Text editing properties
In the case of chemical documents it is necessary to distinguish between two kinds of texts: structural text
(atomic symbols, functional groups, atom labels) and other text
(captions, reaction conditions, annotations etc.). The structural text strings are connected to the atoms, whereas the latter can be placed freely, usually into text boxes and can be edited independently. Of course, in these chemical applications only a minimal amount of text editing features can be found, like the basic manipulation of fonts, styles, sizes and colours. The technique is mostly that of used in other Windows applications.
The editing of structural text is by far the least convenient and limited in Accelrys Draw (obviously only database applications have been taken into consideration). In certain cases, the method used in ChemDoodle is also complicated (e.g. the adding of Greek letters). If nothing else helps, the solution is simply to create a caption text, to position and group it with the parent structure.
Apart from ChemDoodle, the parameters of structural and caption texts are not used globally. There are five independent settings in DrawIt, three in Accelrys Draw and two in the others. The caption text editing properties are the best in ChemSketch and ChemDraw.
While special chemical symbols are available from the programs, the last versions of ChemDraw and ChemDoodle have a full floating character map for quick selecting and pasting of any characters of the installed fonts.
The creation of textual tables is supported in ChemDraw with the aid of the Tab key, but a complete advanced table editor supporting text & structures is also available here. Similarly, the latest ChemSketch also possesses an excellent table editor. DrawIt contains also a good table editor, but for captions only. Apart from the automatic alignment tools in Accelrys Draw, Chemistry 4-D Draw and ChemDoodle, no special help is available for table editing in these three applications..
DrawIt and ChemSketch support the direct creation of framed annotations (callouts), which can be very useful in case of spectra or chromatograms. Although these can be manually assemled in the other programs, too, here they are ready to use and automatically resize when editing their content:
– These programs are widely used all over the world, therefore the support of national characters should be flawless. Unfortunately, 20 years after the rise of MS Windows not all of these program applications are faultless. The test was made using Hungarian accented and Islandic characters:
- Accelrys Draw 4 – no problems
- ChemDraw – version 11: no problem, version 12: incomplete support
- ChemDoodle 4.1 – no problems
- ChemSketch 12 – incomplete support
- Chemistry 4-D Draw – no problems
- DrawIt 9 – incomplete support (foreign characters look OK in ReportIt, but some of them disappear on copy/pasting to other applications)
As the display and keyboard input of foreign characters is OS version, language and setup depending, the above results cannot be generalized.
Templates and group abbreviations
Apart from Chemistry 4-D Draw, these applications contain several ready template pages of different ring systems, amino acids, carbohydrates, etc. and these can be pasted quickly into the document. Other templates, for example laboratory glassware, are also available (except in Accelrys Draw). The programs allow the user to create custom templates. Of course, the technique of the creation and use of the templates are different in each program; perhaps the solution and organization used by ChemSketch is the most advanced one. A large amount of additional chemical, biochemical, biological, manufacturing, etc. templates for ChemDraw are available as downloadable support from the CambridgeSoft's site.
The so-called abbreviated groups (labels, superatoms, nicknames) are shorthand text string representations of functional groups (COOtBu, NO2
), meanwhile they keep their chemical significance with the underlying structure hidden – a highly important feature in the case of databases. There are several methods to add such linear structural formulas (side-chains) with or without chemical significance:
You draw the full structure and contract a substituent to a chemically meaningful text label, if necessary. The process can be reversed, the textual abbreviation can be expanded to structure. This feature is relevant mainly when storing molecules in databases.
- Accelrys Draw: OK
- ChemDraw: OK
- Chemistry 4-D Draw: works only in the case of a few predefined simple substituents
- ChemDoodle: not supported
- ChemSketch: not supported
- DrawIt: imperfect even in the case of very simple side-chains or groups. After abbreviation, the side-chain often cannot be expanded.
- MarvinSketch: OK
- Important, commonly used or user defined substituents are stored and can be added by a few keystrokes as atom labels or expanded structures. This method is available in Accelrys Draw, ChemDraw, ChemDoodle and MarvinSketch. Other programs support it with limitations.
- You add the substituent or side-chain in linear textual form and the parser of the program interprets and expands it. The expression may contain parentheses, too (ChemDraw, DrawIt and ChemSketch). The algorithm of ChemDraw seems to be the most advanced one, you can even add substituents to the linear formula. Previously defined abbreviations may have two connection points. The expansion is a fully automated process and the outlook is not always according to the user's taste.
