def test_rmsd_to_same(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.]])
a2 = np.array([[1., 2., 1.], [0., -1., 0.], [-1., -1., -1.]])
self.assertAlmostEqual(ftme.drmsd(a1, a1), 0)
self.assertAlmostEqual(ftme.drmsd(a2, a2), 0)
self.assertAlmostEqual(ftme.rmsd(a1, a1), 0)
self.assertAlmostEqual(ftme.rmsd(a2, a2), 0)
def test_rmsd_to_same(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.]])
a2 = np.array([[1., 2., 1.], [0., -1., 0.], [-1., -1., -1.]])
self.assertAlmostEqual(ftme.drmsd(a1, a1), 0)
self.assertAlmostEqual(ftme.drmsd(a2, a2), 0)
self.assertAlmostEqual(ftme.rmsd(a1, a1), 0)
self.assertAlmostEqual(ftme.rmsd(a2, a2), 0)
def update(self, sm, step):
if not self.silent:
curr_vress=sm.bg.get_ordered_virtual_residue_poss()
if self.mode=="RMSD":
rmsd=ftme.rmsd(self._reference, curr_vress)
elif self.mode=="dRMSD":
rmsd=ftme.drmsd(self._reference, curr_vress)
if self.best_cgs.can_insert_right((None, rmsd)):
self.best_cgs.insert_right((sm.bg.to_cg_string(),rmsd))
if step % 10 == 0:
for i, bg in enumerate(self.best_cgs):
with open(os.path.join(conf.Configuration.sampling_output_dir,
'best_rmsd{:d}.coord'.format(i)), 'w') as f:
f.write(bg[0])
if self._showMinMax:
if rmsd>self._maxRMSD:
self._maxRMSD=rmsd
if self._showMinMax==True:
if rmsd<self._minRMSD:
self._minRMSD=rmsd
self.history[1].append( self._minRMSD )
self.history[0].append( rmsd )
self.history[-1].append( self._maxRMSD )
if self._showMinMax=="max":
return "{:6.3f} A\t{:6.3f} A".format(rmsd, self._maxRMSD)
else:
return "{:6.3f} A\t{:6.3f} A\t{:6.3f} A".format(rmsd, self._minRMSD, self._maxRMSD)
else:
self.history[0].append( rmsd )
return "{:6.3f} A".format(rmsd)
else:
return
def update(self, sm, step):
if not self.silent:
if self.res_ids:
curr_vress = []
for res in self.res_ids:
curr_vress.append(
sm.bg.get_virtual_residue(res,
allow_single_stranded=True))
curr_vress = np.array(curr_vress)
else:
curr_vress = sm.bg.get_ordered_virtual_residue_poss()
if self.mode == "RMSD":
try:
rmsd = ftme.rmsd(self._reference, curr_vress)
except Exception as e:
self.res_ids = set(self.reference_cg.seq._seqids) & set(
sm.bg.seq._seqids)
self._reference = []
curr_vress = []
for res in self.res_ids:
curr_vress.append(
sm.bg.get_virtual_residue(
res, allow_single_stranded=True))
self._reference.append(
self.reference_cg.get_virtual_residue(
res, allow_single_stranded=True))
curr_vress = np.array(curr_vress)
self._reference = np.array(self._reference)
log.error("Calculating rmsd between %s and %s",
self._reference, curr_vress)
rmsd = ftme.rmsd(self._reference, curr_vress)
elif self.mode == "dRMSD":
rmsd = ftme.drmsd(self._reference, curr_vress)
if self.best_cgs.can_insert_right((None, rmsd)):
self.best_cgs.insert_right((sm.bg.to_cg_string(), rmsd))
if step % 10 == 0:
for i, bg in enumerate(self.best_cgs):
with open(
os.path.join(
conf.Configuration.sampling_output_dir,
'best_rmsd{:d}.coord'.format(i)), 'w') as f:
f.write(bg[0])
if self._showMinMax:
if rmsd > self._maxRMSD:
self._maxRMSD = rmsd
if self._showMinMax == True:
if rmsd < self._minRMSD:
self._minRMSD = rmsd
self.history[1].append(self._minRMSD)
self.history[0].append(rmsd)
self.history[-1].append(self._maxRMSD)
if self._showMinMax == "max":
return "{:6.3f} A\t{:6.3f} A".format(rmsd, self._maxRMSD)
else:
return "{:6.3f} A\t{:6.3f} A\t{:6.3f} A".format(
rmsd, self._minRMSD, self._maxRMSD)
else:
self.history[0].append(rmsd)
return "{:6.3f} A".format(rmsd)
else:
return
def test_drmsd(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.]])
a2 = np.array([[1., 2., 1.], [0., -1., 0.], [-1., -1., -1.]])
r = ftme.drmsd(a1, a2)
self.assertGreater(r, 0)
def test_drmsd(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.]])
a2 = np.array([[1., 2., 1.], [0., -1., 0.], [-1., -1., -1.]])
r = ftme.drmsd(a1, a2)
self.assertGreater(r, 0)