Ramachandran diagram generator

Teh ramachandran diagram generator is my first attempt to put the formalism of my 3D programming experience behind something of practical, if obscure use, in the form of a molecular modeller. The ramachandran diagram was first introduced to me y the fabulous biochemistry textbook by Voet & Voet, and immediately struck me as something of major technical importance that I could pull off, in pascal, on my P233. Essentially, the program does this. A peptide bond in a model polymer of L-amino acid is suimulated in the 3D engine, and the two bonds with free rotation, designated phi and psi respectively, are manipulated through 360 degrees. The stability of the peptide bond under each configuration is tested by seeing if the constituent atoms come within their non-bonding interaction van-der-waals radii, and if a stable configuration is generated, it is marked on the diagram in red or blue with respect to the tortional angles used. In the case of rotating and manipulatable R groups, these have to be taken into acount as well, and the stability is assessed according to the stable form the R group can take on rotation. This means that the rotation and stability measuring procedures often have to be tested through 360 degrees in three, four, or even more dimensions, making the program rather slow in the consideration of Poly-L-Serine and Poly-L-Phenylalanine (although, rather counter-intuitively going by the bulky phenyl group and oxygen's large Van der waals radius, these produce the same diagram as Poly-L-Alanine; only the nonchiral glycine gives the symettrical diagram, as pictured to the left). The 3D models are in vector form, to allow measurement of distances and rotation along bonds to be simply accomplished, and a simple vector rotation procedure, harnessing the cross product (which for some dumb reason isn't taught as part of the maths A-level, forcing me to attempt to piece it together myself) to complete the rotation about bonds of entire sections of the model. Although the coding is rather prosaic, I'm rather proud of my little creation, particularly due to the accurate demonstration of a biochemically useful principal. In the goody bad available I've included the sources and applications to generate ramachandran diagrams for Alanine, Serine, Phenylalanine, and glycine, even though all through appear ... exactly the same. Good to prove it to yourself, mind. Also included is a small program that visually demonstartes the rotation process. I hope this is of some use or entertainment to somebody - Jon

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