GENERATING AND RENDERING STRUCTURES

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

Process of molecule depiction.

Example of various depiction styles.

Example of highlighting styles available in OEDepict.

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

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 link below:

Documentation

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all the OpenEye applications and remaining toolkits are built.

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.

OEChem TK Core chemistry handling and representation as well as molecule file I/O
FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
OEDocking TK Molecular docking and scoring
Omega TK Conformer generation
Shape TK 3D shape description, optimization, and overlap
SiteHopper TK Rapid Comparison of Protein Binding Sites
Spicoli TK Surface generation, manipulation, and interrogation
Spruce TK Protein preparation and modeling
Szybki TK General purpose optimization with MMFF94
Szmap TK Understanding water interactions in a binding site
Zap TK Calculate Poisson-Boltzmann electrostatic potentials