Binary string encoding method

Another set of early studies came from the work of Judson and coworkers [35, 36], which emphasized using GAs for search problems on small molecules and peptides, especially cyclic peptides. A dihedral angle representation was used for the peptides with values encoded as binary strings, and the energy function used the standard CHARMM force field. Mutations were implemented as bit flips and crossovers were introduced by a cut-and-paste of the strings. The small size of the system enabled a detailed investigation of the various parameters and policies chosen. In Ref. [37], a comparison between a GA and a direct search minimization was performed and showed the advantages and weaknesses of each method. As many concepts are shared between search problems on small peptides and complete proteins, these studies have contributed to subsequent attempts on full proteins. 

In the genetic synthesis of the binary string representing the cut order plan, two possible kinds of encoding methods are considered due to search space discrepancy. 

In encoding method 1, each binary string consists of (S + C) binary sub-strings. Each binary sub-string represents the number of garments in S for different sizes, and the number of plies in C for different colours for a particular fabric lay a a= 1,2,.. ., L). As each number of garment and ply could be chosen... 

In encoding method 2, the binary string is shortened with only and binary sub-strings that comprise... 

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