Toolkit Development Platform

OEDepict TK

OEDepict TK

OEDepict TK offers rapid 2D coordinate generation and artful rendering of chemical structures. 2D coordinates can be generated from connection tables (e.g. SMILES) or 3D structures. Multiple image file formats are supported including:

  • PNG (Portable Network Graphics)
  • PDF (Portable Document Format)
  • SVG (Scalable Vector Graphics)
  • Postscript
  • Encapsulated PostScript

In addition to standard depiction routines, OEDepict TK provides a powerful
graphics engine which supports:

  • Basic shape drawing
  • Highly customizable molecule depiction
  • Variety of highlighting styles
  • Customizable layout options (including grids and multi-page formatting)
  • Depictions aligned by MCS or substructure
  • MDL Query and MDL Reaction depictions
For more detailed information on OEDepict TK, check out the links below:


 Documentation   >   Evaluate
Process of molecule depiction.
Process of molecule depiction.
Example of various depiction styles.

Example of various depiction styles.

Example of highlighting styles available in OEDepict.

Example of highlighting styles available in OEDepict.

oeprepare-aligned-depiction.jpg

Example of molecule alignment based on MCS. The single bonds of the fit molecule are rotated to maximize its overlap with the reference structure.

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all of the OpenEye applications and remaining toolkits are built. The Cheminformatics suite is a collection of seven individual yet interdependent toolkits that are described in the table below.

  Toolkit Major Functionality
  FastROCS TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
  OEChem TK Core chemistry handling and representation as well as molecule file I/O
  OEDepict TK 2D Molecule rendering and depiction
  Grapheme™ TK Advanced molecule rendering and report generation
  GraphSim TK 2D molecular similarity (e.g. fingerprints) 
  Lexichem TK  name-to-structure, structure-to-name, foreign language translation 
  MolProp TK Molecular property calculation and filtering 
  Quacpac TK Tautomer enumeration and charge assignment
  MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics

 

Modeling

The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can therefore be used to create new or extend existing functionality associated with those applications.

  Toolkit Major Functionality
  OEChem TK Core chemistry handling and representation as well as molecule file I/O
  OEDocking TK Molecular docking and scoring
  Omega TK Conformer generation
  Shape TK 3D shape description, optimization, and overlap
  Spicoli TK Surface generation, manipulation, and interrogation
  Szmap TK Understanding water interactions in a bind site
  Szybki TK General purpose optimization with MMFF94
  Zap TK Calculate Poisson-Boltzmann electrostatic potentials