From: Rajarshi G. <rg...@in...> - 2006-08-25 17:40:58
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Hi, I had sent a mail to cdk-help regarding some issues with the IBioPolymer interface and internal representation of Monomer names. One issue is that Monomer names can be arbitrary. This is fine. However when reading in a PDB, we will get 3-letter codes. When creating a peptide sequence by hand we will get 1-letter codes. Should we not standardize on the internal representation? So that when reading a PDB, the 3-letter code gets converted to a 1-letter code? Thus when I query an object that implements the IBioPolymer interface, I can be sure of getting one type of monomer name. Of course, if I were to provide my own names, that would break the standardization - but then I would also assume that I would have code that would understand the non-standard names. Second, the IBioPolymer interface provides a method to get all the Monomer names, but no equivalent method to get all the Monomer objects themselves. I realize that I could get the Strand names, then get the Strand objects and then get the Monomer's from each Strand object. Would it be better to include this within the BioPolymer class? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Alone, adj.: In bad company. -- Ambrose Bierce, "The Devil's Dictionary" |
From: Rajarshi G. <rg...@in...> - 2006-08-25 20:34:46
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On Fri, 2006-08-25 at 13:40 -0400, Rajarshi Guha wrote: > Hi, I had sent a mail to cdk-help regarding some issues with the > IBioPolymer interface and internal representation of Monomer names. [snip] Another problem I faced that does not seem to be handled is the identification of the N-terminal residue in a peptide sequence. Given that the monomer names (and monomers themselves) are stored in a hash table, I cannot assume that the the first one is the N-terminal AA. Would it be a good idea to store the information at creation time. That is, when ProteinBuilderTool or PDBReader is used, can it store the information regarding the N-terminal and C-terminal residues? Thanks, ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "A fractal is by definition a set for which the Hausdorff Besicovitch dimension strictly exceeds the topological dimension." -- Mandelbrot, "The Fractal Geometry of Nature" |