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Solutions for Cheminformatics. Migration from ISIS environment. Szabolcs Csepregi et al. November 200 8. Migration - Topics. ChemAxon - Product Overview F rom Isis/Host and MDL Direct to JChem Cartridge Alternatives to Cheshire (Standardizer) From ISIS/Base to Instant JChem

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solutions for cheminformatics
Solutions for Cheminformatics

Migration from ISIS environment

Szabolcs Csepregi et al

November 2008

migration topics
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

chemaxon embedded examples
ChemAxon Embedded - examples

Workflow

Pipeline Pilot, Inforsense, and KNIME.

ELN

Agilent, Contur, DeltaSoft, Kinematic, etc.

SAR

Spotfire, Synaptic Science, Omniviz

Databases

Aureus, GVK, Jubilant Biosys, Patcore

Web

Thomson Reuters, Wiley, Houghton Mifflin, Cengage, Prentice Hall, Collaborative Drug Discovery, RCSB PDB, BindingDB, NIH/NLM ChemIDPlus, Molport etc

the marvin family

MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.pptMarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt

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

The Marvin family

MarvinSketch MarvinView MarvinSpace

Available as Java applets for HTML pages and Java beans for standalone apps (full API)

Publication quality macromolecule visualization

Individual and structure table visualization

Structure, query & reaction editing

marvin d evelopment histor y
Marvin Development History

1999

2000

2001

2002

2003

1998

SDF, RDF, XYZ animations, CML, templates, compressed formats, Swing, 3Dmodels

SMILES, SMARTS, PDB, Rgroups, isotopes, shortcuts, Marvin Beans

Ball and stickJPG, PNG, SVG, Cut&Paste with Isis/ChemDraw, 2D cleaning, (de)aromatization, reaction drawing

Applets, Molfiles, stereo support, Windows, Unix

Mac support, signed applets, Java Web Start, atom mapping

Partial charge, pKa, logP/logD,3Doptimization, radicals,abbreviated groups

2008

2007

2006

2004

2005

Tautomers, resonance, lone pairs, conformers, 3D sketching, MarvinSpace,

Topologyanalysis,presentation quality graphics,...

More Plugins,

more R-groups,

EMF, PDF and Mol2,

Improved property storage in MRV, SDfiles and Rdfiles.

.NET support in MarvinBeans.

Name to structure, OLE 2,

Chemical Terms

Customizable GUI

Marvin file format, enhanced stereo, shapes, text boxes, multiple groups, link nodes, TPSA, recursive SMARTS, Donor/Acceptor,electron arrows,

Structure to name, Coordination compounds, Polymer drawing, OLE, Markush enumerationplugin

Configurations

calculator plugins

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

Calculator Plugins

A variety of structure based calculations are available from the Marvin GUI, cxcalc command line tool and the API. The calculations are widely used within several JChem tools and are available as functions of Chemical Terms expressions.

  • Elemental Analysis
  • IUPAC Name
    • Standard IUPAC Name
  • Protonation
  • pKa, Major Microspecies, Isoelectric Point
  • Partitioning
  • logP, logD
  • Charge
  • Charge, Polarizability, Orbital Electronegativity
  • Isomers
  • Tautomerization, Resonance, Stereoisomer
  • Conformation
  • Conformer, Molecular Dynamics
  • Geometry
  • Topology Analysis, Geometry, Polar Surface Area (2D), Molecular Surface Area (3D)
  • Markush enumeration
  • Other
  • Hydrogen Bond Donor-Acceptor, Huckel Analysis, Refractivity
chemical naming
Chemical Naming

Structure to Name/ Name to structure

Supported nomenclatures :

  • Chains, Monocycles/ Traditional names with and without heteroatom/ Spiro ring systems/ Ethers/ Common characteristic groups, Ionic compounds/ Unlimited number of atoms and rings/ All atom types /Stereochemistry/ etc.

Usage:

  • drag&drop or copy&paste to MarvinSketch
  • Label updated in real-time
  • Automatic format recognition
  • Batch from command line
jchem development history
JChem development history

2000

2001

2002

2003

2004

Oracle, MySQL, SQLServer, Access, hashed fingerprints,substructure and similarity search

Clustering, diversity

DB2, PostgreSQL, Rgroup searching

Reaction searching, fragmentation,reaction processing, standardization, pharmacophores, screening

Cartridge, enhanced stereo searching, recursiveSMARTS,Chemical Terms, virtual synthesis

2005

2006

2008

2007

Position variation queries,

Instant JChem:

  • - Federated search,
  • - Cartridge support...
  • JChem for Excel

Calculated columns, Installer,

Tautomer Duplicate filtering, Query tables,Markush tables,

Speed enhancementsforJChem Cartridge,

form design, relational data for Instant JChem ...

