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Scientific & technical presentation Marvin Sketch and MarvinView. May 200 8. Instead of Introduction. File types to read/write: MRV, CDX, SKC MOL, SDF, RXN, RDF (V2000/V3000) SMILES, SMARTS/SMIRKS (recursive) XML based format MRV, CML, InChi, MOL2, XYZ, Gaussian Cube

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technical features
File types to read/write:

MRV, CDX, SKC

MOL, SDF, RXN, RDF (V2000/V3000)

SMILES, SMARTS/SMIRKS (recursive)

XML based format MRV, CML, InChi, MOL2, XYZ, Gaussian Cube

PDB, 1 and 3 letter peptide

IUPAC and traditional name

Flexible

Customizable menu/toolbar

Custom templates

Calculation plugins

Custom formatting

Image export into BMP, JPEG, PNG, PPM, POV, SVG, EMF, PDF

Printing, multipage documents

3D models, Java or OpenGL rendering (with MarvinSpace)

Available as

Java (signed) applets

Applications, deployment with installer, Java Web Start

JavaBeans

System Requirements:

Java 1.5 (or later version) platforms (Windows, Mac, Solaris, Linux/Unix) or

.NET (Windows)

Technical Features
various file formats
Various File Formats
  • Molecule source file can be edited and saved or imported/exported in different formats
  • Possible to insert into a long file of many compounds at a given location
  • Also possible to read a structure from a given position of a long file
  • Append current structure to an existing file

ChemAxon Marvin Documents | CML | CDX CDXML | SKC | MDL Molfile Extended Molfile Rxnfile Extended Rxnfile RDfile SDfile | Peptide sequence | IUPAC InChI IUPAC Name | SMILES SMARTS | Tripos SYBYL molfile Mol2 | Gaussian Cube | PDB | XYZ

image export
Image Export
  • Create raster or vector graphical image from your structure.
ole component for documents
OLE component for documents
  • Editable molecules in Office documents
system compatibility
System Compatibility
  • 100% pure Java
  • .NET integration
    • Through JNBridge
  • Windows
    • 95, 98, Me, NT, 2000, XP, Vista
  • Mac OS X
  • Unix/Linux
    • Linux, Solaris, etc.
distributions marvin beans
Marvin Beans

Desktopapplications(deployment with Java or .NET Installer or Java Web Start)

Full API (with JavaBean or .NETsupport) for developers to use Marvin components in applications

Documentation and examples

Recommended for end-users

Easy installation

Support Java 1.5 or .NET capable platforms (Windows, Mac OS X, Linux/Unix)

Command line molecule converter

Applications are free for end-users

Recommended for developers

Quick GUI building

Easy customization

Direct manipulation of molecules

Free for open access, non commercial websites

Free for academic research and teaching

Free for Evaluation

Distributions / Marvin Beans
distributions marvin applets
Marvin Applets

Browser-independent solution for Marvin integration into web pages

Wide range of layout customization

API to control the applets fromJavaScript

Documentation and examples

For web developers

Simple web base deployment

Modular architecture ensures short download time

Minimum requirement (Java 1.5 capable browsers)

Free for open access, non commercial websites

Free for academic research and teaching

Free for Evaluation

Distributions / Marvin Applets
web browser compatibility
Web Browser Compatibility
  • Internet Explorer
  • Firefox
  • Mozilla
  • Netscape
  • Safari
  • Opera
applet specific features
Applet Specific Features
  • Using Swing GUI components, the appropriate version for the browser / JRE is automatically selected
  • Signed (trusted) applets enable access to local files, system clipboard and allow printing.
  • Applet API accessible from JavaScript to
    • fetch the current structure from the applet and send it to the server for further processing.
    • change the structure or display options of the applet without reloading the page.
developing with marvin beans
Developing with Marvin Beans
  • Use Marvin Beans to add MarvinSketch or MarvinView as a graphical component to your standalone application

Additional API is accessible for

- Import / Export

- Performing calculations with plugins

- 2D and 3D cleaning ofstructures

- All operations accessible in the GUIs are also available in the API.

molecule sketching features
Easy sketching

Click-drawing, sprout

Templates, aliases, pseudo atoms

Toolbars, shortcuts

Stereo features:

tetrahedral (R/S)

double bond (E/Z)

diastereomer (Abs/And/Not)

Reaction (Inv/Ret)

Groups

Abbreviated, multiple, repeating unit, generic,polymer related groups

On-the-fly expanding

Bold bonds for projected drawing

Bracket objects for Sgroups

Attached data

Textboxes

Graphic objects (arrows, boxes, ellipses, brackets)

Curved electron arrows

Multi-page layout

Rich compound format:

