OSRA 2.0.0 is available for download.
OSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or MOL files –
- Significantly improved recognition rates. Full details of the validation are available.
- Added recognition of Iodine, wavy bonds, etc.
- Completely modified confidence function (values not compatible with the earlier versions).
- Updated table detection and removal routines.
- Created binary package for Linux (statically linked, should work on all modern Linux systems).
- Windows and OSX versions now support multi-threading processing of PDF files.
With this release the distribution model has been changed a bit: while the source code is available free as before, to offset the development costs the installable packages for Windows, Mac OSX and Linux can be purchased for a fee.
The Open Chemistry Group have just announced the availability of the first beta release of a suite of software packages for chemists.
It consists of Avogadro 2 an update to the well established molecular editing package, see a recent paper describing it for more details “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform” DOI.
Some notable new features of Avogadro 2 include:
- Scalable data structures capable of addressing the needs of large molecular systems.
- A flexible file I/O API supporting seamless addition of formats at runtime.
- A Python-based input generator API, creating an input for a range of quantum codes.
- A specialized scene graph for supporting scalable molecular rendering.
- OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
- Unit tests for core classes, with ongoing work to improve coverage.
- Binary installers generated nightly.
- Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.
The final element of this first beta release is a chemically aware database MongoChem built on MongoDB intended to address the need for researchers and groups to be able to effectively store, index, search and retrieve relevant chemical data. It uses Open Babel to provide the cheminformatics input
There is a slide presentation describing the project in more detail here/
Marvin 5.12.3 has been released with a couple of bug fixes
- Name to Structure (n2s)
- Names with ylium and uide suffixes are now supported.
Calculation NMR (HNMR, CNMR Prediction, ...)
- Coupling of a nucleus with a group of magnetically equivalent nuclei was not handled properly.
- NMR Predictor did not consider negative coupling constant values.
JSDraw has been updated as part of the Cheminformatics DevSuite 2.5.1 Release.
There is an online demo of 3D structure generation here using JSME and JSmol.
I just noticed that an update for ChemDoodle was available on my iPhone.
According to the release notes this includes
- Support for the iPhone 5
- IUPAC Naming
- 3D coordinate generation and viewer
- Added empirical formula to calculations
- Added rotatable bond count to calculations
- Added total electron count to calculations
- Added vdW volume to calculations
- Added complexity to calculations
- Fixed slow performance issues on iPad in landscape mode
- Fixed MolGrabber search issues
- Fixed issue where the back button wouldn’t appear on the last help page
- Fixed login issues
- Performance improvements
- General improvements and fixes
There is a page of mobile science applications here.
Marvin 5.12.2 has been released with a couple of bug fixes
- Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand.
- Non ring bond information were imported as query strings from SMARTS.
- After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.
New features and improvements
S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML.
Painting, Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off. When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other. The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.
Editing, Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").
Import/Export, MRV and CML export wrote out characters incorrectly which are not supported by the character set. SDF files having invalid header could not been imported. Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL). MolExporter.exportToObject() added an extra newline to SMILES. Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation. Absolute stereo flag was missing during InChi export/import and InChiKey export.
Molecule Representation, Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.
Calculation, After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases.
There are two main occasions when a chemical drawing package is needed, firstly as a front-end to a chemical database for creating structure-based queries, and secondly for creation of chemical structures in publications. Whilst many drawing packages are fine for query construction some are far from ideal for creating publication quality output.
This paper from Alex Clark (DOI: 10.1002/minf.201200171">10.1002/minf.201200171) discusses the issue in detail.
The creation of 2D molecular structure diagrams that make full use of the capabilities of modern display systems, using only input data expressed in file formats used for cheminformatics, is a complex task that requires a number of additional algorithms. Assuming that atom positions have been well chosen, the rendering engine is required to micromanage the precise positioning of atom labels, bonds and atom adjuncts, in such a way that the final output is correct, consistent with convention, and as pleasing to the eye as a diagram produced by a graphic designer. The techniques must be equally applicable when creating output for low-resolution screens and high resolution printed output, and make use of contemporary graphics file formats in such a way that the largest possible number of software platforms are able to display the output at any resolution without degradation or inconsistency. The main issues involved in meeting these criteria are discussed, and algorithms for satisfying them are presented.
