July 2009

Szilárd Dóránt

Scientific & technical Presentation

Pipeline Pilot Integration

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 : 1.6 (as of September 2009)

– Requires: • JChem / Marvin 5.1.3 or newer• 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)

• Conformer generation

Calculator

Easy access for the most important calculations

More on Calculator plugins

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

Maximum freedom trough Chemical Terms Expressions for the expert user

More on Chemical Terms

Standardizer

Flexible transformation / canonicalization engine

• Simple actions (checkboxes)

• Configuration string (simple or XML)

• Configuration file

More on Standardizer

Easy to use, but expert configurations are also accessible:

Molecular Table ViewerInteractive display of molecules using Marvin View applets

More on MarvinView

Chemical Terms Filter Filtering with powerful Chemical Terms expressions

More on Chemical Terms

Reactor

• Supports smart reaction rules to produce synthetically feasible products

• Sequential or combinatorial mode

• Product or reaction output

• Select products to include in output

• Use tagger components to distinguish inputs of multi-reactant reactions

• Synthesis code generation

• Output reaction mapping

• Advanced options: – Unambiguous only– Ignore rules:

• Reactivity and Exclude• Selectivity• Tolerance

More on Reactor

Virtual reaction processing

Combinatorial Reactor Example

Naming components

Example “roundtrip” protocol:

More on name recognition

Structure to name and name to structure conversion

Clustering with LibMCSMaximum 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:

More on LibMCS

• 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 EnumerationEnumeration of generic structures

More on Markush Enumeration

TautomerizationComponent 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

More on Tautomerization

Conformer generation

Component for 3D conformer generation

• Calculation modes:– Multiple conformers– Lowes energy conformer

• Options:– Maximum number of conformers– Diversity limit– Optimization limit, hyperfine option– Time limit– Generate with explicit H atoms– Energy unit kcal/mol or KJ/mol,

into arbitrary property

More on conformer generation

MolConverter“Swiss army knife” for molecular format conversion• 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

More on supported file formats

Database Connection

• Provides a convenient way to define a JDBC connection parameter set within a protocol

• Other JChem Base components refer to this parameter set by a symbolic name (e.g. “myConnection”)

• Multiple instances may be used in a protocol if needed

• Each component creates its own JDBC connection to the database according to these parameters

JChem Base Insert

• Returns cd_id (primary key) values

• Two input modes:– read structure source from a

specified property– if property not specified uses

Pipeline Pilot input molecule

• Insert into additional data fields

Inserts structures into a JChem Base table • Duplicate filtering option (using Pass and Fail ports)

More on JChem Base

• Wide range search options

• Output can be primary key (cd_id) or Molecule

JChem Database Search

Structural search in a JChem Base table

JChem Query Guide

JChem Base demo protocol

System information

Protocol for checking configuration

Displays the most important environment information in a text editor

Release history - major changes

• Version 1.6, August 2009– New component: "ChemAxon 3D Conformers"

• 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”

• Version 1.2, March 2008– New components: “ChemAxon Reactor”, “Drop JChem Base

Table”, “Create JChem Base Table”– Several components upgraded

Planned development

Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development.

• Support for JChem Cartridge for Oracle

• Improve Molecular Table Viewer (Marvin View)

• Integration with Instant JChem

• Documentation

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:– pp@chemaxon.com

• More resources:– http://www.chemaxon.com/forum/ftopic4604.html

Visit other technical presentations

MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt

MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt

JChem Base http://www.chemaxon.com/JChem_Base.ppt

JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

Standardizer http://www.chemaxon.com/Standardizer.ppt

Screen http://www.chemaxon.com/Screen.ppt

JKlustor http://www.chemaxon.com/JKlustor.ppt

Fragmenter http://www.chemaxon.com/Fragmenter.ppt

Reactor http://www.chemaxon.com/Reactor.ppt