Standardizer
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Feature Animations
Overview
Standardizer is a structure canonicalization tool in JChem for converting molecules from different sources into standard representational forms. Standardizer can automate the identification of mesomers and tautomers and can be used for counter-ion removal.
Flexible molecule transformation engine:- hydrogen manipulations
- aromatic bond transformations
- mesomers
- tautomers
- template based cleaning
- counter ion and solvent removal (by size, counter ion list)
- generation of 2D and 3D coordinates
- set or remove chiral flag, remove stereo features
- enumerate stoichiometry constants
- user defined canonicalization rules
FAQ
What is Standardizer?
Standardizer is a customizable chemical structure conversion tool of ChemAxon.
What is Standardizer good for?
It is good for the uniformization of functional groups and for restoration of chemical structures stored in old system.
Why the uniformization of functional groups is important?
The most important application of standardization is the uniformization of structures stored in databases. The same chemical compound can be represented by different structural graphs. Mesomeric forms of functional groups like nitro or azide, or tautomeric forms like oxo/enol or enamine/imine, or salts containing various counterions frequently cause problems in database searching. If these functional groups of the chemical structures are stored in a uniform manner, graph-based structure search methods will find the corresponding compounds correctly.
Can Standardizer automatically handle the content of a structure table?
Yes, a standardization configuration (an XML) can be set for each structure table and then all compounds inserted will be standardized accordingly. Upon searching, all query structures will be standardized in the same way, so matching will be accurate.
When a chemist adds a chemical structure to a standardized database table, will the original structure be modified by the standardization?
No, the original structures always remain intact as the chemist drawn it. A standardized version is stored in a compact form in a second database column (in the index in case of JChem cartridge).
Can I specify my own standards for the representation of chemical structures?
Yes, the standardization configuration is completely customizable. ChemAxon provides some example configuration files to start with, that can be downloaded from this link.
What if I later would like to change my standardization method?
Since the original structures are always stored, the standardized forms are regenerated automatically when the standardization configuration changes
Why the restoration of chemical structures is needed?
Older chemical databases had serious limitations in the representation of some chemical structures like organometallics with valence errors, isotopes represented by rare elements, or abbreviations represented by aliases. The chemical structure having information stored in these structures in a non-standard way can be converted to the current standards.
Does Standardizer support the generation of canonical files?
Canonicalization is is a two-step procedure. The first is to convert functional groups to a uniform representation. This can be done with the help of Standardizer. The second step is to export the atoms/bonds of the structure to the file in a canonical order. This is an option of the export of some file formats, like SMILES.
Do I need standardizer to generate canonical/unique SMILES?
No, the canonical/unique SMILES mostly mean aromatization and canonical atom order only, that is provided as an option of our SMILES export.
Do I need standardizer to generate canonical InChI?
No, InChI has its own standard, wired-in method for generating canionical output.
How can I specify a Standardization configuration?
An easy to use graphical edior is provided for the design of standardization configuration, that consists of a list of actions.
Can I batch convert files with Standardizer?
Yes, a command line utility and a graphical wizard application is available for the batch standardization of chemical structure files.
I am a software developer, can I integrate Standardizer within my application?
Yes, a programming API if provided with standardizer.
What programming language I can use to access the functionalities of Standardizer?
Standardizer functions are available in Java, .NET API and can also be accessed from many scripting languages like php, perl or ruby via the JChem Web Services. JChem cartridge users can call Standardizer functions by SQL statements.
There are many actions available in standardizer, can I specify own standardization “rules”?
Yes, you can specify your own conversion rules by drawing simple unimolecular transformation schemes to the Transform action (single reactant, single product). These transform actions can have own names and can be saved as templates as well.
How Standardizer is licensed?
Standardizer has been licensed by the number of users accessing the functionalities since 2010.
Is Structure Checker included with Standardizer?
Structure Checker API and batch mode execution requires Standardizer license to run, except for Marvin Sketch where individual molecules can be checked without a Standardizer license.