Sprouting of bonds from the "letters" of the side-chain is possible in ChemDraw and DrawIt. While in DrawIt they are pure graphics only, ChemDraw interprets them on-the-fly chemically.
- Accelrys Draw: not supported.
- ChemDraw: any text label can be added, even complex and branched ones are interpreted and expanded.
- Chemistry 4-D Draw: any textual linear form can be added, but only the very basic ones can be expanded.
- ChemSketch: any textual linear form can be added and even complex ones are interpreted and expanded.
- ChemDoodle: any textual linear form can be added and not very complex ones are interpreted and expanded.
- DrawIt: any textual linear form can be added, but only the very basic ones can be expanded.
- MarvinSketch: not supported.
- The crude method: when chemistry is unimportant, you can simply create a text string and group it to the structure. Apart from MarvinSketch, it can be done in every program.
: These methods are the most advanced in ChemDraw and ChemSketch in the second place. If underlying chemistry is unimportant, all programs are similar. It is difficult to decide which of the above methods is the better one for the addition of substituents: predefined structures or on-the-fly interpretation of linear formulas. Each of them has its own advantages and weak points.
ChemDraw and DrawIt allow the use of stacked labels.
Chemistry 4-D Draw provides its own solution. The Pro version also has an intelligent chemical nomenclature module. Therefore it contains only a few built-in templates (the most important rings and substituents). In addition, every molecule can be saved as a fragment (like the cephem ring in the right figure) that can later be recalled by its name, even in substituted form. A similar mechanism exists in Accelrys Draw, too. The structure resolver includes a feature that allows the user's internal database to be updated with the name/structure pairs.
Chemical intelligence, nomenclature
As it has already been discussed, several programs are capable of parsing the linearized forms of substituents and convert them into structures. With the exception of ChemDoodle all programs are able to assign systematic names to structures according to IUPAC rules, and vice versa
. Therefore, these are very convenient when you are generating chemical names.
These modules are very intelligent and are difficult to cheat, although not faultless, especially on slippery fields of nomenclature, such as carbohydrates. Some of their databases can be customised by adding trivial names. There are a few restrictions, anyway, for example multicomponent ionic structures will not be interpreted in DrawIt or Chemistry 4-D Draw while this is not a problem inside ChemSketch Name or ChemDraw. The presence of these usually extra features are depending on the purchased version or edition of the applications (see the next table). Older Accelrys (Symyx) Draw versions need ACD Labs Name add-in (not compatible with the last version 4). The basic ChemSketch contains the structure-to-name feature only, the opposite is to be purchased separately or available through the online service ACD/I-Lab. ChemDraw Ultra also possesses an appropriate module. From ChemDraw 9.0 on a praiseworthy auto-update feature has been added that renames the structure as you modify it. A more advanced nomenclature modul was introduced with ChemDraw 12 capable of dealing with more complicated polycyclic condensed ring systems. Basic DrawIt contains only demo capabilities. If you need more, try the ACD/Name application, which wins in a canter even in the jungle of oligosaccharides. (Example
Summary of IUPAC modules in the different versions of the applications
||Structure to name
||Name to structure
|Accelrys Draw 4, free academic
and comm. versions
||Ultra version only
||Ultra version only
|ChemSketch 12, freeware
|yes, up to 50 atoms/3 rings
|Chemistry 4D Draw 8, Standard
||yes (without stereochemistry)
|DrawIt 9, free academic
|up to 10 heavy atoms
|up to 10 heavy atoms
(often odd stereochemistry)
Of the program applications in Accelrys Draw and Chemistry 4-D Draw is possible to define and add full structures with trivial names to the internal database, as already mentioned above. The names and structures then become available in name-to-structure and structure-to-name conversions.
In addition, all of the programs including MarvinSketch are able to assign the stereochemistry to all asymmetric tetrahedral atoms and double bonds according to Cahn-Ingold-Prelog (CIP) priority rules. All but ChemSketch do this on-the-fly while editing the structure. The method used in ChemSketch is quite clumsy: when editing the structure, you have to delete manully the previous R and S markers and ask for re-assignement of stereochemistry.:
The commercial version of ChemSketch includes an integrated dictionary of over 30 000 structures with 165 000 trivial and trade names, which can be searched by name, structure and a series of abbreviations, drug code numbers, therapeutic categories or inhibited enzymes.
