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MODGRAPH PRODUCTS:
smi2image
smi2image.cgi - Web CGI to create images from SMILES
Description
smi2image.cgi is a CGI program that converts SMILES into images using the
Daylight Depict Toolkit, for showing molecules in a web page. It can
either create a drawing ``from scratch'' using Daylight's depict algorithm,
or it can use X/Y coordinates supplied in the URL. Images can be GIF, PNG
or JPEG format.
smi2image.cgi is designed to be used with the Apache web server (see
http://www.apache.org/ ) but should work with any
CGI-compliant web server.
smi2image.cgi is written in Perl, and uses the DayPerl2.pm module, which
is freely available. (Contact Modgraph, http://www.modgraph.co.uk if you
need the source code for DayPerl2.)
URL PARAMETERS
All parameters are specified in the URL, for example:
- smiles
-
The SMILES string of the molecule that is to be drawn. This is the only
required parameter.
Note that SMILES must be properly ``quoted'' to eliminate characters that are disallowed or have special meaning in a URL. In particular, the following characters that are legal in a SMILES must be ``escaped'', or converted to the three-character %NN code:
% %25 / %2F # %23 < %3C $ %24 > %3E & %26 [ %5B * %2A \ %5C + %2B ] %5D - %2D | %7C - coordinates
-
X/Y coordinate pairs for each atom in the SMILES. Coordinates are
specified in SMILES order, two numbers per atom, and are separated by
commas. For example:
- width
- Image width in pixels (default: 300)
- height
- Image height in pixels (default: 200)
- colorscheme
- cob, cow, bow, wob, for color-on-black, color-on-white, etc. These are actually filenames in the colorscheme directory, for example ./colorscheme/blue_theme would be '-c blue_theme'. Other colorschemes can be created in a subdirectory called 'colorscheme' in the current directory. Colorscheme names must be lowercase. If no colorscheme is specified, or if the specified colorscheme can't be found, color-on-black is used.
- highlightAtoms
-
Colors the atoms by highlighting the atoms indicated in the parameter's
string. The string is in canonical-smiles order, and each character is a
single number that corresponds to the colors in the colorscheme file
(i.e. 0 = first color, 1 = second color, ...).
For example, the following would color the first two atoms (the N-C) using the second color in the color scheme, and the rest of the atoms in the cyclohexane using the first color in the color scheme:
- transparent yes | no
-
If ``transparent'' is ``yes'', uses a transparent background for GIF
or PNG images (ignored for JPG images). This has the effect of drawing the
atoms and bonds on top of the background color or texture of the web page.
(Default: no)
(NOTE: Incredibly, Internet Explorer can't show transparent colors in PNG images. They are shown non-transparent. Other browsers such as Firefox will show the transparent images correctly.)