R-decomposition,R-enumeration, reaction library, custom fingerprints, random synthesis, link nodes…

Tautomer search,Instant JChem reaction similarity, LibraryMCS, GUI for Standardizer/ Reactor …

jchem base

DB2

Structural Searchhttp://www.chemaxon.com/Structural_Search.ppt

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

JChem Base

Features

  • Fast and sophisticated searching(chemical and non-chemical data, Chemical Terms filter, many options)
  • Custom standardization
  • Calculated columns
  • Combinatorial Markush structure tables

Interfaces

  • Integration with most relational database engines
  • JChem Cartridge for tight Oracle SQL integration
  • JSP integration – open source web example
  • Desktop-ready through Instant JChem
searching in combinatorial markush structures
Searching in combinatorial Markush structures
  • Combinatorial Markush structure registration and search
  • Markush features handled insearch & enumeration:
    • R-groups (nesting to any depth)
    • Atom lists, bond lists
    • Position variation bond
    • Link nodes
  • Compatible Markush enumeration plugin
  • Not all query features supported
  • Detailed description:
  • http://www.chemaxon.com/product/markush_search.html
jchem cartridge for oracle
Access JChem functionality via SQL functions

All search features of JChem Base

JChem index for chemical data in arbitrary database structure

Chemical filters and property predictors using Chemical Terms

Standardization (structure canonicalization) during registration

Structure format conversions

2D, 3D image generation

Library enumeration using virtual reactions and Markush structures

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

JChem Cartridge for Oracle
instant jchem
Instant JChem

Instant JChem: http://www.chemaxon.com/conf/Instant_JChem.ppt

Desktop application for local and remote chemical database management, search and structure based prediction

  • Simply connect to external databases and share your native database simultaneously
  • Powerful search functionalities
  • Scalable – explore large datasets (106 +)
  • Dynamically predict properties using Calculator Plugins
  • Apply canonicalization rules for import and viewing
  • Wide import / export options
  • Merge data sets into a single set
  • Very active development – what do you want to do?
jchem for excel
JChem for Excel

Microsoft Excel integrated solution for Marvin and JChem functionality

Use Excel’s powerful features: Functions, Sorting, Filtering, Charts…

Implemented in C# .NET, and Visual Studio

Proof that ChemAxon APIs can be used in a Java-less .NET environment

Easy to install and deploy

UNDER DEVELOPMENT

canonicalization with standardizer

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

Canonicalization with Standardizer
  • Structure canonicalization
    • Mesomers
    • Tautomers
    • Solvent and counter ion removal
    • Aromatization, dearomatization
    • Explicit/implicit hydrogen conversion
    • Stoichiometry expansion
    • Stereo manipulations
    • 2D cleaning
    • Template based cleaning
  • Custom rules
  • Availability
    • JChemBase, Cartridge & IJC
    • API (Java and .NET)
    • Batch processing
    • GUI
migration topics18
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

slide19

Contents

  • A short introduction of JChem Cartridge
  • MDL/Symyx features in JChem
  • Migration from MDL/Direct and ISIS/Host
  • Migration case studies and user feedback
slide20

Purpose of JChem Cartridge

  • Access JChem functionality using SQL:
    • SELECT count(*) FROM nci WHERE jc_contains(structure, 'Brc1cnc2ccccc12') = 1
    • Access JChem in any programming environment offering Oracle connectivity (.NET, Java, Perl, PHP, Python, Apache mod_plsql...)‏
  • Execute SQL queries efficiently using extensible indexes
    • Precompute chemical information on structures by creating jc_idxtype indexes:
    • CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype
    • The jc_idxtype implementation scans the indexed column for eligible structures in one single performance-optimized operation: domain index scan
slide21

Features of JChem Cartridge

  • Adds chemistry knowledge into the SQL language of Oracle (SELECT, INSERT, UPDATE, ...)‏
  • Substructure, superstructure, exact structure, similarity searching
  • Fast: typically 10k hits in 3M structures within a second
  • Complex chemical expressions using the Chemical Terms language that includes logP, pKa, ...
  • Automatic property calculation during registration
  • Standardization (canonicalization) during registration
  • Structure format conversions (MRV, Molfile, SDfile, RDfile, SMILES, CML, etc.)‏
  • 2D, 3D image generation
  • Structure enumeration using reaction rules
  • Interaction with Oracle optimizer
slide22

Operators and functions

  • jc_compare: substructure/similarity/exact searching combined with Chemical Terms expressions
  • jc_matchcount: number of occurences of the query structure in the target
  • jc_evaluate: Chemical Terms evaluation
  • jc_molweight: molecular weight
  • jc_formula: molecular formula
  • jc_react: structure enumeration based on virtual reactions
  • jc_standardize: structure canonization
  • jc_molconvert: conversion to different formats (image generation is supported)
  • jc_tanimoto: similarity search
  • jcf.hitColorAndAlign: substructure coloring and alignment

