Transcript Pipeline Pilot Integration Szilard Dorant Solutions for Cheminformatics The Component Collection: Quick facts • Provides access to ChemAxon tools from Pipeline Pilot • Free of.

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, atomand 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
Maximum freedom trough Chemical Terms
Expressions for the expert user
• 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
Improved error reporting
From 1.3, upgraded in 1.5
• 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.
Reactor
Upgraded in 1.4
Improvements:
• 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
Options:
• 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)
New in 1.4
Markush Enumeration
Enumeration of generic structures
• 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)
New in 1.5
Tautomerization
Component for tautomer generation
• 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
New in 1.5
MolConverter
“Swiss army knife” for molecular format conversion
• Input and output can either be
– File
– Property
– Pipeline Pilot Molecule
• Specified input format or autodetection
• 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 in 1.5
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:
– [email protected]
Find out more
• Product descriptions & links
www.chemaxon.com/products.html
• Forum
www.chemaxon.com/forum
• Presentations and posters
www.chemaxon.com/conf
• Download
www.chemaxon.com/download.html