As a whole, the structure-to-name service is a very useful feature for every organic chemist; the name-to-structure conversion is usually less practical: long and complicated names are difficult to enter without typo or syntax error (they can be copy/pasted from different sources, though) while short names are usually quicker to enter immediately as graphics.
Spectra and chromatograms
Some novelties in these programs are the spectral data publishing features, spectrum interpretation and database management tools. UV, IR, NMR, MS spectra and chromatograms can be imported and embedded into the documents and join with structures etc. The most versatile are DrawIt and ChemSketch: a wide range of filters are available (usually only when purchasing the appropriate modules). ChemDraw supports JCAMP and Galactic files, ChemDoodle JCAMP files. The curves can be resized, zoomed, scaled, corrected, annotated, and peak list and tables are easy to create. Finally, they can be embedded into the final document. Of course, only formation and editing of the curves are possible. Basic spectrum manipulations, such as Fourier transformation of the FID signals are not possible. Full processing capabilities are available using the ACD/SpecManager product suite which is integrated into ChemSketch. All of the three applications enable the user to assign structures to spectra. One can then display the structure associated with a specific peak by placing the pointer on that peak. Before making any decision, it is highly recommended
to check that what spectrum and database formats are supported by the current versions.
With the freely available NMR- or SpecViewer add-ons ChemSketch's capacity can be also extended to the handling of NMR, UV etc spectra of different origins:
Different chemical and other adds
It is not easy for the reviewer to decide what and how to include, because these extras are changing quickly and depending on the owned version (freeware or standard vs
. pro vs
. ultra versions etc.), sometimes add-ins can be installed only into the purchased version, sometimes they are free, sometimes they are to be purchased separately or available as an Internet-based service (see table 1.
too). It is highly recommended
to look for information at the home pages of the manufacturers before making anydecisions.
, and constitution %:
All of the programs.
13C: KnowItAll, ChemDraw, ChemDoodle, ChemSketch (to be purchased or via I-Lab), Accelrys Draw (with ACD/Labs Add-ins), MarvinSketch (NMR Prediction)
1H: KnowItAll, ChemDraw, ChemDoodle, ChemSketch (to be purchased or via I-Lab), Accelrys Draw (with ACD/Labs Add-ins), MarvinSketch (NMR Prediction)
19F, 31P and 15N NMR: ChemSketch (to be purchased or via I-Lab)
The chemical shifts are not ab initio calculated, but determined with the aid of the applied databases; therefore, the precision of the results is a function of the included molecules. The 13C NMR module of the DrawIt/KnowItAll (if the full suite is installed) and ACD/CNMR can show molecules possessing analogue chemical environment similar to those of the carbons in question. ChemSketch has also developed this scheme into their NMR prediction modules through their "calculation protocol" environments.
The MS fragmentation tool mimics the molecular fragmentation in a mass spectrometer and it allows the user to break existing structures across one or more bonds. ChemDraw, DrawIt, ChemSketch and Chemistry 4-D Draw have this tool; the first two applications have the most advanced one, which allows the user to fragment in zigzags and calculate the mass resulting from multiple fragment losses (if you need more, use ACD's MS Fragmenter or a similar package).
: KnowItAll, ChemSketch (with UV-IR Manager add-on):
Manipulation and comparison of IR spectra. (Only as demo version in DrawIt ChemWindow edition).
Other chemical property prediction tools
ChemDraw: logP, CLogP, critical pressure, temperature and volume, Henry's constant, Gibbs energy, heat of formation, MP, BP, molrefraction. Some of these are available in the Ultra version only
ChemSketch: log P (free version). With ACD/PhysChem Suite: molar refractivity and volume, parachor, surface tension, index of refraction, density, polarizability, logP, pKa, Hammett σ etc. Some of the features are available through ACD/I-Lab. Consult ACD-Labs home page for current details.
DrawIt/KnowItAll: logP, logD, pKa, Rule of Five (depending on licence).
Accelrys Draw: Rule of Five, isotopomer distribution, enumerate stereoisomers and Markush structures as well as ACD Lab's Physicochemical and NMR predictors
ChemDoodle: Several topological indices, structural and analytical data, Rule of Five, H-bond donor/acceptor number, molar refractivity and volume, polar surface area, XlogP, many thermodynamic and physicochemical properties, isotopic distribution, etc.
