def symop(self, matrixA, matrixB, title=""):
a = SVD.SVDSuperimposer()
a.set(matrixA[1], matrixB[1])
x = []
x.append(matrixA[0])
x.append(matrixB[0])
COM = self.get_center_of_mass(x)
print "COMPARISON " + title
print "Centroid: "
print COM
a.run()
R = np.transpose(a.get_rot())
print "Rotation Matrix:"
print R
print title + " Rotation Angle: " + self.getangle(R)
angle = self.getangle(R)
print title + " RMSD: " + a.get_rms()
print '-----'
def main(self, filetype):
self.set = 1
for pdb in self.pdbs:
print "Autoloading detected PDB file: %s" % pdb
print ", ".join([str(x) for x in pdb.list_chains()])
commonAA = pdb.commonAA(
123, 531
) #Only use amino acids 123-531 for superimposing and computing RMSD.
f = open('input.txt', 'r')
l = []
matrices = []
matrices.append([])
for line in f:
if line.strip() == "":
matrices.append(l)
l = []
else:
l.append(map(float, line.split(' ')))
flag = 1
while flag:
towrite1 = []
matrix_static = []
matrix_moving = []
towrite2 = []
counter1 = 1
counter2 = 1
input2 = question("What subunit is the static reference? (eg 5A)")
input2 = input2.strip()
matrixID2 = int(re.findall(r'\d+', input2)[0])
chainID2 = re.findall(r'\D+', input2)[0].upper()
input2 = input2.upper()
input1 = question("What subunit is moving? (eg 1A)")
input1 = input1.strip()
matrixID1 = int(re.findall(r'\d+', input1)[0])
chainID1 = re.findall(r'\D+', input1)[0].upper()
input1 = input1.upper()
for pdb in self.pdbs:
for atom in pdb.backbone:
if atom['chain'] == chainID1 and atom[
'res num'] in commonAA:
a = matrices[matrixID1] * np.transpose(atom.coord())
temp = Patom(str(atom), 1)
temp['x'] = float(a[0])
temp['y'] = float(a[1])
temp['z'] = float(a[2])
temp['line num'] = counter1
counter1 += 1
towrite1.append(temp)
if atom['chain'] == chainID2 and atom[
'res num'] in commonAA:
a = matrices[matrixID2] * np.transpose(atom.coord())
temp = Patom(str(atom), 1)
temp['x'] = float(a[0])
temp['y'] = float(a[1])
temp['z'] = float(a[2])
temp['line num'] = counter2
counter2 += 1
towrite2.append(temp)
file = open("output/%s%s.pdb" % (filetype, input1), 'w')
for i in towrite1:
file.write(str(i) + '\n')
file.close()
file = open("output/%s%s.pdb" % (filetype, input2), 'w')
for i in towrite2:
file.write(str(i) + '\n')
file.close()
matrix_static = self.coordmatrix(towrite1)
matrix_moving = self.coordmatrix(towrite2)
a = SVD.SVDSuperimposer()
static = [towrite1, matrix_static]
moving = [towrite2, matrix_moving]
self.symop(static, moving, "%s-to-%s" % (input1, input2))
continue_check = question("Continue? (Y/n)",
['', 'y', 'Y', 'n', 'N'])
if continue_check not in ['', 'y', 'Y']:
flag = 0
