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

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.

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.

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.