def testIdentityMatrixNonTurbo(self):
assert_array_almost_equal(FASTA_EYE,
buildSeqidMatrix(FASTA, turbo=False))
def testIdentityMatrix(self):
assert_array_almost_equal(FASTA_EYE, buildSeqidMatrix(FASTA))
def testIdentityMatrix(self):
assert_array_almost_equal(FASTA_EYE, buildSeqidMatrix(FASTA))
def testIdentityMatrixNonTurbo(self):
assert_array_almost_equal(FASTA_EYE, buildSeqidMatrix(FASTA, turbo=False))
import prody.sequence as sequence
import prody
import matplotlib.pyplot as plt
alignment = prody.MSAFile("pkinase.fasta")
#get positions -> by hand for now
positions = [72, 83, 117, 119, 194, 251, 354, 355, 357, 429, 432]
#user alignSequenceToMSA instead to derive positions automatically
#set up webservice to get correspondance between MSA position and a particular PDB structure
alignment.setSlice(positions)
prody.writeMSA("test.fasta", alignment)
pa = prody.parseMSA("pocket_type1.fasta")
labs = pa.getLabels()
seqidmatrix = prody.buildSeqidMatrix(pa)
scamatrix = prody.buildSCAMatrix(pa)
tree = prody.calcTree(names=labs, distance_matrix=seqidmatrix)
plt.figure()
show = prody.showTree(tree, format='plt')