Similarity search example displaying ID, SMILES code, and molweight:

SELECT cd_id, cd_smiles, cd_molweight FROM my_structuresWHERE jc_tanimoto(cd_smiles, 'CC(=O)Oc1ccccc1C(O)=O') >= 0.8;

structure search features
Structure search features
  • Wide range of query atoms
  • Query properties
  • R-group queries
  • Full SMARTS support
  • Coordination compounds
  • Link nodes
  • Position variation
  • Pseudo atoms
  • Lone pairs
  • Relative stereo
  • Reaction search features
  • Hit coloring

See detailed information on structure search:

www.chemaxon.com/conf/Structural_Search.ppt

s earch options
Search options
  • Chemical Terms filter constraint
  • Tautomer search
  • sp hybridization state check
  • Stereo on/off
    • Ignore charge/isotope/radical/valence/mixture brackets
    • Vague bond matching modes: „or aromatic”; ignore bond types
    • Inverse hit list
  • Maximum search time / numberof hits
  • SQL SELECT statement for pre-filtering
  • Ordering of results
  • etc.
compatibility and integration
Compatibility and integration

File formats:

  • SMILES
  • MDL molfile (v2000 and v3000)
  • MDL SDF
  • RXN
  • RDF
  • MRV
  • IUPAC name, InChI

Operating systems:

  • Windows
  • Linux
  • Solaris
  • HP-UX
  • etc.

DB engines:

Oracle versions 9i R2 or above

for alternative RDBMS systems, see the JChem Base presentation: http://www.chemaxon.com/JChem_Base.ppt

slide26

Index parameters

  • Index parameters affect:
    • Fingerprint attributes
    • Standardizer configuration
    • Table space and storage options of the index table
  • Examples:
  • Standardization by stripping hydrogens and using basic aromatization:
    • CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype PARAMETERS('STD_CONFIG=dehydrogenize:optional..aromatize:b')‏
  • Add structural keys to fingerprint for more efficient substructure searching (structural keys are defined in table stfp_keys):
    • CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype PARAMETERS('STRUCTURALFP_CONFIG=select structure from stfp_keys')‏
slide27

Supported Column Types

  • VARCHAR2: typically for short formats, e.g. SMILES
  • CLOB
  • BLOB

for longer formats, e.g. MDL molfile,

Marvin (mrv)

mdl feature compatibility
MDL Feature Compatibility
  • Generic atom types and bond types
  • Atom query properties
  • Atom Lists/ not lists
  • Aliases
  • Pseudo atoms
  • Atom values
  • Group and brackets
    • Abbreviated groups
    • Multiple groups
    • Repeating units
    • Polimers
    • Mixtures
    • Attached Data
  • Link Nodes
  • R-groups, R-logic
  • Stereochemistry
    • Chiral flag
    • Parity
    • Double bond stereo
    • Enhanced stereo (abs/end/or)
    • inv/ret
  • Reacting center on bonds
  • Reaction mapping
  • Topology (ring/chain)
  • Option for ISIS-like look
  • Others…

The learning curve of chemists familiar with ISIS is very short. After having some practice, Marvin is reported a more productive drawing environment. The most of the MDL features are available in Marvin and JChem, and many others not available in MDL technology.

mdl feature compatibility29
MDL Feature Compatibility
  • Polymer search (coming in 5.2)
  • Attached data S-group search (coming in 5.2)
  • 3D special features
  • Exact change flag (reaction)

What is missing:

migration from mdl direct cartridge
Migration from MDL/Direct cartridge
  • 2 alternatives:
    • JChem indexes need to be created on structure columns of existing tables, or
    • Structural data migrated to new tables with JChem Cartridge indexes
  • The MDL/Direct SQL operators need to be changed to JChem operators in all uses.
  • Non-chemistry tables: no need for migration
migration from isis host
Migration from ISIS/Host
  • Molecule source need to be accessible for JChem:
    • Through exporting SD/Rdfiles from ISIS and importing into new tables with JChem index, or
    • Setting option in ISIS/Host to include molfile in RCG tables, and:
      • Use SQL to insert mol field into JChem tables, or
      • Add JChem index on original tables
  • ISIS/Host interfaces need to be rewritten to use SQL only, referencing JChem operators.
  • Hviews and GUI-s need to be replaced separately. (See further slides later.)
  • Non-chemistry tables: no need for migration
an independent comparison
An Independent Comparison

FMC migrated from MDL® ISIS/Base ISIS/Host to ChemAxon’s JChem. They later published their detailed scientific comparison.

