Using ChemAxon toolkits through .NET

1. Using ChemAxon toolkits through .NET GergelyKovács / Viktor Hámori

2. ChemAxon .NET product family Custom products by our customers JChem for SharePoint Search JChem for SharePoint JChem for Excel JChem .NET API

3. JChem .NET API package installer download Entry points ChemAxon .NET (workflow based API => future plan) Presentation focus ChemAxon .NET Windows Forms ChemAxon .NET Base ChemAxon .NET IKVM ActiveX/COM/ OLE .NET (assemblies) IKVM compilation Java (Jars)

4. MoleculeData Base What do we mean by Molecule Data? It is a very basic and important component in the ChemAxon.NET chemical object model. Structural approach Usability approach Known format consists of: Format Stream • MOL • MRV • SMILES • NAME • … String Unknown format • CDX • SKC • … Binary When the format is not known it takes a bit longer to get recognized when being loaded into a molecule. ∑: All ChemAxon supp. formats

5. IKVM Molecule What is the purpose of introducing a new molecule object? To have a central (mediator) object providing services for us. It gives real chemical knowledge to the Molecule Data and its data stream. • Lazy loading of Molecule Data (when necessary, requested by a service) • Clonable, renderable, comparable • Construction from • Another Molecule (copy construction) • Another molecule with shallow copy • Molecule Data (simple representation) • Special Multiple representation (base64 coded, zipped Molecule Data) • Gives Services • Basic services • Mass • Formula • ID (Corporate ID support) • Properties (for SDF file representation) • Advanced service • Rendering • Representations • Transformations • Calculations

6. IKVM Molecule Basic Services • Construction: • From Molecule Data: • From another Molecule: • From Native (low level molecule of Java API) Molecule: • From multiple Molecule(Representation)Data(please see how to represent aggregated data later) Properties: Simple Custom

7. IKVM Molecule Advanced Services - Rendering Purpose of the molecule rendering interface is to give .NET compliant façade for our customers that suits to the System.Drawing and System.Drawing.Imaging namespaces. • 1 line code to get an image from molecule datavarimg = new JChemMolecule(new MoleculeData("C=C", MoleculeFormat.SMILES)).Renderer.RenderToImage(ImageFormat.Emf); • This is most frequently requested support question (how to render …) • Easy to use • Supporting multiple mediums • Service for both web and desktop applications • Chemical Rendering Settings Stream/IO Device

8. Molecule Advanced Services - Controls Windows.Forms Predefined controls as molecule renderers in ChemAxon .NET API • MarvinView Control (Molecule Panel) • Windows Forms compatible • Designer compatible • Bindable • Drag & Drop support (from file) • Copy & Paste support • Rendering Settings • Editing extension => MarvinSketchForm • MarvinSketch Form (dialog) • IMoleculeEditorViewinterface support • Easy to use class editor workflow support (yes/no transaction) • MarvinEditor Control • Windows Forms compatible • Copy & Paste support • Native java Marvin support • In-place editing

9. IKVM Molecule Advanced Services - Representations Representations service gives you the molecule back in the requested format. The result obviously is an individual new molecule data you can continue your work with, e.g. creating a brand new Molecule, or store the internal stream in your program. Read, write representations Single (MoleculeData) Batch (IO) • Special: • HTTP encoded • BASE64 encoded • Crypto hashes • GZIP • Custom: • Own format can be implemented • String: • MOL • SMILES • MRV • Binary: • CDX • SKC • LoadFromFile • SaveToFile • LoadAllFromFile • SaveAllToFile Aggregated ( multiple MoleculeRepresentationData)

10. IKVM Molecule Advanced Services - Calculations Purpose of the calculations service is to perform “read-only” calculations on a molecule and return the calculated result numbers or the result molecule. Interface functions look like “Get something from the molecule”. Result categories Calculated molecules Calculated values • logP • pKa • Atom charge • … • (Get)logP(Molecule) • (Get) pKa(Molecule) • (Get)Charge(Molecule) • … • Fragments • Largest Fragment

11. IKVM Molecule Advanced Services - Transformations Transformations are such specific calculations, where logically/chemically modifications are made on the molecule. Therefore the returning value is always a new molecule and the interface contains functions look all like “DO something with molecule”. Actions Single actions Batch actions • Standardization (Standardize) • Structure checking (CheckStructure) • Structure fixing (FixStructure) • Aromatization (Aromatize) • Dearomatization (Dearomatize) • Hydrogenization (AddHAtoms) • Dehydrogenization (RemoveHAtoms) • 2-D Clean (Clean2D) • 3-D Clean (Clean3D)

12. Molecule Advanced Services – Grid View Windows.Forms Grid View is defined to visualize batch of compounds in a browseable control. • Windows Forms compatible • Custom Designer • Bindable • Supports Data formats (for binding) • Binding list (of Molecules) • Data Table with • Molecule string • Byte stream • Displaying more than one molecule column • Formula subscript (C6H12O6) • Copy & Paste support • Rendering Settings • Editing extension => MarvinSketchForm

13. IKVM Workflow Based Services – R-group Decomposition Our first supported workflow doing chemical calculation is the R-group decomposition process. • What we need is: • Query molecule (with R-groups) • List of JChem Molecules for Targets … • Reusing Grid View Control to display results

14. JChem .NET API package Presentation focus ChemAxon .NET Windows Forms ChemAxon .NET Base ChemAxon .NET IKVM installer download

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