Another method to compare two matrices proposed by Marcel and Good operator definition

Three advices are valuable:

1. Start from small. I should take a look at short chains of similar interfaces (how to define similar interfaces) and get the right intuition.

2. Good comparison operator should, to some extend, output small distance value for two matrices generated from biologically known similar interfaces, large distance values for matrices generated from biologically known different interfaces.

3. The compatibility problem can be done in one of the following two ways:
i. Suppose A is a big matrix and B a small one. Locate in a sub-matrix C (compatible with B) in A such that dis(B, C) is smaller than any other sub-matrix from A.
ii.Select entries from A in the order that they appear in A to form a sub-matrix D, such that dis(B, D) is smaller than any other D-like sub-matrix from A.

After the results are got, they can be compared with those got from my enlarging small matrices method, and report the better one or both.

In this weekend, it is better to know the sizes of those 11,000+ matrices. This info will help in deciding if enlarging small matrices method is good.