Bit-string

Figure 2-65. This fingerprint was received by hashing, whereas only one part of all the substructures is specified in the illustration. The asterisk indicates the address of a collision in the bit string, generated by the algorithm.

Thus, if the chromosome is represented as a bit string, the mutation operator will change one bit in the string as illustrated in Figure 9-30. Usually, the mutation operator is applied with only a small probability. 

If each parameter is a 4-bit string, the configuration in Figure 10.38 would be represented by... 

Table 11.3 shows the intermediate steps of the first pass through the above six steps of the basic GA recipe. Step 1 is to construct six random bit-strings... 

Matter/Energy States Information Bit-Strings Propositions Strings... 

Figure 8.3 Example of a 2D similarity search, showing a query molecule and five of its nearest neighbors. The similarity measure for the search is based on 2D fragment bit-strings and the Tanimoto coefficient.

Although such a fragment-based measure clearly provides a very simple picture of the similarity relationships between pairs of structures, it is both efficient (because it involves just the application of logical operations to pairs of bit-strings) and effective (in that it is able to bring together molecules that are judged by chemists to be structurally similar to each other) in operation. 

Known molecules queried with n biotransformation rules to annotate observed metabolites as a binary bit string... 

XuE, L, Godden, J., and Bajorath, J. Database searching for compounds with similar biological activity using short binary bit string representations of molecules./. Chem. Inf. Comput. Sci. 1999, 39(5), 881-886. 

Holliday, J. D., Hu, C.-Y., and Willett, P. (2002) Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings. Combi. Chem. High Through. Screen. 5, 155-166. 

Testing should include network transactions under normal and high loads. For this test, refer to verifications in the TCP/IP transfer protocol. The advantage here is that this is built into the system and will be performed on an ongoing basis. However, this is not 100% accurate, as there are rare situations where the test does not work. To be on the safe side, use routines (e.g., MD5 hash calculation routines based on 128-bit strings). Ask the vendor of your application software sometimes, such tests are built in. 

Because of the numerous choices for molecular descriptors, weighting factors, and similarity coefficients, there are many ways in which the similarities between pairs of molecules can be calculated. The most used molecular descriptors for defining similarity are probably the 2D fingerprints (22). The bit strings of the molecular fingerprints are used to calculate similarity coefficients. Table 2.3 lists several selected similarity coefficients that can be used with various 2D fingerprints (23). The Tanimoto coefficient is the most popular one (22). 

The information content of such bit strings can be usefully quantified in terms of entropy H as defined by... 

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