  • Used 1.8 million vendor compounds to create a testing database
  • Prepared 115 different query structures for comparison
  • 51 simple sub-structure search
  • 51 similarity search
  • 64 complex search

Identical search hits in almost all cases, major differences result from MDL’s incorrect aromatic bond definitions in case of 5 member aromatic rings. ChemAxon's approach is the chemically correct and their performance is higher (faster).

vague bonds
Vague Bonds

For the sake of perfect compatibility with MDL searching ChemAxon provides vague bond options to retrieve results according to MDL systems.

technical comparison
Technical Comparison
  • Supported Platforms
    • ISIS®: Sun Solaris, Windows Servers
    • JChem: Sun Solaris, Windows Servers, Linux, Irix, MAC
  • Supported Databases
    • ISIS: Oracle
    • JChem: Oracle, MySQL, SQL Server, PostgreSQL, Access, DB2
  • Processing SD Files
    • ISIS: 31 hours, Pipeline Pilot & ISIS
    • JChem: 11 hours, JChem
  • Technology Transparency
    • ISIS®: Unclear Data/Table Structures
    • JChem: Clear Understanding of
      • Flow of Data
      • Structure of Data
      • Execution Process

Native Oracle Tables and Procedures

  • Performance
    • ISIS®: Slow similarity search
    • JChem: Fast similarity search
comparison conclusions
Comparison Conclusions
  • Technical Conclusion
    • Clear and straightforward understanding of data representation and system architecture
    • Integrated system
    • Quicker and less error-prone
    • Less hassle for software development

From technical point of view, ChemAxon is favorable

  • Business Conclusion

ChemAxon was the better choice

migration experience questionnaire
Migration Experience Questionnaire

Five companies were interviewed about their JChem Cartridge migration experiences in the form of a questionnaire containing 14 questions.

  • A UK based service/biotech company
  • A Swedish biotech company
  • A US branch of a Swiss pharmaceutical company
  • A Japanese pharmaceutical company
  • A US branch of a Japanese pharmaceutical company
migration experience
Migration Experience

1. What was the platform you used before the migration?

  • All systems were run using the Daycart cartridge on Linux servers
  • MDL Cartridge running on Sun Solaris
  • Daycart
  • We used ISIS/Host as a server, the client was ISIS/Base customized using ISIS/PL
  • Daylight and IDBS Chembridge

2. How long did it take to migrate?

  • Very simple, hardly any time at all, just a few hours to uninstall old cartridge, install new cartridge and build indexes. Then modify a few SQL statements in the code to use the new cartridge functions.
  • It took a full weekend to switch over and convert all old databases.
  • Since we use SQL for structure searches, the actually change in the application code are few. Code changes takes about 1 day. However, we spent at least two weeks to compare the daylight and jcart.
  • It took 1 year for planning, and another 1 year for designing and developing the system. 1-year-migration time includes all of the operation that is needed. That means our technical people worked for this project 1 year. We migrated the data structure of HView, but the form was re-designed in order to fit our existing (wet) workflow.
  • Two months
migration experience40
Migration Experience

3. How many technical people were required in the migration process?

  • It was fairly simple so just one developer with all round programming, database, and chemistry knowledge.
  • One person
  • 2 people
  • 6 technical people. 2 were contacting with users. For the system design, 11 users were involved from chemistry, HTS, eADME groups.
  • 1.5

4. Why did you decide on leaving the previous platform? (problems)

  • Purely the cost. We found the Daycart system to be very good, very stable, fast, and the API was well thought out. However, it was just too expensive for us.
  • Old technology not offering new functionality. High cost, in particular for new licenses.
  • Daycart (at least at that time) did not take MOL query, not all query structures could be correctly presented as smiles/smarts.
  • Two main reasons were the maintainance cost, and the accessibility. We had to suppress the raising system (software) cost, and at the same time we had to enlarge the number of users and client PCs from which we could use DB system.
  • Cost, maintenance and risk
migration experience41
Migration Experience

5. What alternative platforms were considered/evaluated?

  • Prior to selecting ChemAxon we looked at all the cartridges available at the time
  • The Accord cartridge was also evaluated. Some others did not qualify for evaluation.
  • None
  • Accord (Accelrys), and ChemOffice (Cambridge Soft) were two major alternatives.
  • Symyx/MDL Direct Oracle cartridge

6. Why did you choose ChemAxon technology? (advantages)

  • Cost was a major factor, but also because we felt we could work with ChemAxon to develop the tools further as we wanted to use them. A very open approach. Another reason was that all the tools we needed were available from a single vendor, i.e. Oracle cartridge for searching, and sketching and viewing tools.
  • Almost as good as Accord but with better impact on improvement and support.
  • Marvin Sketch and JCart represent the molecules in MOL using exactly the same backend library. MOL is used instead of smiles/smarts. Much faster search. Price is good .
  • We could keep the cost lowest by using ChemAxon, and more than that, the affinity for the web technology was favorable to our future vision of the cheminformatics system.
  • The greatest advantage is the low cost and great support. We have always had MDL/Direct cartridge, but the greatest advantage is the low cost and stellar support speaks specifically to ChemAxon.
migration experience42
Migration Experience

