def compute_psi_dict(amino_acids, aa_descriptors):
"""
This function pre-compute the square Euclidean distance
between all amino acids descriptors and stock the distance
in an hash table for easy and fast access during the
GS kernel computation.
amino_acids -- List of all amino acids in aa_descriptors
aa_descriptors -- The i-th row of this matrix contain the
descriptors of the i-th amino acid of amino_acids list.
"""
# For every amino acids couple (a_1, a_2) psiDict is a hash table
# that contain the squared Euclidean distance between the descriptors
# of a_1 and a_2
psiDict = {}
# Fill the hash table psiDict
for i in xrange(len(amino_acids)):
for j in xrange(len(amino_acids)):
c = aa_descriptors[i] - aa_descriptors[j]
psiDict[amino_acids[i], amino_acids[j]] = np.dot(c,c)
return psiDict
gs_kernel_slow.py 文件源码
python
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