16 years of the Chemistry Development Kit (CDK)
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A talk at the Molecular Informatics Open Source Meeting (MIOSS) at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, Cambridge, United Kingdon
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16 years of the Chemistry Development Kit (CDK)
- 1. 16 Years of the Chemistry Development Kit (CDK) Christoph Steinbeck and the CDK Developers
- 2. http://cdk.sourceforge.net The Chemistry Development Kit (CDK) Open Source Cheminformatics in Java
- 3. The CDK after 16 years •16,521 commits made by 115 contributors •564,171 lines of code •mostly written in Java •well established, mature codebase •maintained by a large development team •with stable Y-O-Y commits •estimated 151 years of effort (COCOMO model) •first commit in October, 2000 •most recent commit 1 day ago The Chemistry Development Kit (CDK) Open Source Cheminformatics in Java
- 4. A bit of history
- 5. 1990
- 7. Computer-Assisted Structure Elucidation (CASE) Steinbeck, C.; Angewandte Chemie. International Ed. in English 1996, 35, 1984-1986 Steinbeck, C.: J. Chem. Inf. Comput. Sci. 2001, 41, 6, 1500 1992 - now
- 8. A bit of history
- 10. Bibliometrics
- 15. Build your own Blue Obelisk
- 16. The Doctor Who Model of Open Source
- 17. The Doctor Who Model of Open Source Egon Willighagen
- 18. The Doctor Who Model of Open Source Rajarshi Guha Egon Willighagen
- 19. The Doctor Who Model of Open Source John May Rajarshi Guha Egon Willighagen
- 20. Development Model • Open Source Principles • Release Early, Release Often • All the Raymond stuff (Cathedral … • Persistance • People contribute what they need • You need a Doctor Who who cares • code quality, build systems, etc
- 22. • Maven describes how a project is built and it’s dependencies. • Simplifies both building from source or linking a distributed JAR. • Dependencies are dynamically downloaded and kept in sync. • “Convention over configuration” • Many new Java projects choose Maven, CDK is 15+ years old this was a challenge. • Splitting a one source tree into 76 interdependent modules. • Modularisation started by Egon Willighagen modularisation in Ant. • Test Fail=Build Fail, Required resolving 150+ existing regressions. • CDK 1.5.10+ available from The Central Repository a geographically distributed collection of dedicated servers. Maven Switch Over tinyurl.com/cdk-mavencentral
- 23. 1.5.x: Cleaner, More Efficient, More Robust, More Stable Example: Generate depiction of a molecule. 1.4.x 1.5.x + Improved Layout + Improved Render + Easy highlighting + Abbreviations
- 24. Try it: http://cdkdepict-openchem.rhcloud.com/ Error 1.4.x1.5.x Examples 1-4: Clark A, et al, 2D structure depiction. JCIM, 46, 1107-1123 (2006) 1.5.x: Cleaner, More Efficient, More Robust, More Stable Molecule 2D layout and rendering from SMILES
- 25. Try it: http://cdkdepict-openchem.rhcloud.com/ 1.4.x 1.5.x 1.5.x +abbr +colmap Reaction: Lowe, D. Extraction of chemical structures and reactions from the literature. PhD Thesis. 2012 1.5.x: Cleaner, More Efficient, More Robust, More Stable Reaction 2D layout and rendering from SMILES
- 26. CHEMBL590010 (ChEMBL website) CHEMBL590010 (from SMILES with CDK 1.5.x)
- 27. Example: SMARTS match for intramolecular Hydrogen Bonds: O=[C,N]aa[N,O;!H0] in NCI Aug00 (~250,000 molecules) [1-3] 1.4.x: 16 mins (64 err) 1.5.x: 16 secs (0 err) + Lazy algorithm + Stereochemistry Match + Component Grouping + Adaptive (e.g. ring membership only if needed) + New Pattern API, hides differences between SMARTS/Substructure/ Isomorphism queries 1.5.x: Cleaner, More Efficient, More Robust, More Stable [1] Weininger D. Chemistry Cartridge CGI Examples. EMug (1998) [2] Sayle R. Cheminformatics Toolkits: a personal perspective, RDKit UGM (2012) [3] May J. All The Small Things. http://efficientbits.blogspot.co.uk/2013/10/
- 28. Robustness CDK 1.5.x moves away from default atom type perception/sanitisation. + Much faster + High fidelity IO: round trip [CH2] though SMILES/InChI/Molfile + Exact Kekulization + Exact ring perception + Portable canonical Kekulé SMILES + Multiple aromaticity models, “Horse for courses” + Accurate MMFF94 partial charges Stability Java APIs can be more fluid than native: aim to keep public API fixed. Continuous integration and regression testing with Jenkins and Travis. 1.5.x: Cleaner, More Efficient, More Robust, More Stable
- 29. Stereochemistry Tetrahedral, CisTrans, Extended Tetrahedral (Allene) Representation and round tripping between formats Query Matching Perspective conversion (Haworth, Chairs, Fischer) File Formats Molfile Sgroup support: Repeat Units, Display Shortcuts CXSMILES Coming soon: HELM 2.0 Fingerprints Count fingerprints Efficient Circular Fingerprint and Model Building Clark et al. JChemInf. 6:38 (2014) Coming soon: FPS readers, mmap indexes Updated and Super Quick Fundamental Algorithms Ring Finding - May and Steinbeck. JChemInf. 6:3 (2014) Subgraph Isomorphism Canonical labelling Aromaticity Kekulization Molecular Hash Codes, Automorphism Group, and much more Other Features of 1.5.x
- 30. Acknowledgement • All CDK developers • The Blue Obelisk Community • You for your attention