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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 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 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 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 Mesomerize Neutralize 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 Conversion of neutral form of nitro to the ionic, in Standardizer The same in command line Structure Checker Framework The new Structure Checker framework will provide plenty of validation and correction functions to detect and repair defective or unpreferred structures. • • • • • • • • • • • • • • • • • • • • • 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 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.
