Post on 18-Nov-2014
description
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.