Scientific & technical presentation MarvinSketch and MarvinView May 2008.
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Transcript of Scientific & technical presentation MarvinSketch and MarvinView May 2008.
Scientific & technical presentation
MarvinSketch and MarvinView
May 2008
Instead of Introduction
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)
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
Multirecord file open in MarvinSketch
Converting Images to Structure using OSRA
Image Export
• Create raster or vector graphical image from your structure.
OLE component for documents
• Editable molecules in Office
documents
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– Desktop applications
(deployment with Java or .NET Installer or Java Web Start)
– Full API (with JavaBean or .NET support) 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 Applets
• Marvin Applets– Browser-independent
solution for Marvin integration into web pages
– Wide range of layout customization
– API to control the applets from JavaScript
– 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
Web Browser Compatibility
•Internet Explorer
•Firefox
•Mozilla
•Netscape
•Safari
•Opera
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.
Custom Marvin Applets Layout
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 of structures
- 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
Click-drawing, sprout, on-the-fly expansion
Stereo Features, Lone Pairs
Reactions
Templates
Bold bonds and their juncitons
Brackets as graphical objects
Abbreviated and Multiple Groups
Other Sketching Goodies
electron flow arrows
attached data
link nodes
3D sketching
Rich formatting
Configuration setting
ChemDraw configuration
ISIS/Draw configuration
Formatting, customizing
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
• 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
R-group Queries
Structure Cleaning
CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1
3D2D
topology
• Cleaning Options• 2D
– optional optimization– wedge bonds cleaning
• 3D– fast clean– find low energy
conformer– optional
hydrogenization– optional optimization– generate 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
Structure checker in MarvinSketch GUI
Direct search in ChemSpider
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
• 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
• 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
• Single structure or table views
• Animated views in viewer
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
• 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
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.
Visit other technical presentations
MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt
MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt
Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt
JChem Base http://www.chemaxon.com/JChem_Base.ppt
JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt
Standardizer http://www.chemaxon.com/Standardizer.ppt
Screen http://www.chemaxon.com/Screen.ppt
JKlustor http://www.chemaxon.com/JKlustor.ppt
Fragmenter http://www.chemaxon.com/Fragmenter.ppt
Reactor http://www.chemaxon.com/Reactor.ppt
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