Pipeline Pilot Integration

Transcription

1 Scientific & technical Presentation Pipeline Pilot Integration Szilárd Dóránt July 2009 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 or newer Pipeline Pilot or newer

2 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) Conformer generation

3 Easy access for the most important calculations Calculator More on Calculator plugins Use arbitrary Chemical Terms expressions Chemical Terms Calculator Maximum freedom trough Chemical Terms Expressions for the expert user Results stored to arbitrary properties A wide range of ChemAxon functionality can be accessed as Chemical Terms functions More on Chemical Terms

4 Standardizer Flexible transformation / canonicalization engine Easy to use, but expert configurations are also accessible: Simple actions (checkboxes) Configuration string (simple or XML) Configuration file More on Standardizer Molecular Table Viewer Interactive display of molecules using Marvin View applets More on MarvinView

5 Chemical Terms Filter Filtering with powerful Chemical Terms expressions More on Chemical Terms Virtual reaction processing 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 Reactor

6 Combinatorial Reactor Example Example roundtrip protocol: Naming components Structure to name and name to structure conversion More on name recognition

7 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) More on LibMCS 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) Markush Enumeration More on Markush Enumeration

8 Component for tautomer generation Tautomerization 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

9 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 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

10 Inserts structures into a JChem Base table 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 JChem Base Insert Duplicate filtering option (using Pass and Fail ports) More on JChem Base JChem Database Search Structural search in a JChem Base table Wide range search options Output can be primary key (cd_id) or Molecule JChem Query Guide

11 JChem Base demo protocol Protocol for checking configuration System information Displays the most important environment information in a text editor

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

13 Resources Download: Technical support forum: More resources: Visit other technical presentations MarvinSketch/View MarvinSpace Calculator Plugins JChem Base JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor