Scientific & technical presentation
MarvinSketch and MarvinView
May 2008

Instead of Introduction

Technical Features
• File types to read/write: • Printing, multipage documents
– MOL, SDF, RXN, RDF • 3D models, Java or OpenGL
(V2000/V3000) rendering (with MarvinSpace)
– SMILES, SMARTS/SMIRKS • Available as
(recursive)
– Java (signed) applets
– XML based format MRV, CML,
InChi, MOL2, XYZ, Gaussian – Applications, deployment with
Cube installer, Java Web Start
– PDB, 1 and 3 letter peptide – JavaBeans
– IUPAC Name • System Requirements:
• Flexible – Java 1.4 (or later version)
platforms (Windows, Mac,
– Calculation plugins
Solaris, Linux/Unix)
– Custom templates
– Custom formatting
– Image export into BMP, JPEG,
PNG, PPM, POV, SVG, EMF,
PDF

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 • Recommended for developers
– Desktop applications – Quick GUI building
(deployment with Installer,
– Easy customization
Java Web Start)
– Full API (with JavaBean – Direct manipulation of
support) for developers to use molecules
Marvin components in
applications • Free for open access, non
– Documentation and examples commercial websites
• Recommended for end-users • Free for academic research
– Easy installation and teaching
– Support Java 1.4 capable • Free for Evaluation
platforms (Windows, Mac OS X,
Linux/Unix)
– Command line molecule
converter
– Applications are free for end-
users

Distributions / Marvin Applets
• Marvin Applets • For web developers
– Browser-independent – Simple web base
solution for Marvin deployment
integration into web pages – Modular architecture
– Wide range of layout ensures short download
customization time
– API to control the applets – Minimum requirement
from JavaScript (Java 1.4 capable
– Documentation and browsers)
examples
• 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, • Link nodes
reactions, residues • Attached data
• Isotopes, charges, • Graphic objects (lines,
radicals arrows, boxes, text)
• Stereo features: • Curved electron arrows
– tetrahedral (R/S) • Multi-page layout
– double bond (E/Z)
– diastereomer • Rich compound format:
(Abs/And/Not) – Fonts
• Reaction (Inv/Ret) – Colors
– Bond thickness
• Templates, aliases, – Journal drawing styles to
pseudo atoms load/save
• Abbreviated groups, • 3D sketching
Multiple groups

Isotopes, Charges, Radicals

Stereo Features, Lone Pairs

Reactions

Templates

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 • Basic chemistry functions:
– Generic atoms, generic bonds – Aromatization/dearomatization
– Atom lists/not lists – Automatic stereo configuration
– Query properties: hydrogen (R/S, E/Z)
count, connection count, – Automatic reaction component
number of explicit connections, identification
ring count, smallest ring size, – Automatic reaction mapping
ring bond count, substitution – Cleaning 2D layout
count, unsaturation,
aromatic/aliphatic atom – 3D geometry optimization
– Topology (ring/chain)
– Reacting center
– R-group queries
– Occurence
– RestH
– If-Then conditions
– Recursive SMARTS

R-group Queries

Structure Cleaning
• Cleaning Options
• 2D
CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1
– optional optimization
– wedge bonds cleaning
topology
• 3D
– fast clean
– find low energy
conformer
– optional
hydrogenization
– optional optimization
– generate conformers
2D 3D

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