scientific & technical presentation standardizer january 2008

Scientific & technical presentation

Standardizer

January 2008

Why standardize structures?

To recognize the same compound represented with different chemical forms

Custom transformations

Custom transformationsBuilt-in functions

Availability

Mesomers

Tautomersoxo-enol, enamine-imine

Tautomerspyridone-pyridol

Solvent removal

Specific counterion removal

Built-in functions

Custom transformations

Built-in functionsAvailability

Fragment removal

Aromatization

Dearomatization

Hydrogen conversionsconverting implicit hydrogens to explicit

Hydrogen conversionsconverting explicit hydrogens to implicit

2D Cleaning

Template-based Cleaning2D-coordinate calculation of macrocycles or bridged systems

query

Template-based Cleaningaligning search results to the query

Stereo manipulations removing absolute R/S and E/Z stereo configurations

Stereo manipulations setting the absolute stereo (chiral) flag for stereo molecules

Stoichiometry expansionexpanding reaction stoichiometry

Stoichiometry expansionexpanding salt stoichiometry

Group manipulation

Availability

Custom transformations

Built-in functions

Availability

API and command line interface

Standardizer st = new Standardizer(new File("standardize.xml"));st.standardize(mol);

standardize input.sdf -c config.xml -o output.smiles

Graphical User Interface

Features

General– aromatize/dearomatize– add/remove explicit

hydrogens

Transforms– mesomers

– tautomers

– functional groups

Removals– solvents– counterions by list– remove smallest fragment– keep largest fragment– R-groups

Stereo– remove stereo features– set the absolute stereo flag

Sgroups– expand/contract/ungroup– clear/set the absolute stereo

flag– expand stoichiometry of

attached data

Cleaning– partial– full– template based

Features

Compatible– MOL, SDF, RXN, RDF (V2000/V3000)– SMILES, SMARTS/SMIRKS (recursive too)– MRV, CML, PDB

Flexible– customizable parameters– customizable conversions

Available– full API– command line interface– integration with JChem Base and Cartridge– documentation and examples– free for the Academic community

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