Pipeline Pilot Integration Szilard Dorant Solutions for Cheminformatics

The Component Collection: Quick facts Provides access to ChemAxon tools from Pipeline Pilot Free of charge Open source : Java sources are also included Available from ChemAxon or Accelrys Latest version : 1.5 –Released in May 2009 –Requires JChem / Marvin or newer –Requires Pipeline Pilot or newer

Available functionality (1/2) Standardizer: structure canonicalization Chemical Terms expressions for filtering and calculations (including logP, logD, pKa, HBD, HBA, Isoelectric point, PSA and more) Reactor : smart virtual reaction processing Maximum Common Substructure (MCS) based clustering IUPAC Name Molecule conversion (both directions) JChem chemical database: insertion, search and retrieval of structures; create and drop structure tables

Available functionality (2/2) Marvin applets: structure visualization and editing Major microspecies (major protonation form) Microspecies distribution Burden eigenvalue descriptor (BCUT) MolConverter: conversion of the wide range of structure formats supported by ChemAxon Markush enumeration: enumeration of Markush (generic) structures (e.g. R-groups, link nodes, atom- and bond lists and many more) Tautomerization: tautomer generation (all, dominant, major, canonical, generic)

Release history - major changes Version 1.5, May 2009 –New components: "ChemAxon MolConverter", "ChemAxon Tautomerization", "ChemAxon Markush Enumeration" Version 1.4, November 2008 –New components: "LibMCS Clustering", "Molecule to IUPAC Name", "Molecule from IUPAC Name –Major upgrade of "ChemAxon Reactor" component Version 1.3, July 2008 –New component: Chemical Terms Calculator –New, improved error reporting system Version 1.2, March 2008 –New components: ChemAxon Reactor, Drop JChem Base Table, Create JChem Base Table –Upgraded: ChemAxon Standardize, JChem Base Insert, JChemSearch, documentation upgrade for most components

Calculator Easy access for the most important calculations

Chemical Terms Calculator Use arbitrary Chemical Terms expressions Results stored to arbitrary properties A wide range of ChemAxon functionality can be accessed as Chemical Terms functions New in 1.3 Maximum freedom trough Chemical Terms Expressions for the expert user

Improved error reporting Helps to track down problems quicker, more efficient support More information is displayed in the error dialog: JChem version, the current structure, etc. An even more detailed error report including the full stack trace is appended to the file pp_error_.txt" in the \chemaxon\logs directory (new file every day). The log directory can be changed be setting the environment variable CHEMAXON_PP_LOG_DIR. From 1.3, upgraded in 1.5

Reactor Improvements: Upgraded in 1.4 Synthesis code generation Output reaction mapping Advanced options: –Unambiguous only –Ignore rules: Reactivity and Exclude Selectivity Tolerance

Combinatorial Reactor Example

IUPAC naming components IUPAC Name to Molecule Molecule to IUPAC Name Example roundtrip protocol: New in 1.4

Clustering with LibMCS Maximum Common Substructure (MCS) based clustering Size of smallest common substructure to consider Three levels of heuristics: –Exact (no heuristics) –Fast –Very Fast Bond type, atom type, charge can optionally be ignored Disallow breaking rings (default) Options: New in 1.4

File input Enumeration type: –Sequential –Random Number of enumerated structures can be limited (per input structure) Valence filter Scaffold alignment Markush code generation. The scaffold ID can be: –fetched from data field –generated (prefix + number) Markush Enumeration Enumeration of generic structures New in 1.5

Tautomerization Component for tautomer generation New in 1.5 Calculation modes: –All tautomers –Canonical tautomer –Generic tautomer –Major tautomer –Dominant tautomer distribution Options: –Protect aromaticity, charge, double bond stereo, tetrahedral stereo –Exclude antiaromatic compounds –Single fragment mode –Consider pH at specific value

MolConverter Swiss army knife for molecular format conversion New in 1.5 Input and output can either be –File –Property –Pipeline Pilot Molecule Specified input format or auto- detection Various output formats or custom format string Option to halt or continue on error, error messages put into property 2D cleaning (coordinate generation) only when needed (default). Unconditional 2D or 3D cleaning or no cleaning can also be selected

New Java class: ChemAxonComponent Parent class for component classes, implements com.scitegic.pilot.Component Error reporting: all exceptions thrown in onInitializeBody(), onProcessBody(), onFinalizeBody() are caught, logged and reported (re-thrown with added information) Parameters and context always readily available Utility functions for conveniently accessing parameters and properties, e.g.: findStringParameter(String name) Reduced code redundancy, better readability

Planned development Conformer generation Improve Molecular Table Viewer (Marvin View) JChem Cartridge for Oracle Integration with Instant JChem Documentation Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development.

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