1. Pipeline pilot Components
February 2017, Version

2. 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

3. 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

4. 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

5. 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)

6. Calculator Easy access for the most important calculations
More on Calculator Plugins

7. 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

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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. Combinatorial Reactor Example
More on Reactor

19. 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

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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 …

29. 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

30. HTML Molecular Spreadsheet (2/2)
More on MarvinView

31. 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

32. 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

33. 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

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

35. 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

36. 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

37. JChem Base demo protocol
More on JChem Base

38. 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

39. 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

40. 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

41. 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

42. 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

43. Resources Download: Technical support forum: More resources:
Technical support forum:
More resources:

44. end of presentation