Pipeline pilot Components February 2017, Version 17.2.13

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 (weekly release) Pipeline Pilot 9.2 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 Compliance Checker 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 for Office import and export (Word, PowerPoint) JChem Oracle Cartridge: database search and information components JChem PostgreSQL Cartridge search component JChem Web Services database 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

Available functionality (3/3) Microspecies distribution, Major Microspecies at pH MolConverter: conversion of the wide range of structure formats supported by ChemAxon 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 Maximum freedom trough Chemical Terms Expressions for expert users Use arbitrary Chemical Terms expressions Results stored to arbitrary properties A wide range of ChemAxon functionality can be accessed as Chemical Terms functions More on Chemical Terms

Chemical Terms Filter Filtering with powerful Chemical Terms expressions More on Chemical Terms

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

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

JChem for Office Writer Exports live JChem for Office structures to Word and PowerPoint Single structure or multi-structure output Export of properties One property can be treated as ID, can be retrieved on import later Support for several journal styles More on JChem for Office

JChem for Office Reader Imports JChem for Office structures from Word and PowerPoint Reads back structures as molecules Imports ID if present Returns page / slide number More on JChem for Office

Reactor 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 Synthesis code generation Output reaction mapping Advanced options available More on Reactor

Combinatorial Reactor Example More on Reactor

Naming components Structure to name and name to structure conversion IUPAC name Traditional name CAS number (uses public Web Service) Name to Structure Supports recognition of company IDs via company web service More on Naming

Document to Structure 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) More on name recognition

Structure Search filter In-memory structure search Substructure, Superstructure, Duplicate, Full Structure and Full Fragment search Extensive set of search options Hit highlighting JChem Query Guide

Formula Search Filter 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 More on sophisticated chemical formula search

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, radicals, isotopes can optionally be ignored Disallow “breaking” rings (default) More on LibMCS

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) 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 Lowest 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 All formats supported by ChemAxon are available 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 generation High-quality ChemAxon-rendered images 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 …

HTML Molecular Spreadsheet (1/2) Scalable molecule and data display 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 Marvin View Applet pop-up Wide array of display options More on MarvinView

HTML Molecular Spreadsheet (2/2) More on MarvinView

Database Connection Defines a JChem Base 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 More on JChem Base

JChem Base table creation Creates a JChem Base table Different table types supported 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 More on JChem Base

JChem Base Insert Inserts structures into a JChem Base table Duplicate filtering uses Pass and Fail ports if set 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 More on JChem Base

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

JChem Database Search (2/2) Highlighted component features: 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 More on JChem Base

Delete from JChem Base table Deletes rows from a 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 More on JChem Base

JChem Base demo protocol More on JChem Base

JChem Oracle Cartridge Search Search in a JChem Oracle Cartridge indexed table Extensive set of search options Scales better to larger database sizes than the JChemSearch component More on JChem Oracle Cartridge

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

JChem Web Services Database Search Database search via web service Can handle larger tables than JChemSearch No need for Oracle or PostgreSQL cartridge More on JChem Web Services

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

Compliance Checker Compliance checking of structures Hit return or filter mode Search in all or specific categories Search by regulations effective on a certain date Additional component to obtain the available categories More on Compliance Checker

Resources Download: Technical support forum: More resources: https://www.chemaxon.com/download/pipeline-pilot-components Technical support forum: https://www.chemaxon.com/forum/forum88.html More resources: https://www.chemaxon.com/forum/ftopic4604.html

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