The Cambridge Polymer Builder.
July 10, 2007 1 Comment
The first “proof of concept” product of the Cambridge Polymer Informatics Group is up on the web. It is a demo application of a polymer builder, which uses Chemical Markup Language, Polymer Markup Language and Jumbo to build various types of polymers.
The polymers are constructed from small fragments, such as CH, CH2, CO etc. groups with the associated connection table defined in CML. Polymer Markup Language (PML) then contains a set of instructions in terms of how these fragments are “glued” together, how torsions (in 3D representations) are dealt with etc and it can also deal with distributions (of torsional angles just as much as molecular weights) and probabilities (e.g. for random compolymerizations etc.). (More details in a forthcoming paper).
The polymer builder subsequently takes the fragments and the relating PML document as an input to enumerate a full connection table for a macromolecule in CML. (We have not implemented ensemble building in this demonstrator).
Right now we can build most structural motives, such as homopolymers, block- and random copolymers, dendrimers and branched systems. In this demonstrator, we have not currently implemented bump checking and a number of other controls, but we are working on them as I write. The demonstrator app is available as a webservice here. Please go out and take it for a spin. And, by the way, we are grateful for feedback….so let me have your thoughts and comments via the comments function on the blog.