3 0.647556 *c1cn(C)c(=O)c2[nH]ccc12
      4 0.644948 *c1nc2cc[nH]c2c(=O)n1C
      5 0.640279 *C1(O)C(=O)Nc2ccccc21

      when I see the program option carefully

      –full Print the full (fused) ligand structure.

      which means that I can print full ligand structure or smiles

      but when I use –full

      I got following result

      [] Error: couldn’t process mol.
      [
      ] Error: couldn’t process mol.
      [*] Error: couldn’t process mol.
      # Score SMILES
      1 0.619665 <err>
      2 0.612966 <err>
      3 0.608838 <err>
      .
      .

      what could be the problem with my running envirionment ?
      Any kind of suggestion will be appreciated

      Thanks

    • #73333 Reply
      Paulette Greenidge
      Guest

      I am experiencing the same issue. The "full" option for multiple fragments is the main benefit of the command line implementation of DeepFrag.

    • #74231 Reply
      Paulette Greenidge
      Guest

      I observed that the "full" option functions correctly if you remove a fragment (cname, rname) rather than just generate fragments to be added to a hydrogen atom, so there is a work around.

      My new issue is that the smiles from the "full" output seems to have lost the bond type information. Is there a way to fix this without manual curation ?

      Thanks

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