MarvinSketch: protonation and pKa, logP and logD, charge and polarizabiltiy, generation of tautomers, conformation and molecular dynamics (using the Dreiding force field), 3D alignement, topology, surface area, Hückel analysis (HOMO, LUMO, localization energy, etc.), H-bond donor/acceptor properties. The results of several of these calculations are shown graphically as isosurfaces as well. All of these are available in the basic/free version. You can try these calculator plugins online at http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
These calculated properties are to be handled with critic.
A bunch of handy utilities can be found in these extensions, among others handling of multipage documents, conversion to HTML, VRML or SDF formats, peptide, carbohydrate and nucleic acid builders.
This is a handy utility for the synthetic chemists to calculate the molar quantities of reagents and products and the yields of the reaction (Accelrys Draw has a similar calculator as separate add-in):
An ample amount of printed documentation is included with ChemDraw (it is available in pdf format on the program CD as well). DrawIt, Chemistry 4-D Draw and ChemSketch have no printed documentation (but are available in pdf format). The available on-line documentation (Help) is good in the case of Accelrys Draw, ChemSketch and Chemistry 4-D Draw. It is practically the same as the printed one in the case of ChemDraw. The documentation found in the Chemistry 4-D Help is incomplete, several modules have no descriptions at all, no information could be found about the so-called Plasmid modul even from the website of the program and it is dated from 2002. Friendly solution of Accelrys Draw that its Help contains a special section aimed at old ISIS/Draw users. A pdf file is available in the case of ChemDoodle, unfortunately, without index.
Worthy of note that for the sake of the user's convenient, the Help of the purchased version of ChemSketch contains a huge number of internet links to the instructions-for-author pages of chemical journals, moreover, and the majority of these instructions are available off-line in pdf format, too.
Drawing programs and the Web
Nowadays there are more and more applications (or rather, browser plug-ins or Java applets), which can be used for entering chemistry directly into the browser, for example to search an on-line database. A Java applet version of ChemSketch is available at no cost from the ACD website (via the ACD/Structure Drawing Applet). This is a full featured Java-based structure drawing editor including templates and periodic table. The afore-mentioned I-Lab add-on to ChemSketch is also an Internet-based service. The ChemDraw Plugin automatically turns the web browser into ChemDraw whenever a page containing an embedded ChemDraw document is encountered. DrawIt can use spectroscopic databases. However, we do not deal with these this time. Several Java applet versions are found among the programs mentioned in the What else out there
Latest versions of ChemDraw, ChemSketch, ChemDoodle, Accelrys Draw and MarvinDraw support the direct access of chemical databases. ChemDraw can search ChemACX and return information about structures, ChemSketch can conduct a direct search for the drawn structure in the PubChem, eMolecules and ChemSpider web databases of chemical information. ChemDoodle can search for chemical suppliers for drawn structures. Some other web-features, such as direct e-mailing of a sketch in pdf format or the RSS newsfeeds to receive announcements on the dedicated bottom toolbar of ChemSketch belong already to the "bells-and-whistles" category.
On browsing the different chemistry-related forums or lists, it turns out that many user faces the problem how to create an image from a chemical sketch to publish it on the web. It takes a few second for an advanced user, but problematic for the novice. Apart from DrawIt, all of the reviewed programs already support this. As it has already been mentioned, a rule of thumb that never use the jpg format for sketches, but the GIF format or PNG instead! To know more about the GIF and JPG (JPEG) formats, read this sidebar
Apart from small corrections, no new features can already be added to the drawing functions of pure chemistry. Of course, little additions and corrections are continuously made, especially database functionalities are enhanced, such as the support for Markush structures, polymers, etc. are enhanced – this in mind the developers are recently concentrating on the intelligent to-and-fro chemical naming modules, and the tools for viewing and representing spectra of different formats.
For the time being, ChemDraw and ChemSketch are the most powerful chemical drawing applications. Old ChemWindow has been replaced by the DrawIt/ReportIt modules of the KnowItAll Analytical Systems package – no special novelties but excellent team-work with spectroscopy and chromatography. Similarly, the successor of ISIS/Draw can not show up any important novelties as its drawing features are concerned. Chemistry 4D Draw has not been developed for several years either. The far more sophisticated ChemSketch 12.0 is also freely available via the Internet.
Progress never stops, hardware keeps growing stronger and stronger, and the developers have to add something new every year, therefore the originally really drawing-only applications have evolved into a complex of
- full-featured editors of chemical, textual, spectroscopical and graphical objects for
- publication (classical or web-based) or
- e-notebook type data storage.