With the release of Marvin 5.12.0 users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. I thought it might be useful to have a look at this new feature however I don’t have a corporate web service that I can use. This is where use of the Chemical Identifier Resolver (CIR) comes into play
In addition Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call. Users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. Typing abbreviated group names is now case sensitive, When pasting unrecognised format onto the canvas, "Import as" dialog appears, and the user can choose the correct format. Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats. The MMFF94 forcefield has been added to Generate3D and can also be used in the Conformer Plugin and Molecular Dynamics Plugin.
The complete release notes are available here
There is a page of mobile science applications here.
Chocolat a text editor for Mac OS X, that combines native Cocoa with powerful text editing tools has been updated.
There are more text editors here.
MacVector Inc have released a free version of MacVector.
If you used a temporary trial license, then when the 21 days were up, MacVector would simply refuse to start unless you entered a new valid license code. With the release of MacVector 12.7 we have changed that behavior. Now, when the trial license (or any annual license) expires, MacVector will give you the option of continuing to work, but with reduced functionality. All of the functions in the Analyze menu become disabled, but you can still open, edit, save and print MacVector documents, or save MacVector files in other formats.
ichemlabs have announced the release of ChemDoodle Web Components 5.
ChemDoodle Web Components 5 is a massive update. The most notable addition is a Full Sketcher, for drawing multiple molecules, shapes and figures, in addition to the Single Molecule Sketcher already provided. iChemLabs Cloud services and the ChemDoodle JSON format have been updated and drastically improved. The entire codebase has been reoptimized and cleaned, doubling the performance in desktop browsers and more than quadrupling the performance in mobile browsers. All Canvases now handle managing multiple molecules and shapes. Many new additions have been added and dozens of bug fixes have been implemented. We will be unrolling our new proprietary options over the next month, but of course, everything is available for free today under the GPL license!
There is a tutorial for using ChemDoodle web components here.
As I mentioned in my recent review of MOE 2012 there is now support for using Marvin as an external 2D chemical drawing package, but what happens if you want to use another drawing package? Well that is where Applescript comes to the rescue, using Applescript support for shell scripts and one line of SVL (scientific vector language) we can use ChemBioDraw as the external editor. Full details of the script are here.
The Applescript section contains more tutorials, scripts and resources.
They are looking for input to prioritise future developments.
There are more chemical editors here.
Serious problems with the security of the java browser plugin, together with a series of ongoing (and unresolved) stability issues mean that this developer is looking elsewhere.
Given the nature of the newly-disclosed Java Plugin security exploits and ongoing stability issues, ChemWriter’s clipboard paste functionality will likely be removed altogether in a future release. Those currently using this feature are encouraged to find an alternative.
Marvin from ChemAxon has been updated to version 5.11
New features and improvements
- Image I/O
- Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style). Documentation
- MSketch GUI
- A new "imageImportServiceURL=[URL]" program argument was added to the MarvinSketch application.
- MSketch applet
- A new "imageImportServiceURL" was added as an applet parameter.
- Graphical object handling
- When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.
- Document to Structure (d2s)
- Names broken over two lines with a hyphen (-) are now recognized.
- Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin11") are now recognized.
- Name to Structure (n2s)
- In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.
- If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.
- Image I/O
- Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.
- MOL, SDF, RXN, RDF
- Aliphatic query properties of atoms with query string were not read from MDL formats.
- After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.
- Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.
- SDF import returned structure with incorrect S-group embedding.
- SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.
- Molecule Representation
- Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.
- Valence Check
- Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.
- Clean 2D
- Terminal methyl-group in phosphate-ester was cleaned incorrectly.
