Transcript Product presentation

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
•
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
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:
–
–
–
•
Search types
–
–
–
•
Molecule
Formula string
Molecule source
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:
–
–
•
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
–
–
•
•
Hit return mode
Flow-trough (“Query filtering”) mode
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:
– 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
END OF PRESENTATION