7. What were the most problematic issues occurred during the migration? (negative impressions)

  • Understanding the finer points of all the search functions / options i.e. precisely how things like aromaticity, stereochemistry, etc. are handled. We've also had to spend time considering how to restandardise structures and how to rewrite SQL. When doing a straight forward structure search (i.e. benchmarking), the JChem cartridge performs very well against other systems such as Daylight, however, if you want to incorporate joins between tables can considerably affect the query times even when using what we call ChemAxon SQL.
  • Structure matching bugs in the cartridge and undocumented actions needed to be performed.
  • JCart installation was not so smooth 3 years ago. Much better now. Most of the problem and issues are because some structures are interpreted different between the two software. Some are Daylight bugs and others are jchem bugs. JChem has fix all their share.
  • There were little problem, what I remember is that the response was slower than expected when the chemical object was included in the page.
  • Identifying all the integration points.
migration experience43
Migration Experience

8. How could you overcome in these difficulties? (resolutions)

  • We spent a lot of time experimenting with the different functions/options so we completely understand what they do.
  • The structure search bugs was overcome by rewriting the registration procedures, undocumented actions were overcome by hard work.
  • Wait until major bugs in JChem are fixed. We live with about 0.01% of inconsistencies and work it out later.
  • The needless chemical objects were replaced by pictures.
  • Availability and quick turn around to patch any

9. Did you expect any other problem, that did not occur? (positive impressions)

  • We though there may be problems running two different cartridges on the same table but this worked fine
  • Not really. Most MDL features were available in JChem. This was one of the selection criteria, particularly important for chemical registration.
  • No
  • We expected that the transfer of the existing data might be problematic, and that the system change might be inconsistent with existing 'wet' workflow. That was why we organized 11 users as a system designing team, and I think the team worked well.
  • Migration went very smooth
migration experience44
Migration Experience

10. What additional components were purchased together with the JChem Cartridge?

  • Most of them!
  • Descriptor calculations.
  • None. User probably should consider plug-ins for calculating HBD, HBA, logp, psa, etc. We did not because we need to stick to CLOGP in order to be consistent with the rest of the company.
  • Standardizer.
  • Standardizer.

11. How much technical support did you need from ChemAxon for the migration?

  • Initially quite a lot, though the products have been developed a lot since then. We haven't required much support for structure migration, but we've also migrated a load of SMIRKS and we've needed support for that mainly because of the way in which they were handled in the old system (non-standard).
  • A few needed support cases where filed on the support forum and fairly quickly resolved.
  • Lots, we had close communication with dev team during the migration.
  • Our technical people sent e-mail several times to your support team.
  • Little.
migration experience45
Migration Experience

12. Were/Are you satisfied with the ChemAxon support?

  • Yes. Support has always been good.
  • Yes very satisfied. The support has always been very fast and accurate.
  • Yes.
  • Yes.
  • Yes.

13. Did the migration reach its original goals?

  • So far, yes! The systems are up and running.
  • Yes.
  • Yes.
  • Yes.
  • Yes.
migration experience46
Migration Experience

14. Are you satisfied with the performance/functions of the ChemAxon powered system?

  • The number of functions available and flexibility of the JChem tools is excellent, and allows us to develop very interesting and useful drug discovery software for our scientists.
  • Yes.
  • Yes.
  • Yes.
  • Yes.
slide47

Useful migration resources

ChemAxon's Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v 4.0)Seong Jae Yu, David Roush*, Usha Ganesh, Young Moon, Henry Liu, FMC Corp.

http://www.chemaxon.com/conf/FMC_ChemAxon_JCHEM_Cart_xnotes.ppt

User Group Meeting presentations:

http://www.chemaxon.com/UGM/ugm_land.html

migration topics48
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

cheshire alternatives from chemaxon
Cheshire Alternatives from ChemAxon

What is Cheshire?

“Cheshire is a scripting language that enables you to write scripts to validate, modify, or gather information about chemical structures, such as molecules and reactions.”

What alternatives can ChemAxon offer?

