JOHN MAYFIELD EGON WILLIGHAGEN CHEMISTRY DEVELOPMENT KIT V2.0
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1 JOHN MAYFIELD EGON WILLIGHAGEN CHEMISTRY DEVELOPMENT KIT V2.0 CINF 64: ACS Fall 2017, Washington, D.C.
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3 INTRODUCTION HISTORY Project started in contributors, key people: Christoph Steinbeck, Egon Willighagen, Dan Gezelter, Rajarshi Guha Originally based on Christoph s compchem (1997) Lineage in Compute Assisted Structure Elucidation
4 INTRODUCTION ABOUT ME Joined CDK Project 2012 During Cheminformatics for Genome-Scale Metabolic Reconstructions BBSRC-CASE (Unilever) funded PhD At NextMove Software since Oct 2014 Thesis:
5 INTRODUCTION CDK IN ACTION Stephan Beisken (EMBL-EBI). KNIME-CDK: Workflow-driven cheminformatics. Rajarshi Guha (Indiana/NIH). RCDK: Chemical Informatics Functionality in R Chun Wei Yap (National University of Singapore), PaDEL-descriptor: molecular descriptors and fingerprints Ola Spjuth, Bioclipse: Workbench for life science Kazuya Ujihara, NCDK:.NET port TU Dortmund, Scaffold Hunter: Visual analysis of large and complex data sets IDEA consult Ltd. AMBIT: open-source cheminformatics data management Scooter Moris (UCSF), chemviz2: Cheminformatics Plugin for Cytoscape Pistoia Alliance, HELM 2.0: Hierarchical Editing Language for Macromolecules NextMove Software Ltd. Casandra: Real time alerting server for Electronic Lab Notebooks Kevin Lawson (Syngenta), LICSS System (excel-cdk): MS Excel Integration Edmund Duesbury (University of Sheffield), et al. MCS-based Data Fusion in Similarity Searching etc
6 INTRODUCTION THIS TALK Key improvements and innovations in 2.0: Speed many core algorithms replaced or optimised Quality correctness of results These two today Robustness tolerance and recovery to unexpected input Testing continuous integration of passing 20,000+ test Future plans - what s missing
7 FEATURES - STEREOCHEMISTRY STEREOCHEMISTRY I Disparate support pre 2.0 Central representation SMILES 2D molfile CML IStereoElement InChI 0D molfile 3D molfile Image: E Willighagen et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminf (2017) 9:33
8 FEATURES - STEREOCHEMISTRY STEREOCHEMISTRY II Substructure matching SMARTS [C@,Si@@] [!@!@@] Haworth, Chair, and Fischer projections Image: E Willighagen et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminf (2017) 9:33
9 FEATURES - IO SMILES Memory footprint matters Daylight CIS databases could keep SMILES in memory Most toolkits ~ same per molecule SDfile SMILES CDK RDKit OB Babel NCI Aug KB KB 14.9KB 12.1KB ChEMBL KB KB 20.6KB 16KB emolecules KB 8.7KB 13.8KB
10 FEATURES - IO SMILES Beam sub-library for SMILES (github.com/johnmay/beam) Very fast parser and generator Kekulization algorithms Benchmark Input FMT Skipped Elapsed Per Min Skipped Elapsed Per Min Improve Count Heavy ChEBI 149 ChEMBL 22.1 smi s 108.2K sdf s 355.4K smi 0 8m39.3s 193.9K sdf 0 3m17.29s 510.4K
11 FEATURES - IO SMILES Beam sub-library for SMILES (github.com/johnmay/beam) Very fast parser and generator Kekulization algorithms Benchmark Input FMT Skipped Elapsed Per Min Skipped Elapsed Per Min Improve Count Heavy ChEBI 149 ChEMBL 22.1 smi s 108.2K s 2.9M sdf s 355.4K 25 3s 854.1K 2.4 smi 0 8m39.3s 193.9K s 9.4M sdf 0 3m17.29s 510.4K s 1.9M 3.7
12 FEATURES - IO CTFILE SGROUPS Annotation layer over part of a structure Round-trip via ChemAxon Extended SMILES 75% 25% Display Shortcut Polymer Mixture Data Gushurst et al. The substance module: the representation, storage, and searching of complex structures. J. Chem. Inf. Comput. Sci. (1991) Blanke G. Sgroups Abbreviations, Mixtures, Formulations, Polymers, Structures with Statistical Distribution and Other Special Cases. Online - StructurePendium Technologies GmbH
13 FEATURES - IO/DEPICTION SGROUP LAYOUT AND RENDERING Generated from ChemAxon Extended SMILES (CXSMILES): US 2007/ (I) US 2017/ A1 (Synthetic scheme 5) Praline, NextMove Software Ltd John May, et al. Sketchy Sketches: Hiding Chemistry in Plain Sight. Seventh Joint Sheffield Conference on Cheminformatics. 2016
14 FEATURES - DEPICTION LAYOUT AND RENDERING ERROR 2.0 Try it: Examples 1-4: Clark A, et al, 2D structure depiction. JCIM, 46, (2006)
