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 5.1.3 or newer– Requires Pipeline Pilot 6.1.1 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 1.3Maximum 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_<date>.txt" in the “<user_home>\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.

Resources

• Download:– http://www.chemaxon.com/integration/download.html– http://accelrys.org/pipelinepilot/chemistry.html

• Technical support forum:– http://www.chemaxon.com/forum/forum88.html

• E-mail:– dorant@chemaxon.com

Find out more

• Product descriptions & linkswww.chemaxon.com/products.html

• Forumwww.chemaxon.com/forum

• Presentations and posterswww.chemaxon.com/conf

• Download

www.chemaxon.com/download.html