  • ChemAxon’s Java API (also available from .NET)
  • Chemical Terms
  • Standardizer
java api for cheminformatics from chemaxon
Java API for Cheminformatics from ChemAxon

ChemAxon’s class library consists of more than 1500 chemistry related classes tuned for usability and high performance.

chemical terms
Chemical Terms

Chemical Terms offers more than a hundred popular chemistry functions opening up the power of cheminformatics for those scientists who focus on quick results instead of the details of programming and scripting. The integration of Chemical Terms makes make chemistry applications smarter and more customizable.

charge() and match(amine) or match(hydrazine)

standardizer for batch conversion
Standardizer for Batch Conversion

Standardizer is a batch conversion utility providing many useful and customizable functions for the canonicalization of chemical structures and restoration renovation chemical information in structures from older databases.

standardizer actions
Standardizer Actions

Transform

Clear Stereo

Aromatize

Set Absolute Stereo

Dearomatize

Remove Absolute Stereo

Add Explicit Hydrogens

Convert Wedge Interpretation

Remove Explicit Hydrogens

Convert Double Bonds

Clean2D

Alias to Group, Alias to Atom

Clean3D

Contract Group

Wedge Clean

Expand Group

Clear Isotopes

Ungroup

Remove Fragments

Expand Stoichiometry

Remove R-groups

Map Reaction

Tautomerize

Unmap

Neutralize

Mesomerize

counting groups cheshire
Counting Groups – Cheshire

Counting O=S=O groups in Cheshire

counting groups java api
Counting Groups – Java API

Counting any functional groups with ChemAxon’s Java API

Counting O=S=O groups in Chemical Terms

adding explicit hydrogens cheshire
Adding Explicit Hydrogens - Cheshire

Adding explicit hydrogens and cleaning the molecule in Cheshire

adding explicit hydrogens java api
Adding Explicit Hydrogens – Java API

Adding explicit hydrogens and cleaning the molecule with ChemAxon’s Java API

adding explicit hydrogens standardizer
Adding Explicit Hydrogens – Standardizer

Adding explicit hydrogens and cleaning the molecule with Standardizer

The same in command line

group conversions cheshire
Group Conversions – Cheshire

Conversion of neutral form of nitro to the ionic one in Cheshire

group conversions java api
Group Conversions – Java API

Conversion of neutral form of nitro to the ionic one with ChemAxon’s Java API

group conversions standardizer
Group Conversions – Standardizer

Conversion of neutral form of nitro to the ionic one in Standardizer

The same in command line

structure checker framework
Structure Checker Framework
  • ValenceChecker
  • AromaticityChecker
  • OverlappingAtomsChecker
  • OverlappingBondsChecker
  • CrossedDoubleBondChecker
  • WigglyDoubleBondChecker
  • WedgeBondsChecker
  • BondLengthChecker
  • BondAngleChecker
  • AliasChecker
  • PseudoAtomChecker
  • AbbreviatedGroupChecker
  • MultiComponentChecker
  • QueryChecker
  • MoleculeChargeChecker
  • RadicalChecker
  • IsotopeChecker
  • ExplicitHydrogenChecker
  • StereoDoubleBondChecker
  • TetrahedralStereoAtomChecker
  • UnspecifiedStereoDoubleBondChecker
  • ChiralFlagChecker
  • CovalentSaltChecker
  • FerroceneChecker
  • CumulatedRingBondChecker
  • UnbalancedReactionChecker
  • MultistepReactionChecker
  • AtomMapChecker
  • MissingAtomMapChecker
  • AtomMapStyleChecker
  • RgroupQueryChecker
  • MarkushChecker
  • 3DCoordinateChecker
  • MolfileChecker
  • RxnfileChecker
  • SmilesChecker
  • SmartsChecker
  • InchiChecker
  • PeptideSequenceChecker
  • CmlChecker
  • PdbChecker

The new Structure Checker framework will provide plenty of validation and correction functions to detect and repair defective or unpreferred structures.

summary
Summary

ChemAxon’s Java API provides similar freedom and flexibility to Cheshire for programmers to develop chemistry functions for any tears like web clients, desktop applications, server systems and Oracle stored procedures.

Java is a standard language with worlwide community, rich resources and lots of well educated developers. (The ChemAxon Java API is also accessible from .NET.)

Chemical Terms provides more than a hundred high level, ready to use functions substituting dozens of lines of complex Cheshire code.

Chemical Terms expressions can directly be used in database filters, virtual reactions, pharmacophore definitions or other cheminformatics applications.

Standardizer is an easy to use batch tool and graphical interface for chemists to create conversion rules without writing a single line of code.

The upcoming Structure Checker will provide and extensible set of quick “problem detection” functions that can be integrated in any applications and will be added to Marvin and Standardizer as well.

migration topics64
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

instant jchem is
Instant JChem is…
  • An “out of the box” desktop application designed for biologists and chemists
  • A modular platform for developing chemistry applications
instant jchem lets users
Instant JChem lets users…
  • Create or connect to existing structure databases
  • Easily manage relational data
  • Import/export/merge/edit data
  • Build forms for reporting
  • Run combined structure + data searches
  • Perform structure based predictions
  • Access sophisticated chemistry features
  • Collaborate with other users
ijc architecture
IJC Architecture
  • Built on modular platform
    • Allows easy extension by ChemAxon, customers and 3rd parties
    • Strong enforcement of APIs
  • API
    • Allows extension
    • IJC functionality is built upon these APIs
current architecture
Current architecture

