GraphemeTM TK 1.3.5

New features

  • A new function, OERenderUnpairedInteractionMap, has been added to visualize clash and unpaired interactions.

    Examples of visualizing clash and unpaired interactions

    PDB: 1S2A

    PDB: 3K6L

    ../../_images/pdb1s2a-unpaired.svg ../../_images/pdb3k6l-unpaired.svg
  • OERenderActiveSite now depicts covalent and cation-pi interactions.

    Examples of depicting covalent and cation-pi interactions

    PDB: 5WQX

    PDB: 3ARW

    ../../_images/complex2img-pdb5wqx-optimized.svg ../../_images/complex2img-pdb3arw-optimized.svg
  • The style for depicting stacking interactions has been simplified.

    Examples of stacking interaction depiction




    ../../_images/complex2img-stacking-t-2017-Oct.png ../../_images/complex2img-stacking-pi-2017-Oct.png


    ../../_images/complex2img-stacking-t-2018-Feb.png ../../_images/complex2img-stacking-pi-2018-Feb.png
  • The color scheme used to visualize interaction types when depicting protein-ligand interactions has been updated to accommodate the two new interaction types.


    New interactions color scheme

  • A new method, OE2DActiveSiteDisplay.IsValid, has been added that is checked by all Grapheme TK API points.

  • The OEResidueSVGStandardMarkup class now takes a separator option.

  • The following API, introduced in the 2017.Jun release for marking up residue circles in SVG images generated by the OERenderActiveSite function, is no longer preliminary and is now also available in both Java and C#:

Minor bug fixes

  • The algorithm used by the OE2DActiveSiteDisplay function to scale and position residues around ligands has been improved.

  • OERenderActiveSite is now able to generate images when some ligand atoms have identical 2D coordinates.

  • OERenderActiveSite now throws a warning if an interaction cannot be rendered.

Java-specific changes

  • The API for marking up residues in SVG images is now fully supported in Java (see the list above).

C#-specific changes

  • The API for marking up residues in SVG images is now fully supported in C# (see the list above).