15 FEATURES - DEPICTION REACTION DIAGRAMS Try it: Alex Clark. Rendering Molecular Sketches for Publication Quality Output. Molecular Informatics. 2013
16 FEATURES - DEPICTION DEPICTION API
17 FEATURES - RINGS RING PERCEPTION Rewrote and optimised: Membership - fundamental Cycle basis (SSSR, Elementary Cycles, Relevant Cycles) All Rings - useful for delocalising rings
18 FEATURES - RINGS RING PERCEPTION II Stress test Was 73 seconds Now seconds Efficient Bits
19 FEATURES - RINGS RING PERCEPTION II Benchmark Input FMT Skipped Elapsed Per Min Skipped Elapsed Per Min Improve Membership SSSR All Rings ChEBI 149 ChEMBL 22.1 ChEBI 149 ChEMBL 22.1 ChEBI 149 ChEMBL 22.1 smi s 106.3K sdf s 294.2K smi 0 8m45.78s 191.5K sdf 0 4m12.01s 399.6K smi s 88.9K sdf s 216.4K smi 0 12m4.62s 139K sdf 0 7m9.58s 234.4K smi s 53.8K sdf s 70.1K smi 88 12m40.2s 132.5K sdf 90 8m5.64s 207.4K
20 FEATURES - RINGS RING PERCEPTION II Benchmark Input FMT Skipped Elapsed Per Min Skipped Elapsed Per Min Improve Membership SSSR All Rings ChEBI 149 ChEMBL 22.1 ChEBI 149 ChEMBL 22.1 ChEBI 149 ChEMBL 22.1 smi s 106.3K s 2.3M sdf s 294.2K s 823.9K 2.8 smi 0 8m45.78s 191.5K s 5.9M sdf 0 4m12.01s 399.6K 0 1m6.54s 1.5M 3.79 smi s 88.9K s 1.7M sdf s 216.4K s 677.8K 3.13 smi 0 12m4.62s 139K s 3.7M sdf 0 7m9.58s 234.4K 0 1m8.17s 1.5M 6.3 smi s 53.8K s 1.9M sdf s 70.1K s 730K smi 88 12m40.2s 132.5K s 4M sdf 90 8m5.64s 207.4K 0 1m5.68s 1.5M 7.39
21 FEATURES - STRUCTURE SEARCHING STRUCTURE MATCHING I Previously MCS based UniversalIsompormismTester Reaction SMARTS (substructure queries) New lazy Pattern API
22 FEATURES - STRUCTURE SEARCHING STRUCTURE MATCHING II Counting automorphisms Structure Matched UIT SMSD Ullmann VentoFoggia n t (s) t (s) t (s) t (s) ferrocene (n=180?) fullerene C (n=1) fullerene C70 60 n/a 9.8 (n=1) fullerene C n/a n/a n/a Roger Sayle, Efficient matching of multiple chemical subgraphs. 9 th ICCS, Noordwijkerhout, 2011 Efficient Bits,
23 FEATURES - STRUCTURE SEARCHING STRUCTURE MATCHING II Find O=[C,N]aa[N,O;!H0]in NCI Aug 00 (250K) Death by a thousand paper cuts - majority of gain from overheads (String finding, aromaticity, SMILES) Version Matched Errors Time (Machine A) Time (Machine B) , s 860 ms , s 725 ms 1.5.4a 11, s 639 ms 1.5.4b 10, s 713 ms 1.5.4c 10, s 18 ms 8 s 126 ms , s 446 ms Improvement from last slide D Weininger. Chemistry Cartridge CGI Examples. EMug 98 Efficient Bits,
24 FEATURES - FINGERPRINTS FINGERPRINTS Benchmark Input FMT Skipped Elapsed Per Min Skipped Elapsed Per Min Improve Path Fingerprints MACCS 166 Circular Fingerprint ChEBI 149 ChEMBL 22.1 ChEBI 149 ChEMBL 22.1 ChEBI 149 ChEMBL 22.1 smi m38s 24.9K s 236.9K 9.53 sdf 0 2m11.03s 19.6K s 196.6K smi 0 42m56.15s 39.1K 9 6m34.67s 255.2K 6.53 sdf 0 47m5.58s 35.6K 0 7m52.32s 213.2K 5.98 smi h37m35s s 124.8K sdf 48 1h44m17s s 120.6K smi h24m57s 1.4K 9 13m31.21s 124.1K 90.6 sdf h41m46s 1.1K 0 13m26.41s 124.9K smi 0 NA s 557.4K sdf 0 NA s 376.2K smi 0 NA - 9 2m43.45s 616.1K sdf 0 NA - 0 3m42.01s 453.6K Circular Fingerprint - Clark A, et al. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0. J. Cheminf (2014) 6(1):38
25 SUMMARY FUTURES New connection table implementation (in progress) Minor write performance trade-off, major read performance gain (see blog) More types of stereochemistry (in progress) Complete: Atropisomerism Planned: Square-Planar, Octahedral, etc Maybe: Enhanced stereochemistry? Structure Transforms (SMIRKS) Currently provided by AMBIT 3D Coordinate Generation - Can you help?
26 SUMMARY CONCLUSIONS Many improvements in CDK 2.0 Performance now competitive with commercial toolkits Relative comparisons are deceptive Progress required Robustness APIs - some still very complex/convoluted Training materials Push performance even further
27 ACKNOWLEDGEMENTS CDK Project Egon Willighagen Christoph Steinbeck Stephan Beisken Venkata Chandrasekhar Nainala Rajarshi Guha All CDK Contributors and Users Discussions/Papers Roger Sayle (NextMove Software) Noel O Boyle (NextMove Software) Daniel Lowe (MineSoft) Alex Clark (CDD)
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