scores[pdbs[i]] = {}
PhyloM.append([])
scoresM.append([])
scores[pdbs[i]][pdbs[j]] = score
scoresM[i].append(score)
else:
print '{:->3.2%}\t{} {}\t{}'.format( s/total, pdbs[i], pdbs[j], "error")
if pdbs[i] not in scores:
scores[pdbs[i]] = {}
PhyloM.append([])
scoresM.append([])
scores[pdbs[i]][pdbs[j]] = 0
scoresM[i].append(0)
print_matrix("Scores", scores, pdbs)
scoresM = TreeConstruction._Matrix([x[x.rfind('/')+1:] for x in pdbs], scoresM)
distances = {}
for i in range(leng):
distances[pdbs[i]] = {}
for j in range(i+1):
distances[pdbs[i]][pdbs[j]] = (scores[pdbs[i]][pdbs[i]]+scores[pdbs[j]][pdbs[j]])/2.0 - scores[pdbs[i]][pdbs[j]]
PhyloM[i].append(distances[pdbs[i]][pdbs[j]])
PhyloM = TreeConstruction._DistanceMatrix([x[x.rfind('/')+1:] for x in pdbs], PhyloM)
print_matrix("Distances", distances, pdbs)
tree = TreeConstruction.DistanceTreeConstructor().upgma(PhyloM)
Phylo.draw_ascii(tree)
tree.ladderize()
#Phylo.draw_graphviz(tree, node_size=0)
def hide_inner(node):
PhyloM.append([])
scoresM.append([])
scores[pdbs[i]][pdbs[j]] = score
scoresM[i].append(score)
else:
print '{:->3.2%}\t{} {}\t{}'.format(s / total, pdbs[i], pdbs[j],
"error")
if pdbs[i] not in scores:
scores[pdbs[i]] = {}
PhyloM.append([])
scoresM.append([])
scores[pdbs[i]][pdbs[j]] = 0
scoresM[i].append(0)
print_matrix("Scores", scores, pdbs)
scoresM = TreeConstruction._Matrix([x[x.rfind('/') + 1:] for x in pdbs],
scoresM)
distances = {}
for i in range(leng):
distances[pdbs[i]] = {}
for j in range(i + 1):
distances[pdbs[i]][pdbs[j]] = (scores[pdbs[i]][pdbs[i]] + scores[
pdbs[j]][pdbs[j]]) / 2.0 - scores[pdbs[i]][pdbs[j]]
PhyloM[i].append(distances[pdbs[i]][pdbs[j]])
PhyloM = TreeConstruction._DistanceMatrix([x[x.rfind('/') + 1:] for x in pdbs],
PhyloM)
print_matrix("Distances", distances, pdbs)
tree = TreeConstruction.DistanceTreeConstructor().upgma(PhyloM)
Phylo.draw_ascii(tree)
tree.ladderize()
