def parsegene_hbonds_site_reference(c, ref=None):
if ref is None:
ref = c.structures[0]
# First, calculate molecules, molecule sites and hydrogen bonds
MoleculeSites.get(ref)
HydrogenBonds.get(ref)
MoleculeSites.get(c)
HydrogenBonds.get(c)
# Now for the actual comparison we need to compile a list of Hbonds
# for each structure, expressed in terms of molecular sites
reflabels = HydrogenBondTypes.get(ref)
hblabels = HydrogenBondTypes.get(c)
# And now to actually create a comparison
distL = []
for hb_lab in hblabels:
distL.append(list_distance(hb_lab, reflabels))
return np.array(distL)
def parsegene_hbonds_site_compare(c):
# First, calculate molecules, molecule sites and hydrogen bonds
MoleculeSites.get(c)
HydrogenBonds.get(c)
# Now for the actual comparison we need to compile a list of Hbonds
# for each structure, expressed in terms of molecular sites
hblabels = HydrogenBondTypes.get(c)
# And now to actually create a comparison
distM = np.zeros((c.length, c.length))
for hb_i1, hb_lab1 in enumerate(hblabels):
for hb_i2, hb_lab2 in enumerate(hblabels[hb_i1 + 1:]):
d = list_distance(hb_lab1, hb_lab2)
d /= (len(hb_lab1) + len(hb_lab2)) * 0.5
distM[hb_i1, hb_i1 + hb_i2 + 1] = d
distM[hb_i1 + hb_i2 + 1, hb_i1] = d
return distM
def test_labelprops(self):
from soprano.properties.labeling import (MoleculeSites,
HydrogenBondTypes)
a = read(os.path.join(_TESTDATA_DIR, 'nh3.cif'))
nh3_sites = MoleculeSites.get(a)[0]
# Check the name
self.assertEqual(nh3_sites['name'], 'H[N[H,H]]')
# Check the sites
self.assertEqual(set(nh3_sites['sites'].values()),
set(['N_1', 'H_1']))
# Now we test hydrogen bond types with alanine
a = read(os.path.join(_TESTDATA_DIR, 'mol_crystal.cif'))
# We expect 12 identical ones
hbtypes = ['C[C[C[H,H,H],H,N[H,H,H]],O,O]<N_1,H_2>'
'..C[C[C[H,H,H],H,N[H,H,H]],O,O]<O_1>']*12
self.assertEqual(HydrogenBondTypes.get(a), hbtypes)