-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Friday 20 February 2004 12:18, Tommi Hassinen wrote: > On Thu, 19 Feb 2004, Miguel Howard wrote: > > Can you tell me a little about the ghemical?
Will you be using the Ghemical Reader in CDK? BTW, the link is: http://bioinformatics.org/ghemical/ > It's a molecular modelling program written in C++. Currently it is split > in 2 parts: > > libghemical : only contains the core functionality (no graphics > or file I/O), has a built-in molecular mechanics implementation > links to external libs to implement quantum-mechanics methods > (libmopac7 and scientific toolkit from the MPQC program); the > following list shows what can(+) and can't be done(-) currently: > +compute energy/forces > +do geometry optimization > +do a molecular dynamics run > +run different conformational searches > -do a normal-mode analysis (vibrations/IR) > > ghemical : contains a GUI part for gnome. > > > What is the input format? > > There is a native file format, and many other file formats are accessible > through file import/export capabilities that depend on OpenBabel. > > However, I think none of the file formats directly fit into the plugin > use, and a new communication protocol is needed. If you have some time left, I would like to propose CMLComp... Ask Peter Murray-Rust about it... CMLComp is in XML format, which nicely embeds in other XML languages... just consider it. > > > I'll learn about cgi and web servers before I start anything at the > > > server side. > > > > Good. > > Yesterday evening I read a few tutorials about CGI, so here is the current > plan (please correct if needed). > > Indeed using CGI we can achieve more or less the situation where > inputs/outputs of the plugin and the server are connected; the only > limitation seems to be that plugin can only send a single request and > only after the server has received it, it can send a single reply. But > this is not too bad, especially since it makes the server quite simple. > > So the server would read standard input and write into standard output. > Now I see that it doesn't make sense to use the gnome/bonobo > ghemical-server, but instead a completely separate server is needed. Let's > call it "ghemical-cgi"; it will be a rather simple C++ console program > that uses resources from libghemical. Later it could be optimized into > this purpose (say smaller size and on-demand loading of parameter files). > > So a web server should be installed and set functional, and the > ghemcal-cgi program should be copied into the cgi-bin directory. Then the > web server would launch it for each request separately, and connect it > into the plugin. > > The plugin should ask user for server URL, say > > http://www.something.net or > http://www.something.net:80 > > Then internally it should add to URL a path to the cgi program: > > http://www.something.net:80/cgi-bin/ghemical-cgi > > Now if such a request is sent to the web server, it should launch the > ghemical-cgi program, right? Correct. > Ok then the web-server launches ghemical-cgi so that some environmental > variables are set. Now the request form plugin should be sent to the > ghemical-cgi program. Since the request can be a large one (it could > contain the structure of a peptide or a whole protein molecule perhaps) > the simple means are not enough; by this I mean ghemical-cgi should get > the request from standard input. Yes, you will need to use the POST method of HTTP... > How to do that then? My docs say that this the way it works if the html > request the plugin makes is of type POST. How this is done, is still a bit > unclear, and I'm studying it. Basically a socket should be opened to Indeed... I don't know how this is done in C++, but for other languages there exist many tools... so I guess for C++ too... > http://www.something.net:80 > > and a proper html request string should be sent that accesses > /cgi-bin/ghemical-cgi file using the POST method. The data to be sent is > included in this html request. The data should contain a description of > atoms and bonds, and instructions to ghemical-cgi what to do with them. > The protocol could be something like this: > > -a header part for checking protocol versions etc. > "hello, I have a job for you" > > -descriptions of atoms/bonds etc. > "there a x atoms and y bonds ; atom0 = ... atom1 = ..." > > -the comp.chem. method to be used and related settings. > "use molecular mechanics" > "use a semi-empirical QM method, AM1, with total charge = 0" > > -instructions about the operation to be done. > "just calculate the energy" > "do a geom-optimization and send structures after each x steps" > > At this stage ghemical-cgi knows what to do, and can start working. It > should add only a simple header to the data it sends using stdout to the > web server, and then it can send data directly to the plugin; the start > of the reply to web-server and finally to plugin is > > Content-type: text/plain > > this is the first line of reply to the plugin. > > Then the plugin just reads and interprets the reply stream until it ends. > The ghemical-cgi process is shut down and the operation is ready. > > Any comments or enhancements? Talk to Peter... he has been/is doing similar things... Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFANfBsd9R8I9Yza6YRAr3eAJ0etsPJtakqDF9U6oD0yPykypvsewCfZk8l UyU9DkD5vM97Y0v8YJ5IKXU= =NVPp -----END PGP SIGNATURE----- ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. 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