- several chemical toolsets:
- MS fragmentation tool, TLC plate tool, chemical table editor, different templates and alike;
- quick 2D → 3D conversion and visualization for publication purposes;
- conversion of structures to names and vice versa, generation of stereo descriptors;
- Passive (one-way) database use:
- intelligent template-like use: quick look-up of natural or commercial products by their trivial names;
- Retrieval of data or manufacturers of compounds from the internet
- Calculation of spectroscopic data (NMR-shifts) based on databases.
- the input modules of other applications:
- active chemical databases, molecule and reaction retrieval, management of chromatographic and spectroscopical data, peak search, etc.;
- calculation modules (such as physical-chemical data, QSAR parameters etc.);
- available on-line services.
The comparison of the discussed packages is not an easy task, as in each one the potential user can find clear advantages compared to the others as well as weak points, too. The judgment of a program is highly dependent on the routine and knowledge of the user: better results can be achieved with a very well known and mastered, but less sophisticated program than with a partly known one full with bells-and-whistles. The user-friendliness is also relative as those who know well for example the different available keyboard shortcuts of an application can work more efficiently and quickly with this one than with another one. According to my opinion, if only pure chemical drawings are in question, all of the applications can be equally useful. In the case of more complicated drawings ChemDraw or ChemSketch is the most recommendable. ChemDoodle is also very good, the most problematic drawback of the current version is the direct interaction with other programs. When the management of spectra and chromatograms is a must, DrawIt or ChemSketch (the appropriate subsets of the suite) should be preferred. If 3D-modeling is also desired, you may consider ChemDraw + Chem3D. Choose ChemDraw (or preferably its ChemBioDraw edition) when biochemical sketches are in question. Apart from ChemDoodle, these applications serve as the input modules of their appropriate chemical databases – another point of view for the proper judgment of these programs. Chemistry 4-D Draw contains only the minimum drawing features, it can be used as a name generator, too.
A power-user is usually not satisfied with one application only; some features are available in one program only, others are better in another one. File exchange via common formats is usually possible, and the higher-level mutual support of applications of even competitors (such as the ACD add-ins in the CambridgeSoft or Accelrys programs) is clearly beneficial for everybody.
My personal order of preference:
- ChemDraw (the appropriate version according to your demand)
- ChemSketch (the free or commercial version according to your demand)
- Accelrys Draw (free version)
- Commercial versions of Accelrys Draw, DrawIt or Chemistry 4D Draw – only if you need it because of another member of the suite, doesn't worth purchasing solely because of drawing.
What else out there?
Beyond the above-discussed drawing software applications there are several other ones to be considered for general use or only for experimentation. They are freeware or shareware programs, some are highly sophisticated, some are simple ones, some are only in beta-phase. Others are excellent for web applications and/or are running only within a web page as applets. Here are a few of them (apart from MarvinSketch and PLT, no extensive tests have been done)
(Windows, Linux, Mac)
As previously mentioned, MarvinSketch has not been added to the above six software applications, as for the time being, it is not meant for the creation of publication quality complex drawings and several necessary features are missing. However, it has several other tools and features that entitles it for special attention
Although it is only a basic 2D drawing software, it includes some features characteristic only of modelling softwares, for example coloring of the atoms by type or display in ball-and stick and CPK models
It is possible to import 3D molfiles (Sybyl, PDB, XYZ, etc.), it has separated 2D and 3D clean-up modules. InChi, Smiles or Smarts strings are interpreted and cleaned up as well. MarvinSketch is available not only as stand-alone application (javabean), but as Java applet for developers as well and may serve as the graphical input module of on-line databases (therefore query bond and atom types, R-logic, Markush structures, groups, etc. are also supported). It contains several chemical property calculation and prediction tools as already described above. Unique to MarvinSketch that the source of the molecule in the work-space can be inspected and edited in several file formats in the source editor. The browsing of MDL database files is also possible. Partner applications: MarvinView for quick 2D → 3D conversion and display, and MarvinSpace for high performance 3D molecule and surface visualization. It is integrated into a variety of database systems via JChem Base. As already mentioned, it has a name generator for the computation of the IUPAC names of compounds. For more details visit its home page.
The images in MarvinSketch are optionally antialiased on the screen. Therefore MarvinSketch is also excellent for drawing molecules or reactions intended to export as images for web pages The sketches can be exported to JPG, BMP, PNG, SVG, EMF or PDF files.
(Hans J. Reich)
In the first part of the 90s the DOS based PLT was the masochists' drawing program with its dozens and dozens of keyboard shortcut combinations. It concentrates on drawing without the many bells-and-whistles of the above programs. Advanced users could absolutely master the drawing. For example, the height, breadth, slant, and rotation of text could be freely and continuously changed, as well as the fine adjustment of the bond crossings and many other parameters. The Windows version is already more user-friendly, but, unfortunately, some of the uniqueness of the original PLT had to be sacrificed. Even so, beyond the standard Windows fonts allowing only italic and bold formattings, a graphical font is available for free formatting. The technique and conception of drawing in PLT differs considerably from those in the above programs, which may seem odd at first (the program comes with ample help and tutorial). The presence of vector graphics can be strongly felt (the other programs try to conceal it by chemistry; the original PLT produced HPGL plotter files), but these allow many unusual solutions, such as direct embedding of keto or sulfone groups into rings or text labels etc, or creating special bonds by dismantling bonds into lines and reformatting them (such as the up/down double bonds in Figure 28) etc. It reads and writes only its own file format, can export to WMF, EMF, BMP, GIF, smoothed GIF and EPS graphical files or to the clipboard. Several other formats, e.g. MDL MOL or RXN files can be converted to PLT format by Mol2Mol
In addition to chemical drawing, in the Windows version modules for incorporating NMR spectra and producing X-Y graphs have been included. Some unique features: on-click addition of several common moieties, such as carbonyls, CH2
groups with up/down bonds, etc; Bezier, sine, cosine, parabola, circle, Gaussian and Lorenzian curves are available; chemical slide-show (without Powerpoint) etc. Worth trying.
(Windows, Linux, Mac)
Drawing application and suite of programs for 3D conversion, visualization, pharmacophor searching, cheminformatics, etc. Worth to have a close look.
A very useful shareware application, different versions are available (NMR prediction, fast force field based geometry optimisation and 2D → 3D conversion). Worth trying.
XDrawChem is a molecule drawing program for the Unix operating system. It is similar in functionality to other molecule drawing programs such as ChemDraw. It can read and write MDL molfiles, and read ChemDraw text and binary files, allows sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. An old Windows version is also available (WinDrawChem)
(Windows, Linux, Mac)
Java based multiplatform, simple 2D drawing program. Stand-alone and java applet versions are available. Among others supports CML, SVG, Smiles and MDL MOL/SDF formats, and 13
C NMR prediction.
(Windows, Linux, Mac)
BKChem is a free chemical 2D drawing program written in Python, therefore it is a multiplatform application (Mac OS, GNU/Linux, Windows). It has basic drawing features. Supports CML, Adobe SVG graphics, PDF, Post Script, Open Office, etc. formats. Allows embedding good quality antialiased graphics into web pages (needs the Adobe SVG plugin)
Easy to use software for drawing 2D chemical formulae and reactions. Allows you to print and export formulae in other documents.
(T.Volk - M. Kroeker)
Chemtool is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
* * *
Direct molecular structure input by using web browsers as interface is a very important branch of applications as web services have become of general use today. These are usually quite simple applets for generating basic (quiery) structures. Several of them import molecule files and the drawings can be exported to the usual document editors. Instead of going into details we refer here only to a recent overview 
. A few examples are here:
JME Editor 2004.10
(Peter Ertl, Novartis Pharma AG)
The simple and user friendly JME Molecular Editor is a free and often used Java applet which allows the user drawing, editing and displaying molecules and reactions directly within an HTML page. The editor can generate or input files in SMILES, MDL MOL/RXN or proprietary own formats. Its JME Professional version is not an applet but a stand-alone Swing application. Only pure molecules, query structures, and reactions can be drawn and saved/exported as molfiles. Creation of substructure queries is also supported. JME is an excellent tool for developers and may serve as the graphical input module for, e.g., on-line databases or property calculation services.
The applet may be used also in a depiction mode to visualise molecules:
The WebME Molecule Editor
of Molinspiration is a novel variant of the JME editor, based on Web2.0 Ajax technology.
The Accelrys JDraw applet gives application developers a lightweight structure editor for the development of custom web applications that require chemical structure queries and/or chemical structure input and rendering functionality.
