Comments (1)
Hello Joern,
thanks for your interest in CCMpred.
The ordering of the 21 amino acid states is "ARNDCQEGHILKMFPSTWYV-"
Instead of answering the second question, I would like to point you to the python-based parsing code for both the "oldraw" and "MessagePack" raw coupling format available as part of the CCMgen sourcecode. It will parse the raw coupling files into an object with x_single and x_pair matrices available as NumPy arrays. For x_pair, the array indexing is [i, j, a, b] with a corresponding to the amino acid at position i and b corresponding to the amino acid at position b. I hope that this is a lot easier and less error-prone to use than coming up with your own parser.
Best wishes,
Stefan (Seemayer)
from ccmgen.
Related Issues (8)
- Model with 2 states for amino acids ? HOT 1
- AttributeError: 'str' object has no attribute 'decode' (scipy1.7)
- nmut approximation via rounded expectation can be inaccurate in edge cases.
- Pseudo-likelihood optimization does not take pseudo-counts into account
- Error with CCMgen --tree-newick HOT 3
- when gaps included in x_single, there is an error in sampling
- How to use --seq0-file option ? HOT 1
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from ccmgen.