Date post: | 21-Jan-2015 |
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Technology |
Upload: | chemaxon |
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Scientific & technical presentation
MarvinSketch and MarvinView
May 2008
Instead of Introduction
Technical Features
• File types to read/write:
– 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 Name
• Flexible
– Calculation plugins
– Custom templates
– Custom formatting
– Image export into BMP, JPEG,
PNG, PPM, POV, SVG, EMF,
• 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 1.4 (or later version)
platforms (Windows, Mac,
Solaris, Linux/Unix)
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 | IUPAC
InChI IUPAC Name | MDL Molfile Extended
Molfile Rxnfile Extended Rxnfile RDfile SDfile |
Peptide sequence | SMILES SMARTS | Tripos
SYBYL molfile Mol2 | Gaussian Cube | PDB |
XYZ
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 Installer,
Java Web Start)
– Full API (with JavaBean
support) for developers to use
Marvin components in
applications
– Documentation and examples
• Recommended for end-users
– Easy installation
– Support Java 1.4 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 1.4 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
• Drawing molecules, reactions, residues
• Isotopes, charges, radicals
• Stereo features:– tetrahedral (R/S)
– double bond (E/Z)
– diastereomer (Abs/And/Not)
• Reaction (Inv/Ret)
• Templates, aliases, pseudo atoms
• Abbreviated groups, Multiple groups
• Link nodes
• Attached data
• Graphic objects (lines, arrows, boxes, text)
• Curved electron arrows
• Multi-page layout
• Rich compound format:– Fonts
– Colors
– Bond thickness
– Journal drawing styles to load/save
• 3D sketching
Isotopes, Charges, Radicals
Stereo Features, Lone Pairs
Reactions
Templates
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
– Occurence
– RestH
– If-Then conditions
– Recursive SMARTS
• Basic chemistry functions:
– Aromatization/dearomatization
– Automatic stereo configuration
(R/S, E/Z)
– Automatic reaction component
identification
– Automatic reaction mapping
– Cleaning 2D layout
– 3D geometry optimization
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
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
MarvinView Tables
• Display SD files with property
fields
• (Re)customize table layout:
- visible rows/cols
- font size
• (Re)scale molecules in cells
separately or uniformly
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