Xemistry Web Sketcher
A very advanced and useful multiplatform sketcher. As it is a server side application, it does not rely on plug-ins or applets or other components to be downloaded. It supports many formats to export and import chemical structures, among others most string formats (Smiles, InChi, SLN, Cactus, etc.), the most important molecule file formats (MDL MOL, PDB, MOL2, etc.) as well as the export of several graphical bitmap and vector formats (GIF, PNG, SVG, EPS, WMF, PDF, etc.). The sketcher program can easily be used in various web scenarios and linked to different services, etc.
* * *
(University of Cambridge and Microsoft Corp.) (Windows)
Another interesting approach to include chemical information into documents is the chemistry add-in for Microsoft Word, a joint project of Microsoft Research and University of Cambridge. By creating inline "chemical zones" in Word, chemical information can be represented in a variety of ways: 2D chemical structures, names, chemical formulae or different data. In other words, instead of a static picture one can select with a few clicks what information should appear in the embedded fields. Chemical structures (called "zones") can be inserted from the web (PubChem or OPSIN) or from CML files. There is a very simple built-in structure editor in Chem4Word only enough for modification of imported structures. Thus, you need a more advanced drawing application capable of exporting 2D structures in CML format if you can not find and download a given structure. This project is only in experimental phase and can be used only with MS Word 2007 or 2010.
1. Accelrys (Symyx) Draw 4.0 (Symyx Technologies, Inc) URL: http://accelrys.com/products/informatics/cheminformatics/draw/
2. ChemDraw 12.0.2; CambridgeSoft Corporation, Cambridge, MA, USA; URL: http://www.cambridgesoft.com
3. DrawIt 9.0 (KnowItAll Academic Edition); Bio-Rad Laboratories Informatics Division, Philadelphia PA, USA; URL: http://www.chemwindow.com
4. Testing and comparison was made on a PC with Intel Core 2 T7200 CPU, 2 GB memory, Windows XP SP3 and Windows Vista SP2 (International English release). Text editor: MS Word 2003 (English). Printers: HP Laserjet 5, HP Deskjet 600 and 840.
5. a) ACD/ChemSketch 12.0; Advanced Chemistry Development, Inc, Toronto, Canada; URL: http://www.acdlabs.com
b) David Bradley: Chemical Structure Drawing Software, URL: http://www.sciencebase.com/aug04_iss.html (review, accessed 28.12.2011)
6. Chemistry 4-D Draw 8.4.6; ChemInnovation Software Inc., San Diego, USA; URL: http://www.cheminnovation.com.
7. a) MarvinSketch 5.8, ChemAxon Ltd, Budapest, Hungary; URL: http://www.chemaxon.com
b) A Review of Marvin. URL: http://homepage.mac.com/swain/Macinchem/Reviews/ChemAxon_review/Marvin.html (accessed 28.12.2011)
8. a) P. Ertl: Molecular structure input on the web. J. Cheminformatics
:1 (2010); URL: http://www.jcheminf.com/content/2/1/1
b) A comparison of six chemical drawing packages. URL: http://homepage.mac.com/swain/Sites/Macinchem/Reviews/chem_drawing_packages/chem_draw_packages.html (accessed 28.12.2011)
9. a) ChemDoodle 4.1.1, iChemLabs LLC, Piscataway, NJ, USA; URL: http://www.chemdoodle.com
b) ChemDoodle Review. URL: http://homepage.mac.com/swain/Macinchem/Reviews/chemdoodle_review/chemdoodle_review.html
c) Exploring ChemDoodle Web Components. URL: http://homepage.mac.com/swain/Macinchem/Reviews/Chemdoodle/chemdoodle_web_components.htm (accessed 28.12.2011)
10. Other comparative reviews on chemical drawing programs and articles dealing with sketching:
a) Vikas Anand: Comparative Evaluation of Freely Available Chemical Structure Drawing Softwares.
URL: http://www.pharmainfo.net/reviews/comparative-evaluation-freely-available-chemical-structure-drawing-softwares (accessed 28.12.2011)
b) A. M. Clark: Basic primitives for molecular diagram sketching. J. Cheminformatics, 2:8 (2010)
URL: http://www.jcheminf.com/content/2/1/8 (accessed 8.1.2012)>
11. An old version of this document can be found in a reshaped article form at:
a) Internet J. Chem. 3, L 25 (2000) (ISSN 1099-8292)
b) T. Gunda: Magyar Kémiai Folyóirat 104, 25-33 (1998)) (in Hungarian)
12. OSRA: Optical Structure Recognition Application. URL: http://cactus.nci.nih.gov/osra
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