September 2014, Version Szilárd Dóránt Scientific & technical Presentation Pipeline Pilot Integration

The Component Collection: Quick facts Provides access to ChemAxon tools from Pipeline Pilot Developed and directly supported by ChemAxon The component collection itself is free of charge But still needs the corresponding ChemAxon licenses for the tools being used Compatibility: Each version is compatible only with exact same JChem version since Pipeline Pilot 8.5 or newer required

Available functionality (1/3) 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 Structural Search and Formula Search filters Structure Checker

Available functionality (2/3) Name to Structure; Structure to Name; Document to Structure conversion JChem Base chemical database: insertion, search and retrieval of structures; create and drop structure tables JChem for Excel export Marvin applets: structure visualization and editing Major microspecies (major protonation form) Microspecies distribution Burden eigenvalue descriptor (BCUT)

Available functionality (3/3) MolConverter: conversion of the wide range of structure formats supported by ChemAxon Markush (generic structure) enumeration Tautomerization: tautomer generation (all, dominant, major, canonical, generic) Conformer generation Image generation RECAP fragmentation

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

Chemical Terms Filter Filtering with powerful Chemical Terms expressions 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:

Structure Checker Automated checking and fixing of structures Pipeline Pilot molecule or structure source input File or simple action string configuration Fix or check-only modes OCR error structures can be ignored Detected issues, applied fixes and remaining issues are listed in the output More on Structure Checker

JChem for Excel Writer Exports live structures to Excel Pipeline Pilot molecule or structure source input File output Export format is Excel 2007 (.xlsx) Data fields (data record properties) are also exported Overwrite / append option Various formatting options More on JChem for Excel

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

Document to Structure More on name recognition Structure extraction from documents Recognizes IUPAC and other systematic names Common names SMILES, InChi, CAS numbers etc. OLE objects (“live” structures) Supports PDF, TXT, Microsoft Office documents, HTML, XML files and URLs Support for 3 optical structure recognition tools: CLiDE, OSRA, Imago Correction of some OCR errors Start page, end page, OSR filtering options Output: molecule, name, uncorrected name, page number, position, type, OSR confidence

Structure Search filter Substructure, Superstructure, Duplicate, Full Fragment search Extensive set of search options Hit highlighting Support for searching Markush structures JChem Query Guide

Formula Search filter More on sophisticated chemical formula search Input types: Molecule Formula string Molecule source Search types Exact formula Exact subformula Subformula Support for Ranges Multicomponent formula search Isotopes

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, radicals, isotopes 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 Enumeration Enumeration of generic structures More on Markush Enumeration

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 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

Fragmenter RECAP based fragmentation Molecule fragmentation based on predefined cleavage rules Support for marking attachment points -As any (*) atoms -As Al and Ar atoms for aliphatic and aromatic distinction Cut data can be added as atom labels Detailed cleavage data is stored in properties More on Fragmenter

Image formats: PNG, BMP, JPEG Input can be either -Pipeline Pilot Molecule -Structure source (e.g. MRV string) Numerous rendering options, for example: -Image size, background, transparency -Scaling, max scale, atom label size -Various aromatization, dearomatization modes -R/S label, E/Z label, Absolute label options -Mark valence errors -Implicit H display, add/remove explicit H -etc … Image Generation High-quality ChemAxon-rendered images

HTML Molecular Spreadsheet Adds ChemAxon display capabilities to the familiar “HTML Molecular Table Viewer” Pipeline Pilot component Supports ChemAxon hit coloring, advanced Markush features Larger image pop-up Applet pop-up Wide array of display options Scalable molecule and data display More on MarvinView

HTML Molecular Spreadsheet More on MarvinView

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 table creation Non-default fingerprint parameters can be specified Absolute Stereo Flag option Duplicate filtering option Tautomer duplicate filtering Custom Standardizer configuration can be specified Extra column definitions can be added as SQL suffix Creates a JChem Base table Different table types supported More on JChem Base

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 Option to continue on error, error message stored in specified property Inserts structures into a JChem Base table Duplicate filtering uses Pass and Fail ports if set More on JChem Base

An extensive number of search options supported JChem Database Search (1/2) Search in a JChem Base table JChem Query Guide

Modes of operation: -Hit return mode -Flow-trough (“Query filtering”) mode Various output options for DB hits: -cd_id value (primary key) -Pipeline Pilot molecule -Generated MRV source or original source from DB Hit coloring supported Hit alignment -Rotate -Partial clean Markush hit reduction supported (with MRV output) Option for fetching data fields from JChem Base structure table Highlighted component features: JChem Database Search (2/2)

Delete from JChem Base table Delete by input list of cd_id (primary key) values, for example results of a search operation Delete by SQL WHERE clause, e.g. “WHERE cd_id IN (23, 247, 786)” Delete all rows by empty WHERE clause Deletes rows from a JChem Base table More on JChem Base

JChem Base demo protocol

Resources Download: – componentshttp:// components Technical support forum: – More resources: –

Visit other technical presentations MarvinSketch/View MarvinSpace Calculator Plugins JChem Base JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor