"I am looking is a server side code that will generate images (png, jpeg, etc.)"
Try for example the free mol2ps/mol2png depiction tool, and you can use this Perl scripts for batch processing http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html There is a specific thread about this in BOx right now!!! http://blueobelisk.stackexchange.com/questions/38/how-do-i-automate-the-generation-of-3d-images-of-molecules Best regards. > Rolf Huehne wrote: > > Thank you for the quick reply. >> Nina Jeliazkova schrieb: >> >>> Hello All, >>> >>> I am looking for a guide or examples to use JMol in headless mode, for >>> generating images on the server side. >>> >>> I have seen a discussion on the list from 2006, as well as wiki-related >>> threads, but am still not sure if this is possible with the current >>> release. Any examples or just hints where to look in the jmol code >>> will be very useful. >>> >>> >> Nina, please describe more specific what you want to do. >> Is there also an applet and a user-defined view involved? >> > No. >> Or do you just want to use Jmol to create images automatically defined >> by some Jmol script(s)? >> > more or less. >> We do the latter to create the images in the JenaLib atlas pages for PDB >> entries, e.g.: http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1deh >> > There are structures (2D and 3D) of small molecules in a server side > database. Currently 2D images are generated by various means (mainly via > the CDK library). We would like to generate and provide 3D images > (where possible) as well. There is no problem to use JMol applet to > show a single structure, but embedding multiple jmol applets in a single > web page for multiple structures is not the best option, so what I am > looking is a server side code that will generate images (png, jpeg, > etc.) . > > Some examples (with 2D images) at > http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/1?max=10 > > I have a code, embedding Jmol in a Swing application, which runs fine > since few years, but trying to rework it server side was not successful. > > First , the viewer needs a component, which is not available in a server > side application > viewer = Viewer.allocateViewer(component, adapter); > > Second, trying to use a fake Component and a Graphics from a specially > created BufferedImage in viewer.renderScreenImage() just produces an > empty image. Obviously, I am missing something. > > Hope this makes the setup clearer. > > Best regards, > Nina > >> Regards, >> Rolf >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast and >> easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
