February 2013 Szilárd Dóránt Scientific & technical Presentation Pipeline Pilot Integration.

February 2013

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

• Free of charge• Latest version : 2.5 (as of February 2013)

– Compatibility: • JChem / Marvin 5.10.x, 5.11.x • Pipeline Pilot 8.0 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

• Configurable structure cell size

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.

• Supports PDF, TXT, Microsoft Office documents, HTML, XML files and URLs

• Support for OSRA optical structure recognition (from JChem 5.9.x and later)

• Correction of some OCR errors

• Outputs: name, uncorrected name, page number, position

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 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 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 option (using Pass and Fail ports)

More on JChem Base

• A large 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)

JChem Base demo protocol

Planned development

Component release cycle is fast and flexible.

Please advise us on priority and additional functionality for future component development.

• Easier access to JChem Cartridge for Oracle

• Integration with Instant JChem, JChem for Excel

• Improvement of existing components

• Documentation improvements

Resources

• Download:– http://www.chemaxon.com/integration/download.html

• Technical support forum:– http://www.chemaxon.com/forum/forum88.html

• E-mail:– pp@chemaxon.com

• More resources:– http://www.chemaxon.com/forum/ftopic4604.html

Visit other technical presentations

MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt

MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt

JChem Base http://www.chemaxon.com/JChem_Base.ppt

JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

Standardizer http://www.chemaxon.com/Standardizer.ppt

Screen http://www.chemaxon.com/Screen.ppt

JKlustor http://www.chemaxon.com/JKlustor.ppt

Fragmenter http://www.chemaxon.com/Fragmenter.ppt

Reactor http://www.chemaxon.com/Reactor.ppt