Technical presentation

Alternatives to MDL® Cheshire

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

•Chemical Terms

•Standardizer

Java API for Cheminformatics from ChemAxon

ChemAxon’s class library consists of more than 1,500 chemistry related classes tuned for usability and high performance.

Chemical Terms

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

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

Aromatize

Dearomatize

Add Explicit Hydrogens

Remove Explicit Hydrogens

Clean2D

Clean3D

Transform

Wedge Clean

Clear Isotopes

Remove Fragments

Remove R-groups

Neutralize

Tautomerize

Mesomerize

Set Absolute Stereo

Remove Absolute Stereo

Convert Wedge Interpretation

Convert Double Bonds

Clear Stereo

Alias to Group, Alias to Atom

Contract Group

Expand Group

Ungroup

Expand Stoichiometry

Map Reaction

Unmap

Counting Groups – Cheshire

Counting O=S=O groups in Cheshire

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 and cleaning the molecule in Cheshire

Adding Explicit Hydrogens – Java API

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

Adding Explicit Hydrogens – Standardizer

Adding explicit hydrogens and cleaning the molecule with Standardizer

The same in command line

Group Conversions – Cheshire

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

Group Conversions – Java API

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

Group Conversions – Standardizer

The same in command line

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

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

• 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.

• 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.