Transcript Standardization

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.
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ValenceChecker
AromaticityChecker
OverlappingAtomsChecker
OverlappingBondsChecker
CrossedDoubleBondChecker
WigglyDoubleBondChecker
WedgeBondsChecker
BondLengthChecker
BondAngleChecker
AliasChecker
PseudoAtomChecker
AbbreviatedGroupChecker
MultiComponentChecker
QueryChecker
MoleculeChargeChecker
RadicalChecker
IsotopeChecker
ExplicitHydrogenChecker
StereoDoubleBondChecker
TetrahedralStereoAtomChecker
UnspecifiedStereoDoubleBondChecker
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ChiralFlagChecker
CovalentSaltChecker
FerroceneChecker
CumulatedRingBondChecker
UnbalancedReactionChecker
MultistepReactionChecker
AtomMapChecker
MissingAtomMapChecker
AtomMapStyleChecker
RgroupQueryChecker
MarkushChecker
3DCoordinateChecker
MolfileChecker
RxnfileChecker
SmilesChecker
SmartsChecker
InchiChecker
PeptideSequenceChecker
CmlChecker
PdbChecker
Summary
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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.
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Java is a standard language with worlwide community, rich resources and lots
of well educated developers.
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Chemical Terms provides more than a hundred high level, ready to use
functions substituting dozens of lines of complex Cheshire code.
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Chemical Terms expressions can directly be used in database filters, virtual
reactions, pharmacophore definitions or other cheminformatics applications.
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Standardizer is an easy to use batch tool and graphical interface for chemists
to create conversion rules without writing a single line of code.
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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.