Alternatives To Symyx® Cheshire®

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Overview of technologies at ChhemAxon relevant to MDL / Symyx Cheshire®. Particularly relevant for those exploring migration and platform development

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Alternatives To Symyx® Cheshire®

  1. 1. Technical presentation Alternatives to MDL ® Cheshire
  2. 2. Cheshire Alternatives from ChemAxon <ul><li>What is Cheshire? </li></ul><ul><li>“ 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.” </li></ul><ul><li>What alternatives can ChemAxon offer? </li></ul><ul><li>ChemAxon’s Java API </li></ul><ul><li>Chemical Terms </li></ul><ul><li>Standardizer </li></ul>
  3. 3. 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.
  4. 4. 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.
  5. 5. 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.
  6. 6. 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
  7. 7. Counting Groups – Cheshire Counting O=S=O groups in Cheshire
  8. 8. Counting Groups – Java API Counting any functional groups with ChemAxon’s Java API Counting O=S=O groups in Chemical Terms
  9. 9. Adding Explicit Hydrogens - Cheshire Adding explicit hydrogens and cleaning the molecule in Cheshire
  10. 10. Adding Explicit Hydrogens – Java API Adding explicit hydrogens and cleaning the molecule with ChemAxon’s Java API
  11. 11. Adding Explicit Hydrogens – Standardizer Adding explicit hydrogens and cleaning the molecule with Standardizer The same in command line
  12. 12. Group Conversions – Cheshire Conversion of neutral form of nitro to the ionic one in Cheshire
  13. 13. Group Conversions – Java API Conversion of neutral form of nitro to the ionic one with ChemAxon’s Java API
  14. 14. Group Conversions – Standardizer The same in command line Conversion of neutral form of nitro to the ionic, in Standardizer
  15. 15. Structure Checker Framework <ul><li>ValenceChecker </li></ul><ul><li>AromaticityChecker </li></ul><ul><li>OverlappingAtomsChecker </li></ul><ul><li>OverlappingBondsChecker </li></ul><ul><li>CrossedDoubleBondChecker </li></ul><ul><li>WigglyDoubleBondChecker </li></ul><ul><li>WedgeBondsChecker </li></ul><ul><li>BondLengthChecker </li></ul><ul><li>BondAngleChecker </li></ul><ul><li>AliasChecker </li></ul><ul><li>PseudoAtomChecker </li></ul><ul><li>AbbreviatedGroupChecker </li></ul><ul><li>MultiComponentChecker </li></ul><ul><li>QueryChecker </li></ul><ul><li>MoleculeChargeChecker </li></ul><ul><li>RadicalChecker </li></ul><ul><li>IsotopeChecker </li></ul><ul><li>ExplicitHydrogenChecker </li></ul><ul><li>StereoDoubleBondChecker </li></ul><ul><li>TetrahedralStereoAtomChecker </li></ul><ul><li>UnspecifiedStereoDoubleBondChecker </li></ul><ul><li>ChiralFlagChecker </li></ul><ul><li>CovalentSaltChecker </li></ul><ul><li>FerroceneChecker </li></ul><ul><li>CumulatedRingBondChecker </li></ul><ul><li>UnbalancedReactionChecker </li></ul><ul><li>MultistepReactionChecker </li></ul><ul><li>AtomMapChecker </li></ul><ul><li>MissingAtomMapChecker </li></ul><ul><li>AtomMapStyleChecker </li></ul><ul><li>RgroupQueryChecker </li></ul><ul><li>MarkushChecker </li></ul><ul><li>3DCoordinateChecker </li></ul><ul><li>MolfileChecker </li></ul><ul><li>RxnfileChecker </li></ul><ul><li>SmilesChecker </li></ul><ul><li>SmartsChecker </li></ul><ul><li>InchiChecker </li></ul><ul><li>PeptideSequenceChecker </li></ul><ul><li>CmlChecker </li></ul><ul><li>PdbChecker </li></ul>The new Structure Checker framework will provide plenty of validation and correction functions to detect and repair defective or unpreferred structures.
  16. 16. Summary <ul><li>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. </li></ul><ul><li>Java is a standard language with worlwide community, rich resources and lots of well educated developers. </li></ul><ul><li>Chemical Terms provides more than a hundred high level, ready to use functions substituting dozens of lines of complex Cheshire code. </li></ul><ul><li>Chemical Terms expressions can directly be used in database filters, virtual reactions, pharmacophore definitions or other cheminformatics applications. </li></ul><ul><li>Standardizer is an easy to use batch tool and graphical interface for chemists to create conversion rules without writing a single line of code. </li></ul><ul><li>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. </li></ul>

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