- Clean2D could not handle condensed adamantane derivatives. Forum topic
- Other (HBDA, Huckel Analysis, ...)
- The --pH command line option did not work in hydrogen bond acceptor-donor calculation.
- Structure Checker
- If fixer action was not defined, default fixer was not applied in structurechecker command line tool.
ChemDoodle 5 includes significant new features and improvements, including:
- Round-trip editing on Windows via OLE. (Round-trip editing is already provided on Mac OS X)
- Round-trip editing on Linux!
- A revamped shape system for much easier and more precise manipulation of shapes, especially in crowded figures. Also a new quick colors button to now quickly change colours of objects.
- Bezier curves for complex shapes and mechanisms.
- Fragmentation tools.
- More functions for handling chemical data on the clipboard.
- File chooser previews.
- 77 new glassware templates!
- Hundreds of other features and improvements.
Upgrade pricing options are available.
Open Eventory has been updated
2012-09-28: - updated Ketcher molecular structure editor, now also supports reaction equations - added DrugBank for structure-to-CAS and substance data search - fixed a bug that prevented merging of literature datasets - advert in navigation panel no longer covers functionality on smaller screens - added SDF export (experimental) - import of existing substance data is now possible (if you have data not within the online catalogs)
Open enventory is an integrated laboratory journal with a literature database and inventory program.
This version of ChemBioDraw released in August 2012 is the first release since Cambridgesoft became part of Perkin-Elmer and there are a significant number of changes. This is the first version to be released since the introduction of Mac OS X 10.7 and 10.8 and both are now officially supported. In addition the ChemDraw plugin is now supported in 64 bit mode and Microsoft Office 2011 is supported. I’ve written a brief review here.
Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows, Linux and Mac OS X. The source code source is available under the GNU GPLv2.
This release highlights a great deal of new features, including a built-in crystal library, crystallographic editing, building slabs / surfaces with arbitrary Miller planes, support for Abinit (and soon Quantum Espresso), searching for IUPAC names in PubChem, custom atomic colors and radii, and much more.
See the Release Notes: http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0
What does Avogadro do?
- An intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences
- Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization
- Interfaces to many common computational packages
- Designed to help both educational users and advanced research
- Plugins that allow Avogadro to be extended and customized
- Well defined public API, library and Python bindings for development
- Embedded Python interpreter
- Translations available in 19+ languages
For more information: http://avogadro.openmolecules.net/wiki/
ChemDoodle mobile has just been updated
ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a detailed help guide.
Calculations 1. Molecular Formula 2. Molecular Mass 3. Monoisotopic Mass 4. Degree of Unsaturation 5. Hydrogen Bond Acceptors 6. Hydrogen Bond Donors 7. Average Molecular Polarizability 8. Molar Refractivity 9. Polar Surface Area 10. logP Spectra 1. Mass Parent Peak (Isotopic Distribution) 2. 1H NMR 3. 13C NMR
There are more apps on the mobile science page
Elemental is the Dotmatics chemistry sketch utility provided at no charge
What's New in Version 1.0
- Copy image to Camera Roll
- Copy Image to Clipboard
- File association (tap and hold to load in Elemental)
I just noticed ChemDoodle web components have been updated
As part of my day job I maintain Drug Discovery Resources a website intended to act as a resource for scientists undertaking drug discovery. One part of the site has a section on bioisosteres including many examples http://www.cambridgemedchemconsulting.com/resources/bioisoteres/ in which the chemical structures are shown with dropped shadows.
I use ChemBioDraw to draw the structures and then save as PNG files with a transparent background. The structures are then dropped onto webpages created using RapidWeaver, within RapidWeaver there is an option to add dropped shadows to images. I was recently asked whether there was any other way to create the same effect and Matt at macosxtips suggested using ImageMagick. This applescript droplet allows you to do so by simply dropping the file.