IJC Client

Database

Local DB

Remote DB

Oracle cartridge

ijc server architecture

Web Apps

Web services

IJC server architecture

Database

IJC Client

IJC Server

IJC

Services API

Oracle cartridge

IJC server due Q1 2009

hview vs data tree standard tables

IJC Data Tree

Hview vs. Data Tree: standard tables

ISIS Hview

HVIEW my_data

TREE master

DEVICE oracle

USERNAME scott

PASSWORD tiger

TNAME master_table

TREE detail

DEVICE oracle

USERNAME scott

PASSWORD tiger

TNAME detail_table

LINK master (master_table_id) over detail (master_table_id)

One-to-many relationship

master_table

master_table_id

col1

col2

col3

detail_table

detail_table_id

master_table_id

cola

colb

colc

*

hview vs data tree mol rxn tables

compounds

molregno

structure [jc_index]

IJC Data Tree

inventory

inventory_id

molregno

cola

colb

colc

*

Hview vs. Data Tree: Mol + Rxn tables

ISIS Hview

HVIEW cpds_inv

TREE compounds

DEVICE chemicaldb

USERNAME CPD/CPD

PASSWORD

TNAME compounds

TREE inventory

DEVICE oracle

USERNAME scott

PASSWORD tiger

TNAME inventory

LINK compounds (molregno) over inventory (molregno)

< RC tables>

inventory

inventory_id

molregno

cola

colb

colc

*

migration local isis databases
Migration: local ISIS databases
  • Analyse data hierarchy
  • Export data as SDF/RDF
  • Import into IJC
  • Build forms
  • Maybe possible to automate by writing COM application to read data from ISIS and write to Oracle database.
migration isis host databases
Migration: ISIS/Host databases
  • Analyse database tables and Hview
  • Migrate RCG tables to JChem table(s)
  • Connect IJC to the database
  • Promote tables/columns/foreign keys into IJC
  • Assemble IJC Data Tree
  • Build forms
  • May be possible for some automation.
migration topics78
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

jchem for excel79
JChem for Excel

Microsoft Excel integrated solution for Marvin and JChem functionality

Use Excel’s powerful features: Functions, Sorting, Filtering, Charts…

Implemented in C# .NET, and Visual Studio

Proof that ChemAxon APIs can be used in a Java-less .NET environment

Easy to install and deploy

UNDER DEVELOPMENT

isis for excel to jchem for excel
ISIS for Excel to JChem for Excel
  • Import ISIS SARTables (January 2009)
    • Workbook exported from ISIS for Excel
  • Migration of standard ISIS Workbooks?
migration topics81
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

custom applications
Custom Applications
  • Java Applications
    • Swing
  • .NET Applications
    • JNBridge: Commercial Java - .NET Proxy
    • Byte Code to IL (.NET binary) translation (IKMV)
      • Open Source, very good performance
      • No full GUI support at the moment, but coming
      • JChem for Excel is built using IKVM
  • Web Based Applications
    • JSP,ASP.NET, AJAX
  • SOAP
custom components
Custom Components
  • Plans to release custom components
    • Java Swing
    • AJAX Examples
    • .NET
      • Visual Studio integrated
      • Windows Forms (from JChem for Excel),WPF?
      • ASP.NET
      • ASP.NET AJAX, MVC
net integration enhancements
.NET Integration Enhancements
  • Problem : ChemAxon API uses Java Classes,not familiar to .NET developers
  • Higher Level .NET wrappers, components
    • Properties, Events
    • Search results in DataSet, IDataReader
    • LINQ, IEnumerable interfaces
    • GUI Components: DataGridView, Property Grids, Components for Search
custom application migration and development
Custom Application Migration and Development
  • Resources and experience for migrating custom ISIS(Host - Base) based applications
    • ISIS Forms to other applications
    • Procedural Language (ISIS/PL)
  • Consultation
    • Help with custom application development on ChemAxon platform
    • Both in-house (CXN) staff and partner companies are available
    • Custom/prioritised improvements of ChemAxon products
migration topics86
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

ChemAxon for Developers (Resources)

web services
Web Services

Extends ChemAxon functionality to Web applications

Enables interoperability from multiple programming languages with SOAP Protocol

Allows migration of existing web applications to ChemAxon services

Encourages creation new web applications

service modules
Service Modules

Application Building Blocks

DB Searching

Substructure, Similarity, Exact, etc.

Molecular Standardization

Clustering and Diversity

Chemically Intelligent Tools

Shorthand Chemical Terms and Calculator Plugins

Lipinski Rule of 5, pKa, logP, logD, etc.

