June 2016, Version Scientific & technical Presentation Pipeline Pilot Integration

Overview of the Component Collection Provides access to ChemAxon tools from Pipeline Pilot Developed and directly supported by ChemAxon The component collection itself is free of charge The corresponding ChemAxon licenses are needed for the tools accessed via the components Compatibility: Compatible with the exact same JChem version Pipeline Pilot 9.0 or newer required JChem Oracle Cartridge 6.1 or later is supported

Available functionality (1/3) Calculator Component for common calculations (logP, logD, pKa, HBD, HBA, Isoelectric point, PSA, BCUT and more) Chemical Terms expressions for advanced calculations, also as filter Compound Registration components Conformer generation Document to Structure conversion (image and text) Formula Search Filter Image generation JChem Base chemical database: insertion, search, retrieval and deleting of structures; create and drop structure tables

Available functionality (2/3) JChem for Excel import and export JChem Oracle Cartridge: database search and information components JChem PostgreSQL Cartridge search component Markush (generic structure) enumeration Marvin JS – JavaScript based chemical editor MarvinSketch Applet: Java based advanced structure editor Maximum Common Substructure (MCS) based clustering Microspecies distribution, Major Microspecies at pH MolConverter: conversion of the wide range of structure formats supported by ChemAxon

Available functionality (3/3) Name to Structure conversion Reactor : smart virtual reaction processing Standardizer: structure canonicalization Structure Checker Structure Search Filter Structure to Name conversion Tautomerization: tautomer generation (all, dominant, major, canonical)

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 Detected issues, applied fixes and remaining issues are listed in the output More on Structure Checker

MarvinSketch Applet Java Applet chemical editor ChemAxon’s Java based drawing tool with extensive capabilities Browser must support Java Applets CTAB or MRV source output Embedded or pop-up (thumbnail) appearance More on MarvinSketch

Marvin JS JavaScript chemical editor Smart user-oriented editor No client-side installation or Java required CTAB or MRV source output Embedded or pop-up (thumbnail) appearance Task oriented layouts available. (e.g. Reaction, Reporting, Search, etc.) More on Marvin JS

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 Conditional formatting via Pilot Script supported More on JChem for Excel

JChem for Excel Reader Imports live structures from JChem for Excel files Reads all sheets, the active sheet, or a specific sheet by name The range of data cells to import can be restricted Structures-only mode useful for importing a matrix of molecules Data column names can be auto detected above data rows, a specific row may contain them, or the Excel row names may be used 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 Naming Structure to name and name to structure conversion Structure to Name IUPAC name Traditional name CAS number (uses public Web Service) Name to Structure Supports recognition of company IDs via company web service

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, hit context, document section (USPTO XML)

Structure Search filter Substructure, Superstructure, Duplicate, Full Structure and Full Fragment search Extensive set of search options Hit highlighting 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 Technology

Tautomerization Component for tautomer generation Calculation modes: –All tautomers –Canonical tautomer –Major tautomer –Dominant tautomer distribution Options: –Consider pH at specific value –Protect aromaticity, charge, double bond stereo, tetrahedral stereo, ester groups –Exclude antiaromatic compounds –Single fragment mode –Normal (rational) tautomers only –Ring-chain tautomerization 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

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 (1/2) 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 (2/2) More on MarvinView

Database Connection Provides a convenient way to define a JDBC connection parameter set within a protocol Other JChem Base and JChem Oracle Cartridge 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

Extensive set of search options Scales better to larger database sizes than the JChemSearch component JChem Oracle Cartridge Search Search in a JChem Oracle Cartridge indexed table JChem Query Guide JChem Oracle Cartridge product page

Search in a JChem PostgreSQL Cartridge indexed table Basic search options available Continually improved as new features are added to the cartridge JChem Oracle PostgreSQL Search JChem PostgreSQL Cartridge product page

Compound Registration Components for accessing ChemAxon’s Compound Registration System Connection Data component Automatic registration Search by Structure Search / retrieve structure by ID More on Compound Registration

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