Help File and Information

Dates and Features

Form Input

Structure Input
There are several possibilities to input a structure. The upper input field accepts SMILES strings as structure specifications.If you are familiar with the syntax, you can type in simple queries manually. However, most of the time you will want to use some graphical structure editor. If your favorite desktop molecule editor supports Copy&Paste of SMILES strings, you can simply use this editor, put the structure on the clipboard as a SMILES string and paste it into the entry field. Editors which support this operation include ChemWindow and ChemDraw.

If you enter a structure file via the file selector box, it can be in any of the major formats, including MDL Molfile (or SD files), PDB, JCAMP/CS, CIF (Chiron interchange format, not Crystallographic formats), MDL RXN (Reaction file), RDF (Reaction Data File format), XYZ, SMD4, SMD5, CTX, CACTVS (binary, ascii, cbase), SMILES (including SMARTS subset), Compass, 441, Gaussian/Input, Gaussian/Archive, SCF, SHEL-X, XTEL (XTELPlot input format), Cerius (Ascii exchange format of CeriusII Toolkit), Sharc (SHift ARChives format), Alchemy, Hyperchem, Molconn-Z, Sybyl, Sybyl2, SLN (Sybyl line notation). The structure source (smiles string on the input field or data file) and the file format are automatically recognized.

As a third option, you can start a Java editor by clicking on the Start Editor button below the input field. You must use a WWW browser with Java support (Netscape, Internet Explorer) for this to work, and you must have Java enabled, which is an option in the browser configuration panel. A new window with a structure drawing application will open, or come to the top. Read the editor instructions on how to operate the program.

Hydrogen Addition
One of the curses of many of the more popular structure file formats is their lack to specify hydrogen atoms explicitly. It is often unclear whether an atom is a radical center, carbene or saturated. Since most compounds presumably are not exotic structures, we by default add hydrogen atoms (depending on the file format, this may involve heuristics). If you are sure your file specifies all hydrogen atoms there are, you may wish to suppress the hydrogen addition. The hydrogen addition takes place only if the compound is read from file. Smiles strings contain full hydrogen information.

Aromatic Bond Type Resolution
Some conversion software, most notably Babel, converts aromatic bonds in various input files into bond type 4 in MDL Molfiles. Unfortunately, this is not correct. Bond type 4 in MDL files is reserved for query specifications and must not appear in standard structure files. These must use a Kekulé structure representation. Our software by default reads bond type 4 as intended - as a query attribute, which does not possess a bond order. However, since this a problem tends to occur frequently, we have added a resolver procedure which will, if the box is checked, convert these bonds into a Kekulé structure and compensate for the encoding problem.

The Interlace option
The Interlace requests the image file to be formatted in a way which makes the content visible as blurry approximation before all the data has been transferred. On the other hand, the file will become somewhat larger if this option is active. We recommend the activation of this switch only if you create large, multicolored images.

Image Width/Height
These fields specify the size of the image. If image cropping is enabled, these fields only specify the initial drawing area.

The Expanded Symbol Atom Symbol Setting
If Expanded Symbol is selected, it means that in case of atom lists for substructure searches and similar constructions the atom list is expanded into the full form. In the standard Symbol setting, an atom list is displayed as L.

The Special Value of Carbon and Hydrogen Plot Style
Special Only means in the case of carbon atoms that a C symbol is produced only at charged centers etc. For hydrogens it means that a symbol is only plotted in case of aldehydes, hydrogen at a wedge bond etc. Bonds leading to suppressed hydrogen atoms are not drawn, but suppressed carbon atoms are always bond nodes. If both settings are Special Only, normal structure drawing rules are followed.

Color - Atom, Bond, Hydrogens and Background
These fields specify the colors of the atoms, bonds and the image background.
The special value Element-Specific for atoms colors the atoms according to their element type (red for oxygen, blue for nitrogen, etc). If you input file format encodes atom color information, the read information will be used instead if this option is selected. If you set any color except the default value for hydrogen atoms, this color takes precedence over any other color source for hydrogen atoms. In the Bond Color field a special Split on Atoms setting is included. This option requests the splitting of the bond into two segments which are colored in the color of the bonded atoms. Usually this option is combined with a Element-Specific setting for the atom colors.
Atomsplit
The Border Width
This field specifies how close to the border of the image a bond node may approach. Note that atom symbols, which are centered on the bond nodes, may come somewhat closer. The font the atoms are rendered in is selected automatically from the ratio of image width and the Bonds parameter.

The Horizontal Bonds Field
The Horizontal Bonds option is used to indirectly specify the scaling factor for the display coordinates. The basic plot bond length is the width of the image, minus twice the border, divided by the number of bonds. If the actual width of the molecule is less than the available space, it is centered. If it does not fit, it is scaled down until it fits tightly. This mechanism ensures that you can have nice and readable series of plots with identical drawn bond lengths and image sizes, but the occasional oversized molecule in your dataset is accomodated without problems by shrinking it gently. Note that the value range of the original display coordinates in the file (if they are contained) is automatically re-adjusted, so you do not need to provide them in pixels as unit.