The Mobile Molecular DataSheet (MMDS) has been updated. Two major usability enhancements:
(1) Additional tool banks on the left and right side of the sketcher provide simplified drawing tools that are more familiar to users of desktop chemical drawing software.
(2) A tooltip system provides tips, live demonstrations and links to documentation.
I was reminded that whilst scripting menu items was the traditional way of controlling ChemDraw the more recent releases allow control by scripting commands. This is a major advance since menus can change or be translated into other languages. I’ve thus updated the script.
I was asked if it would be possible to do the same thing for other drawing packages such as MarvinSketch?
The answer is yes but because MarvinSketch does not have applescript support we have to do it slightly differently. Rather than using scripting commands we script system events to evoke the “Paste” command.
Full details of the script are here
I’ve added two new applications from Metamolecular to the alphabetical listing.
ChemVector™ offers a modern solution to the chemical structure imaging problem. Features
- Runs with all commonly-used browsers on Windows, Linux, Mac, and iPad. This includes Internet Explorer 6-9 in addition to Firefox, Google Chrome, and Safari.
- Renders structures directly from individual molfiles on a server, or as inline content.
- Renders chemical structure content directly from ChemDraw™ binary files (.cdx).
- Declarative syntax replaces <img> tags with analogous <object> tags, making it easy for both developers and designers to work with the resulting markup.
- Non-blocking implementation makes it possible to render dozens of structures on a single page while maintaining UI responsiveness.
- Structures can be magnified pre- or post-rendering with no pixelation.
ChemCore is the chemiformatics foundation of all of the Metamolecular products and services. Written in Java and cross-compilable to a number of target runtimes and platforms, ChemCore is both fast and flexible.
- Fast subgraph matching
- Powerful graph query capabilities
- Flexible, efficient graph traversals
- Fast file input/output
- A complete system of atomic weights and elemental properties
- Sensible handling of implicit hydrogens
- Molecule validation and correctness-checking
- Molecule transformations, including canonicalization and salt-stripping
- Extensively tested and documented
Chemical Drawing Programs – The Comparison of Accelrys (Symyx) Draw, ChemDraw, DrawIt, ACD/ChemSketch, ChemDoodle and Chemistry 4-D Draw
There is also a comparison of six chemical drawing packages here
- The js file is renamed to Scilligence.JSDraw.js
- Speeded up JSDraw on IE 6/7/8 by adopting Silverlight
- Added fragment-selecting tool ( http://www.scilligence.com/web/fragment-selecting-tool-in-jsdraw-1210.aspx )
- Improved drawing performance
- Being able to expand Amino Acid using right click menu ( http://www.scilligence.com/web/bio-features-expanding-amino-acid.aspx )
- Bug: atom labels overlaps bonds
- Added Bracket object to support polymers ( http://www.scilligence.com/web/polymer-features-comes-to-jsdraw-1210.aspx )
- Added Lasso selecting tool ( http://www.scilligence.com/web/jsdraw-lasso-selecting-tool.aspx )
- Widely supporting SGroup ( http://www.scilligence.com/web/sgroup-in-jsdraw.aspx )
- Being able to Set object colors
CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature. The software saves users hours of redrawing structures from printed material, as it transforms the 'images' into a 'real structures' that can then be input into databases.
The new and improved features of the latest release include:
- support for Windows, MAC and Linux operating systems
- improved structure recognition capability
- improved error reporting
- improved processing of document pages which contain tables, underlined text and page separator lines that touch a few letters
- extended input format support with Word (DOC and DOCX) and HTML
- extended export format support with CML and MRV formats
- integrated support for ChemAxon's Marvin Sketch, Accelrys'Draw and ChemDraw editors
“We have finished our testing of ChemDoodle on Mac OS X Lion, and everything works as expected. ChemDoodle will continue to work for you on your mac, even after you update to Mac OS X Lion.
We regard Mac OS X as a primary platform and will always support it. With ChemDoodle, you can be confident that your work will be unimpeded by major OS updates.”