def testIdentityMatrixNonTurbo(self): assert_array_almost_equal(FASTA_EYE, buildSeqidMatrix(FASTA, turbo=False))
def testIdentityMatrix(self): assert_array_almost_equal(FASTA_EYE, buildSeqidMatrix(FASTA))
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')