【精选】RDKit_Overview.pdfVIP

RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling Greg Landrum glandrum@ Last updated: Feb. 2011 Availability • SourceForge Page: • Source code: – Browse: /viewcvs.cgi/rdkit/trunk/ – Download using subversion: svn co /svnroot/rdkit/trunk rdkit • Binaries: available for Win32 • Licensing: BSD license (except for GUI components, which are GPL) Components End User Developer • Command-line scripts • Python programming library • Python interface • C++ programming library • Database extensions General Molecular Functionality  Input/Output: SMILES/SMARTS, mol, SDF, TDT  “Cheminformatics”: • Substructure searching • Canonical SMILES • Chirality support • Chemical transformations • Chemical reactions • Molecular serialization (e.g. mol - text)  2D depiction, including constrained depiction and mimicking 3D coords  2D-3D conversion/conformational analysis via distance geometry  UFF implementation for cleaning up structures  Fingerprinting (Daylight-like, circular, atom pairs, topological torsions, “MACCS keys”, etc.)  Similarity/diversity picking (include fuzzy similarity)  2D pharmacophores  Gasteiger-Marsili charges  Hierarchical subgraph/fragment analysis  Hierarchical RECAP implementation General Molecular Functionality, cntd  Feature maps and feature-map vectors  Shape-based similarity * functional implementations, but  Molecule-molecule alignment not really recommended for use  Shape-based alignment (subshape