GraphemeTM TK 1.3.3

New features

  • A new function, OERenderContactMap, has been added that generates interactive SVG images. Clicking on any residue circle will highlight those ligand atoms that interact with the given residue.

click on any residue

Example of interactive SVG image generated by OERenderContactMap (PDB: 4HWR)

Preliminary API

Major bug fixes

  • Several problems in the OERenderActiveSite function have been fixed:

    • When depicting protein-ligand interactions, grey lines represent the shape of the binding pocket. The absence of lines indicates solvent-accessible regions. In order visualize the solvent-accessible areas more realistically, waters are now ignored when calculating the molecule surfaces that determine the 2D representation (compare images below).
    • The rare case where the ligand is completely surrounded by water is now handled correctly.
    • The following heuristics are now used to improve the positioning of residue glyphs around the ligand:
      • Waters are more likely to be positioned in solvent-exposed regions.
      • Other residues are only positioned in solvent-exposed regions if it results in a more visually pleasing layout.
    Example of visualizing solvent-accessible regions and water positioning (PDB: 3E3D)
    2017.Feb 2017.Jun
    ../../_images/pocket-2017-Feb.png ../../_images/pocket-2017-Jun.png

Minor bug fixes

  • OEDrawPeptide has been fixed and now allows only amide and disulfide bonds when identifying standard amino acids. No alpha-carbon substitutions are allowed.

    Example of visualizing peptides with OEDrawPeptide
    2017.Feb 2017.Jun
    ../../_images/ceruletide-2017-Feb.png ../../_images/ceruletide-2017-Jun.png

Documentation changes