Marvin 5.1.4

An incredible Java based chemistry software that will definitely help you in your research.
Marvin is a Java based chemistry software, available in various forms:
· Marvin Applets are created for the Web Developer who builds chemical Internet/Intranet sites. The package contains:
· MarvinSketch/Swing and MarvinView/Swing: applets for editing and visualizing molecules on a web page. They are trusted, thus they are allowed to use local system resources, e.g. to open files from the local machine, to save file to the local machine, use the system clipboard of the local machine
· Java, JavaScript and C source for Molfile compression
· Marvin Beans are made for the Software Developer to incorporate molecule drawing or visualizing capabilities into a Java application. The package contains MarvinSketch and MarvinView as JavaBeans.
· MarvinSketch and MarvinView are applications for the Chemist or anyone else who wants to draw or view chemical structures.

Marvin can handle molecules in various file formats including MDL mol, Compressed mol, unique SMILES, CML, XYZ, SMARTS, Sybyl mol, PDB, POV-Ray.

The Marvin Applets support a wide range of Java platforms, from Java 1.3.1 to the latest versions. They work in older web browsers, but if they find themselves in a modern browser, they automatically utilize newer Java features.

Marvin is highly configurable and controllable via applet parameters and Java/JavaScript method calls.

MarvinSketch has many advanced features rarely or never found in other programs, like recent structures, visual fragment placement, ambiguity reduction, and multi-level undo/redo. MarvinSketch was the first structure drawing program to introduce visual fragment placement (1998) and recent structures (1999).

MarvinView can display a 2D or 3D molecule, or many molecules in a table. A molecule table may also contain GUI components: text labels, buttons, checkboxes. Checkboxes and buttons can trigger JavaScript calls from the Java applet, buttons may also trigger CGI script loading.

The applet has a pop-up menu, but the user can also view a molecule in a separate window that has an ordinary menu bar. A viewer window can be easily transformed into a MarvinSketch window, so the user can even edit the molecule(s).

Marvin can be equipped with custom chemical calculation tools by the integrated plugin services. Plugins are loaded dynamically upon request saving download time and system resources.

NOTE: You must register on the developer's website in order to download


Main features of Marvin:

All three programs are available in two forms:

applet to edit and visualize structures on a web page

standalone Java application

MarvinSketch and Marvin view support

stereochemistry,

abbreviated groups and multiple groups,

reactions,

2D and 3D cleaning,

isotopes,

displaying of implicit H atoms,

aromatization and dearomatization of molecules.
Plugins are available:

Elemental Analysis Plugin

Protonation: pKa, Major Microspecies, Isoelectric Point

Partitioning: logP, logD

Charge: Charge, Polarizability

Isomers: Tautomers, Resonance, Stereoisomers

Conformation: Conformers, Molecular Dynamics

Geometry: Topology Analysis, Geometry, Polar Surface Area (PSA), Molecular Surface Area (MSA)

Other: Hydrogen Bond Donor-Acceptor (HBDA), Huckel Analysis, Refractivity

Import/Export features in MarvinSketch and MarvinView

Various molecule file formats are supported.

The molecule file can also be viewed or edited non-graphically, in any of these text based formats.

JPEG, PNG, PPM and SVG image export.

Other features

Copy & Paste, Drag & Drop (in the Swing version).

applet parameters to modify the appearance

MarvinSketch:
Chemically intelligent:

sets charges and implicit H atoms according to valence rules as you draw

warns for valence errors

Periodic Table

Quick access to Template structures.

Creating user defined templates by dragging-and-dropping over template buttons.
Substructure search support:

Query atom types: "any atom", "heteroatom" atom list, 'NOT' list, SMARTS atom

Query bond types: "any", "single or double", "single or aromatic", "double or aromatic", bond topology ("chain", "ring"), reacting center ("center", "make or break", "change", "make and change", "not center"), SMARTS bond expressions (features: - = # : ; & , ! / /? ? @)

SMARTS properties: Hydrogen count, valence, connections (X), Ring count, Ring membership, smallest ring size, aromatic and Aliphatic. Degree, implicit hydrogen count

SMARTS atom expressions: logical expressions ( ; & , !), recursive smarts ($())

R-groups, R-group conditions.
Group creation support:

abbreviated groups and multiple groups (with repeat count).

Graphics objects can be inserted: lines, arcs, arrows, rectangles, text boxes.

Smart user interface

Pop-up menus.

Multi-level undo/redo.

Rectangle and lasso selection.

