Appendix: Selected Examples in Python
These are full listings of programming examples that are excerpted or offered for download, elsewhere in this book.
Depict Toolkit
These examples illustrate use of the Depict tools to create molecule depictions in a variety of graphical file formats. See a guide to available examples in the Depict chapter.
Docking Toolkit
Docking examples illustrate use of the Docking tools for docking and scoring molecules in the context of a protein active site. See the list in the Docking chapter for the set of examples.
FastROCS Toolkit
FastROCS examples illustrate use of the FastROCS Toolkit to make extremely fast shape comparisons. See a full list of examples in the FastROCs chapter.
Grapheme Toolkit
The Grapheme examples illustrate visualization of complex molecular interactions and properties in a clear and coherent 2D format that is the most natural to chemists. See a full list of exaxmples in the Grapheme chapter.
Graphsim Toolkit
These examples illustrate use of the Graphsim Toolkit, provides a facility for encoding 2D molecular graph information into fingerprints. For a full list of examples, see the Graphsim chapter.
MedChem Toolkit
These examples illustrate use of the MedChem toolkit, which provides facilities for fragmentation-based analysis. For a full list of examples, see the MedChem chapter.
MolProp Toolkit
These examples illustrate use of the MolProp toolkit, which provides a customizable framework for molecular property calculation geared toward enabling rapid database filtering. For a full list of examples, see the MolProp chapter.
OEChem Toolkit
These selected examples illustrate use of the OEChem toolkit, which is a powerful programming library for chemistry and cheminformatics. For a full list of examples, also see the OEChem chapter.
Omega Toolkit
These selected examples illustrate use of the Omega toolkit, which generates conformations of molecules. For a guide to programming examples, see the Omega chapter.
Quacpac Toolkit
These selected examples illustrate use of the Quacpac toolkit, which includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage. For a guide to programming examples, see the Quacpac chapter.
Saiph Toolkit
The Saiph toolkit provides facilities for converting data to different formats without changing the meaning of the data. See the Saiph chapter for a guide to programming examples.
Shape Toolkit
The Shape toolkit facilitates the calculation of molecular descriptors for shape (steric multipoles), volume overlap between molecules, and spatial similarity of chemical groups (color force field), as well as the optimization of the latter two quantities. See the Shape TK chapter for a guide to programming examples.
SiteHopper Toolkit
The Shape toolkit facilitates rapid comparison of protein binding sites. See the SiteHopper chapter for a guide to programming examples.
Spicoli Toolkit
The Spicoli toolkit facilitates creating, manipulating, and analyzing surfaces of many types. Programming examples are presented and excerpted with specific features, for example, OEMakeConnectedSurfaceCliques.
Spruce Toolkit
The Spruce toolkit facilitates preparing biomolecules (that is, proteins and nucleic acids) for modeling tasks. See the Spruce chapter for a guide to programming examples. Examples listed here are provided for download in the Spruce chapter.
Szmap Toolkit
The Szmap toolkit provides simple access to SZMAP functionality, for calculating solvent thermodynamic properties near molecular surfaces. For a guide to programming examples, see the Szmap chapter.
Szybki Toolkit
The Szybki toolkit provides facilities for force-field-based optimization and thermodynamic property estimation of small molecule ligands or protein-ligand complexes with small molecule ligands. For a guide to programming examples, see the Szybki chapter.
Zap Toolkit
The Zap toolkit Zap TK produces Poisson-Boltzmann electrostatic potentials and, from them, biologically interesting properties including solvent transfer energies, binding energies, pKa shifts, solvent forces, electrostatic descriptors, surface potentials, and effective dielectric constants. Programming examples are dispersed among the descriptions of parts of the toolkits and in the overall chapter The Way of Zap. Full listings are provided here for examples that are presented as incomplete snippets in the Zap chapters.