A talk at the Molecular Informatics Open Source Meeting (MIOSS) at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, Cambridge, United Kingdon

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

9. Growth over theYears

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

21. CDK
Current status
John May

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

31. iCASE PhD
Studentships