The Marvin project offers a collection of Java tools for drawing, displaying and characterizing chemical structures, substructures and reactions.
Marvin can be easily installed on your desktop and seamlessly integrated into web pages and third party applications via its Application Programming Interface (API).
The Marvin family consists of the following tools:
* MarvinSketch
* MarvinView
* MarvinSpace
* MolConverter
Applets or Beans?
Marvin is available in two packages depending on usage:
* Marvin Applets for the web developer
* Marvin Beans for the chemist's desktop and for the software developer.
Marvin Applets are tools for building chemical web pages, which are compatible with most browsers (Internet Explorer, Firefox, Safari, Opera, etc.) They offer access from/to JavaScript and are customizable by applet parameters.
Marvin Beans are easily installable applications for the desktop and tools for integrating Marvin capabilities into any Java application.
Product's homepage
Requirements:
· Java 2 Standard Edition Runtime Environment
What's New in This Release: [ read full changelog ]
MarvinSketch:
· Public database search in chemicalize.org.
· Possibility to change ligand order in MarvinSketch.
Fog-effect can be controlled in various ways:
· There is a slider on the Display tab of the Preferences dialog in the Sketch/View GUI to set the strength of the fog-effect and a checkbox to switch off the automatic fog-effect.
· Applet and beans parameters are introduced: fogFactor, automaticFogEnabled. (forum topic).
· Attaching to a group attachment point does not automatically ungroup the Sgroup anymore.
· Determination of S-group content: multiple and generic S-groups have to contain the whole subgraph between the bonds crossing the brackets.
· Update of S-group content if bracket positions change: either brackets or the structure is moved.
· S-group embedding and overlap are checked at molecule consistency checks.
· SMARTS import supports aliphatic carbons with double bond (forum topic).
· SMILES import/export supports allenes.
· Generate traditional name for fragments inside a larger compound (e.g. "dextromethorphan hydrobromide").
· Support for CAS number conversion.
· Improved OCR error correction in DocumentExtractor (missing commas, misrecognized parenthesis type, extra spaces, ...).
· Document Extractor on PDF documents now gives the page number of hits.
· Improved support for common names in structure-to-name and name-to-structure. The general support for name import increased by around 5% for common and 10% for systematic names. Conversion speed is increased by about 20%.
· JChem and Marvin Beans installers for Windows also extract shell script for cygwin.
· Preserve exocycyclic groups in Bemis-Murcko frameworks.
· Halogen can have more than one connection during enumeration.
· Aromatic bonds are considered during calculating the number of double bonds for homology property checking.
· Lasso selection mode can be set to be the default in MSketchPane (forum topic).
· A new function, isChiral has been added to TopologyAnalyzer.
· New Chmical Terms functions: isQuery(), fieldAsString().
Bugfixes:
· Name box was not updated after group creation because creating a group did not increase graph invariant change count (forum topic).
· MarvinSketch application did not understand "-{name}" command line parameter.
· When the Structure > Find structure online menu was invoked under Linux, the default browser could not be detected to display result (forum topic).
· The loading of the isotopes.data file from the java cache failed if its uncompressed version was stored in the cache (i.e. if the uncompression was done automatically by the webserver, and not by Marvin). Forum topic, documentation.
· Graphical objects were not displayed in the Geometry Plugin result window.
· On the electron-flow arrow, the blue box for highlighting was missed (forum topic).
· Ligand order was not displayed on the scaffold if the definitions were deleted, even if the "Always" display option was set for "Ligand Orders" on the preferences dialog.
· Index of the multicenter atom became corrupt after exporting into MDL Mol format if it was connected to an R-group.
· Arrow stuck to rectangles was damaged during Mrv import/export (forum topic).
· Import of 1-letter peptide failed at a single Histidine (forum topic).
· Implicit hydrogens were missing by importing from skc.
· Null property value of MolAtom was not exported/imported in Mrv format.
· By importing certain SMARTS, wrong bond type was determined instead of single or aromatic bond.
· Certain brackets imported from Cdx files drawn in ChemDraw were displayed in the wrong direction.
· SMARTS export: 1-atom single bond neighbor of an aromatic ring was exported as single bond instead of single/aromatic.
· Exporting queries with link node and R-groups in SMARTS format were incorrect.
· The H atom handling was ambiguous in SMARTS expressions.
· Mol file comment field import failed.
· Importing of certain SMILES was wrong (forum topic).
· If the template contains a chain part which can be located in the target as a part of a ring (or ring system) we should ignore that part of the template.
· The Fine with Hydrogenize option of Clean3D did not ungroup S-groups automatically (forum topic).
· Molecule.contractSgroups() messed up the molecule coordinates (forum topic).
· Explicit hydrogens were not properly taken into account in Cis/Trans stereochemistry calculation.
· Tautomer generator threw ArrayIndexOutOfBoundsException in some cases.
· Homology enumeration produced inconsistent molecules for some VMN input.
· Incorrect charge count after applying CovalentCounterion fixer.
· The log output format of StructureChecker command line differed from output format of the wizard.
· ChiralFlagErrorChecker did not handle chirality correctly. Instead of calculating chirality from parity data, it used an implementation based on the isChiral method of TopologyAnalyser.
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