EvaluateEnergy: Evaluates the energy corresponding to the sequence lattice configuration determined by the lattice in vector. From the residues positions, the interaction energies are calculated by the energy function For reference on the HP model see: --- R. Santana, P. Larra�aga, and J. A. Lozano (2004) Protein folding in 2-dimensional lattices with estimation of distribution algorithms. --- In Proceedings of the First International Symposium on Biological and Medical Data Analysis, --- Volume 3337 of Lecture Notes in Computer Science, pages 388-398, Barcelona, Spain, 2004. Springer Verlag. INPUTS vector: Sequence of residues ( (H)ydrophobic or (P)olar, respectively represented by zero and one) OUTPUTS energy: Energy evaluation. Last version 4/15/2009. Roberto Santana (roberto.santana@ehu.es)
0001 function[energy] = EvaluateEnergy(vector) 0002 % EvaluateEnergy: Evaluates the energy corresponding to the sequence lattice configuration determined by the lattice in vector. 0003 % From the residues positions, the interaction energies are calculated by the energy function 0004 % For reference on the HP model see: 0005 %--- R. Santana, P. Larra�aga, and J. A. Lozano (2004) Protein folding in 2-dimensional lattices with estimation of distribution algorithms. 0006 %--- In Proceedings of the First International Symposium on Biological and Medical Data Analysis, 0007 %--- Volume 3337 of Lecture Notes in Computer Science, pages 388-398, Barcelona, Spain, 2004. Springer Verlag. 0008 % INPUTS 0009 % vector: Sequence of residues ( (H)ydrophobic or (P)olar, respectively represented by zero and one) 0010 % OUTPUTS 0011 % energy: Energy evaluation. 0012 % 0013 % Last version 4/15/2009. Roberto Santana (roberto.santana@ehu.es) 0014 0015 0016 global HPInitConf; 0017 0018 0019 [Collisions,Overlappings,Pos] = EvalChain(vector); 0020 0021 0022 if Collisions<0 0023 energy = Collisions*(Overlappings+1); 0024 else 0025 energy = Collisions/(Overlappings+1); 0026 end 0027 0028 0029