Zoom in and out.

Maximizable viewing area (visualization mode).

Detachable from the web page.

Alternative layout.

Smart rotation of

template buttons when dragging,

templates when joining,

selection.

Branching at a single click

Easy to recall keyboard shortcuts for

all the element types (C for Carbon, C-L for Chlorine, etc.),

8 bond types (1 for single, 2 for double, 1-2 for "single or double", etc.),

abbreviated groups,

templates, erase mode, undo, redo, etc.

Horizontal/vertical alignment to specified bond.

Horizontal/vertical flipping.

Multipage molecular document for handling of large documents.

Recent structures

Last templates, atom types, copy/pasted parts can be accessed quickly (from the pop-up menu), to ease the creation of many similar molecules.

"Real-time cleaning"

quantized angles and lengths,

smart fragment placement and displacement - automatic move/rotation to join perfectly,

merges close atoms,

deletes ambiguous bonds.

Visual fragment placement

Templates are immediately shown after picking up.

Highlights the joining points,

the atoms to be merged and

the bonds to be deleted.

Customizable

Create your own templates.

Usage of atom and bond types can be allowed or disallowed.

MarvinView:
3D features:

wireframe, "ball & stick", spacefill rendering styles,

animated 3D rotation,

animated XYZ files,

animation saving into a sequence of image files (in the application only),

bonds can be regenerated with user specified cut-off length (in the Swing version only)

Molecule tables for fast display of many search results in one applet.

User-defined labels, buttons, checkboxes, images.

CGI or JavaScript calls triggered by button presses and checkbox state changes.

Zooming of molecules in separate windows.

MarvinSketch can be launched to edit the viewed molecule.

Pop-up menu.

MarvinSpace:

3D visualization of molecules

Draw types: wireframe, ball, stick, spacefill

Color modes: cpk, residue, chain, constant

Labels: atom labels, residue labels, secondary structure label, editable labels, label coloring

Property settings: radii, colors, color schemas, controls keys, mouse control

Enhanced visualization

Optional depth cue, interactive control of fog start and fog end

Clipping planes, interactive translation of near and far clipping planes

Line and poligon anti-aliasing

3D manipulation

Scene: rotation, translation and zoom

Component: translation, rotation, scaling

Individual component selection, hide, show, delete, fade

Multiple cell view, synchronuous transformations of cells

Monitors and controls

Geometry measurements: distances, bond angle, dihedral angle

Controls: translate, rotate molecules individually, change dihedral angle interactively

All monitors are refreshed while components or controls are being changed

Macromolecules

Component recognition and classification: chains, ligands, ions, water molecules

Easy access to individual components

Secondary structure visualization (cartoon, ribbon) and coloring

Molecular surfaces

Various surface types: van der Waals, solvent accessible, Connolly surface; blobby surface

Fast surface calculation, accurate representation

Several display modes: dotted, mesh, filled, transparent

Coloring: by atom type, residue type, chain type, B-factor and other atomic properties; electrostatic potential and other volumetric data

customizable property mapping, property interpolation, property superposition, color blending

Iso surfaces, interactive cut-off


What's New in This Release:

New features and improvements:

MarvinSketch

Arrows group is restructured in the toolbar and in the menubar (forum topic).

The Insert > Groups menu is replaced by a more convenient dialog.

Import/Export

Unique SMILES should implicitize plain Hydrogens (forum topic).

Calculator Plugins

Unique Markush code can be generated for each enumerated structure.

logP and logD calculations are significantly faster.

API

New methods in chemaxon.beans.MViewPane: isViewWindowOpened(int), isSketchWindowOpened(int) and closeSketcher(int).

PDBReader and related classes were moved from chemaxon.modules to chemaxon.marvin.io.formats.pdb.

MacroMolecule and related classes were moved from chemaxon.modules to chemaxon.struc.

Bugfixes:

MarvinSketch

The layout of the Copy As... dialog is polished.

Periodic System button remained pressed on the toolbar even after the dialog was closed.

The Atom > Stereo > Enhanced, Atom > Charge, Atom > Map, Atom > R-group menus are replaced by more convenient dialogs. (forum topic)

Ctrl+Del in MarvinSketch did not delete properties.

Licenses

The command license -l produced bad output, not listing properly installed licenses.

Calculator Plugins

When using Calculator Plugins, the result window of a previous calculation sometimes reappeared (forum topic).

Huckel Analysis Plugin threw exception if the input molecule contained explicit hydrogens.