Molecular Format Conversion

Image Generation

soap protocol
SOAP Protocol

SOAP protocol used by most major web application languages

Programming languages

Java

.Net (C#, ASP.net)

Scripting languages

JavaScript

Perl

Python

Etc.

migration of existing web apps
Migration of Existing Web Apps

ChemAxon Web Services can be called from existing web services

ChemAxon Web Services can directly replace specific functionality

Migrate using Security Standards

WS-Security, WS-Security Policy

Integrate with existing authentication services (e.g. LDAP, Active Directory)

creation of new web apps
Creation of New Web Apps

Standard WSDL files allow for automated client side code generation (Python, Perl, Java, C#, etc.)

AJAX provides asynchronous and desktop application performance

Easily integrate with Marvin applets

migration topics93
Migration - Topics

ChemAxon - Product Overview

From Isis/Host and MDL Direct to JChem Cartridge

Alternatives to Cheshire (Standardizer)

From ISIS/Base to Instant JChem

From ISIS for Excel To JChem for Excel

Migrating Custom Applications

ChemAxon Web Services

Appendix: ChemAxon for Developers (Resources)

api and compatibility
API and Compatibility
  • Java API (Marvin GUI included)
  • Marvin Applets for web applications
  • .NET API over JNBridge (Marvin GUI included)
  • Native .NET solution under development (Marvin GUI included)
  • API from SQL: JChem Cartridge for Oracle
  • SOAP interface (Python, C, .NET, ... over SOAP) under development
  • AJAX interface under development(Marvin GUI included)
  • Instant JChem highly configurable + Java API
  • Integration: Pipeline Pilot, KNIME, Spotfire, ...
java api
Java API
  • Direct manipulation of structures
  • Format conversions, name<=>structure, image generation
  • Structure searching with/without DB access
  • Standardization of structures
  • Property calculations
  • Reaction modelling (enumeration)
  • Clustering
  • Sketcher, 2D/3D viewers (Marvin family)
  • Etc

JChem API

marvin applets for web applications
Marvin Applets for Web Applications
  • All relevant browsers (IE, FF, Safari, ...)
  • Manipulation from HTML page (from JavaScript)
  • Catching drawing events in JavaScript
  • Can be used from .NET applications using the web browser control

Marvin demo

MarvinSketch Applet Examples

MarvinView Applet Examples

MarvinSpace Applet Examples

net api over jnbridge
.NET API Over JNBridge

Tight integration with .NET

Full Java API is mirrored in .NET

Marvin GUI components are also supported

native net s olution
Native .NET Solution
  • Translating the non-GUI elements to Java binary to .NET binary (using IKVM)
  • Building a thin .NET GUI for Marvin and other tools over the core.

Advantages

  • Pure .NET solution, Java is not needed to be installed
  • No license issue
  • No performance overhead of proxying

under development

jchem cartridge for oracle99
JChem Cartridge for Oracle
  • API from Oracle SQL
  • All features needed for structure handling and searching
  • Fast searching, insertion, and indexing
  • Special features:
    • Standardization of structures is tied with structure tables
    • Property calculations
    • Format conversions, name<=>structure, image generation
    • Reaction and Markush based structure enumeration
    • Markush libraries in structure tables (coming soon)
soap interface
SOAP Interface
  • Web services interface to most functionalities
  • Bridges to Python, C, Perl, .NET, Java using WSDL
  • Enables both remote and local access to ChemAxon functionalities

under development

ajax gui
AJAX GUI
  • AJAX components for web applications
  • Customization using CSS and XSL
  • Accesses SOAP interface
  • Structure searching, database handling example
  • Fast and rich GUI
    • Floating windows
    • Scrolling through large database without paging
  • Marvin Applets are integrated

under development

instant jchem for developers
Instant JChem for Developers
  • Sharable forms, queries, lists
  • URL-s to sharable items - Demos
  • Instant JChem API
integrations
Integrations

Several software vendors integrated ChemAxon components

  • Pipeline Pilot
  • KNIME (by Infocom)
  • Spotfire
  • Aureus
  • Integrity (Thomson)
  • Others: (Agilent, Tripos, Symyx, Deltasoft, GVK, Wiley, Genedata, Contur, Inforsense, Kinematik, Houghton Mifflin, Kelaroo, Patcore, Cengage, Prentice Hall, Crossfire Beilstein, etc)
slide104

Visit othertechnical presentations

ChemAxon Overviewhttp://www.chemaxon.com/conf/ChemAxon_Overview.ppt

MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt

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

Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt

Structural Searchhttp://www.chemaxon.com/Structural_Search.ppt

JChem Basehttp://www.chemaxon.com/JChem_Base.ppt

Instant JChemhttp://www.chemaxon.com/conf/Instant_JChem.ppt

JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt

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

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

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

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

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

find out more
Find out more
  • Product descriptions & links

www.chemaxon.com/products.html

  • Forum

www.chemaxon.com/forum

  • Presentations and posters

www.chemaxon.com/conf

  • Download

www.jchem.com/licensefrset.html