Scientific & technical Presentation
Pipeline Pilot Integration
Szilárd Dóránt
September 2014, Version 14.9.1
The Component Collection: Quick facts
• Provides access to ChemAxon tools from Pipeline
Pilot
• Developed and directly supported by ChemAxon
• The component collection itself is free of charge
• But still needs the corresponding ChemAxon licenses for
the tools being used
• Compatibility:
•
•
Each version is compatible only with exact same JChem version
since 14.7.7.0
Pipeline Pilot 8.5 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
Maximum freedom trough Chemical Terms Expressions
for the expert user
• 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
•
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
•
Overwrite / append option
•
Various formatting options
More on JChem for Excel
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
• 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
Combinatorial Reactor Example
Naming components
Structure to name and name to structure conversion
Example “roundtrip” protocol:
More on name recognition
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
More on name recognition
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
• 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 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 autodetection
• 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 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
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
• Applet pop-up
• Wide array of display options
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 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
JChem Query Guide
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
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
Resources
• Download:
– http://www.chemaxon.com/download/pipeline-pilotcomponents
• Technical support forum:
– http://www.chemaxon.com/forum/forum88.html
• E-mail:
– pp-support@chemaxon.com
• More resources:
– http://www.chemaxon.com/forum/ftopic4604.html
Visit other technical presentations
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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