Fonts, colors, bond thickness

Journal drawing styles to load/save

3D sketching

Molecule Sketching Features
other sketching goodies

electron flow arrows

link nodes

attached data

3D sketching

Other Sketching Goodies
configuration setting
Configuration setting

ChemDraw configuration

ISIS/Draw configuration

customizing drawings
Customizing drawings
  • Add graphic objects (lines, arrows, boxes, text boxes)
  • Possible to change font, color, wire thickness
  • Save/load different publication styles
  • Multi-paged documents
marvinspace integration
MarvinSpace Integration
  • Properties calculated by plugins can be visualized using MarvinSpace
query and general chemistry features
Query design features

Generic atoms, generic bonds

Atom lists/not lists

Query properties: hydrogen count, connection count, number of explicit connections, ring count, smallest ring size, ring bond count, substitution count, unsaturation, aromatic/aliphatic atom

Topology (ring/chain)

Reacting center

R-group queries

R-logic

Position variation

Link node

Recursive SMARTS

Basic chemistry functions:

Automatic valence check

Automatic lone pair calculation

Automatic stereo configuration (R/S, E/Z)

Automatic reaction component identification

Automatic reaction mapping

Conversion between aromatic and Kekulé form

Cleaning 2D layout

3D geometry optimizationn

Structure checker

Automatic error checking

Optional fixes for errors

Searching in online databases

ChemSpider exact search

Query and General Chemistry Features
structure cleaning

Cleaning Options

  • 2D
    • optional optimization
    • wedge bonds cleaning
  • 3D
    • fast clean
    • find low energy conformer
    • optional hydrogenization
    • optional optimization
    • generate conformers

CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1

Structure Cleaning

topology

3D

2D

display conformers
Display Conformers
  • Using the conformers plugin one can generate the most likely 3D structures and select a suitable one
  • The corresponding energies are also calculated for a given conformation
advanced plugin based functions
Advanced (plugin based) Functions
  • Elemental Analysis
  • IUPAC Name
  • Protonation (pKa, Major Microspecies, Isoelectric Point)
  • Partitioning (logP, logD)
  • Charge (Charge, Polarizability, Orbital Electronegativity)
  • Isomers (Tautomers, Resonance, Stereoisomers)
  • Conformation (Conformers, Molecular Dynamics)
  • Geometry (Topology analysis, Geometry, Polar surface area (2D), Molecular Surface Area (3D))
  • Markush Enumeration
  • Other (H-bond donor/acceptor, Huckel Analysis, Refractivity)
calculator plugins
Calculator Plugins
  • ChemAxon’s plugin loading mechanism enables Marvin to provide access to a wide range of dynamically loaded calculation tools
  • A set of plugins already provided by ChemAxon for a separate license key (single trial is included in every distributions for plugins)
  • Users can easily add their own calculator plugins to this framework
2d 3d structure visualization
2D & 3D Structure Visualization
  • Accurate representation
  • Rich visualization options
  • Various display modes (wireframe, ball&stick, spacefill, etc.)
    • Enable/disable hydrogen visibility (explicit / implicit, on hetero and/or terminal)
    • Optional display of stereo information
    • Various rotation modes
    • Optional valence and reaction error highlighting in sketcher
further display features
Further Display Features
  • Single structure or table views
  • Animated views in viewer
molecule matrix view
Molecule Matrix View
  • Display SD files with property fields
  • (Re)customize table layout: visible rows and columns; font size
  • (Re)scale molecules in cells separately or uniformly
spreadsheet view
Spreadsheet View
  • Display structures and data field in the same row
  • Resizable and movable columns
  • Search and edit in data fields
  • Fast loading and scrolling of huge SDFiles
summary
Summary

ChemAxon MarvinSketch and MarvinView are chemically aware, flexible applications enabling the chemist to draw and display chemical structures and to perform predictive calculations.

Marvin Beans and Marvin Applets allow developers to integrate these tools into standalone and web applications.

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Visit othertechnical presentations

MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt

MarvinSpacehttp://www.chemaxon.com/MarvinSpace.ppt

Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt

JChem Basehttp://www.chemaxon.com/JChem_Base.ppt

JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt

Standardizerhttp://www.chemaxon.com/Standardizer.ppt

Screenhttp://www.chemaxon.com/Screen.ppt

JKlustorhttp://www.chemaxon.com/JKlustor.ppt

Fragmenterhttp://www.chemaxon.com/Fragmenter.ppt

Reactor http://www.chemaxon.com/Reactor.ppt

links
Links
  • Marvin home page
    • www.chemaxon.com/marvin
  • Full Marvin API:
    • www.chemaxon.com/marvin/doc/api
  • Animated demos and tutorials
    • www.chemaxon.com/demosite/marvin
  • Brochures:
    • www.chemaxon.com/brochures/MarvinSketch.pdf
    • www.chemaxon.com/brochures/MarvinView.pdf
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