Stereochemistry
The plot algorithm is fully stereo-aware. If atom stereochemistry is present, wedges are automatically created for selected bonds. If new coordinates are generated, and stereo double bonds are present, their cis or trans character is taken into account. If the stereochemistry is arbitrary, for example because the input structure was a 3D molecule with random stereogenic centers, it may be desirable to suppress the plotting of atomic stereo attributes. If only the Wedges flag is disabled, solid wedges are drawn as bold lines, and hashed wegdes as dashed thin lines. Disabling also the Dashes flag completely suppressed the drawing of atom stereochemistry. Disabling only the Dashes flag is not useful.

Cropping
If this switch is on, the image will be cropped, i.e. the outer area which is colored exclusively with the background color is removed. The image is constructed with the initial size, but usually shrinks if this option is selected. After the removal, a crop border (by default 2 pixels) is added again in the background color.

Alignment
With the X or Y switch it is possible to align the dominant axis of the structure with the x or y axis of the image. We recommend this option only if you are creating very small images. It is generally desirable to allow the plot algorithm to chose its own orientation, since it has knowledge about the traditional layout of common ring systems. Plot alignment is only possible if new coordinates are computed.

Coordinates
This switch can be used to change the layout slightly. If the pseudo-3D coordinate style is requested, the longest non-ring carbon chain which contains the first non-ring carbon atom is plotted as a zigzag backbone.
Normal coordinates Pseudo-3D coordinates
normal coordinates
JST coordinates
Request New 2D Coordinates
The Request New 2D Coordinates option enforces the recomputation of 2D coordinates, even if they are already present in the input file. By default plot coordinates which are imported from file are kept and only the image is plotted. Note that SMILES strings never contain coordinates, even if you generate this string with the Java editor! So you will always get new coordinates if you draw your structure with this applet. Do not spend too much time to sketch a nice-looking compound, since your efforts will be lost.

Header/Footer
The Header and Footer fields can be used to label the image.

Comment
This option is useful for saving further information in the GIF/PNG file.
If the Property switch is on, the name respectively the formula of the structure will be saved as further information in the file. Some image viewers will allow you to view this information.

Embedded Structure Code
This option allows the hidden inclusion of the structure code (in the formats SMILES, CACTVS and Molfile) in the GIF/PNG file. Some molecule editors like CACTVS csed are able to extract this information from the GIF file and thus can operate on the images like it was a structure exchange file.
When using an external image viewer instead of the internal browser image viewer it is strongly recommended to submit the page with the "and save the image on disk" option. The application of some intermediate image viewers (like xv) leads to the loss of structure code, if these programs are used to save the image to disk!

Image Maps
This additional option can be selected if the generation of an HTML image map associated with the image is desired. This option can be used only if the image is not directly saved to file. The HTML response page contains the image, as usual, and below the image map data in a text area. The image and the map data can can both be saved and used in active Web sites which perform some kind of operation if an atom, bond or molecule is clicked at. The image map will generally require some editing, for exmple, you almost certainly want to change the action URL executed when you click on a displayed item. Three image map types are supported: Molecules (only useful if the image contains more than one structure fragment), atoms and bonds. The action URLs are activated when you click on the molecule area, atom or bond. Invisible atoms (hydrogen, but not carbon which is still displayed as vertex) and suppressed bonds are not clickable. The default action associated with the response page simply pops up a JavaScript alert box, informing about the object clicked at. On MS Internet Explorer, you can view the object identification as a tooltip when you pause over a clickable region.

Technology and Acknowledgments

The CGI script connected to the form runs on a non-GUI version of a class of progammable (in Tcl/Tk and Extensions) general-purpose chemical structure handling programs of the CACTVS system. Using the powerful scripting language interface of these programs, it is possible to implement nearly every graphical or structure handling application very rapidly.

We thank Peter Ertl from Novartis Crop Protection AG for kindly allowing us to use the JME molecular editor. Novartis

The GIFs are plotted with a customized version of the GD GIF drawing library, which includes PNG output patches by Grep Roelofs. The 2D display coordinate generation (in case no 2D coordinates are passed in) is based on the algorithms of C. Shelley (J. Chem. Inf. Comput. Sci. 23 (1983), 61-65). It works nicely for most small and medium-sized organic compounds, but can sometimes fail in case of compounds with a cage structure.

Please contact Wolf-D. Ihlenfeldt, if you have any questions or comments. Commercial variants of this code are available.

Last Change: 2001-01-16 W. D. Ihlenfeldt