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
sequence
|
IUPAC
RDfile SDfile | Peptide
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 endusers
•
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
link nodes
attached data
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
topology
•
•
Cleaning Options
2D
– optional optimization
– wedge bonds cleaning
•
–
–
–
–
–
2D
3D
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