def getBackbone(residues):
phi = [0.0]
psi = []
for i, res_i in enumerate(residues):
N_i = res_i["N"].get_vector()
CA_i = res_i["CA"].get_vector()
C_i = res_i["C"].get_vector()
if i > 0:
res_im1 = residues[i - 1]
C_im1 = res_im1["C"].get_vector()
phi.append(calc_dihedral(C_im1, N_i, CA_i, C_i))
if i < (len(residues) - 1):
res_ip1 = residues[i + 1]
N_ip1 = res_ip1["N"].get_vector()
psi.append(calc_dihedral(N_i, CA_i, C_i, N_ip1))
psi.append(0.0)
return phi, psi
def omega(self, i, rosetta_definitions=True):
"""
Get the Omega Angle of i in radians
Omega is defined as the dihedral angle between the peptide bond of i and i + 1, as in Rosetta.
If rosetta_definitions are False, omega is then treated as being between i and i -1
:param i: int
:param reverse_rosetta_definitions: bool
:rtype: float
"""
res = self.all_residues[i]
try:
n = res['N'].get_vector()
ca = res['CA'].get_vector()
c = res['C'].get_vector()
if rosetta_definitions and i < len(
self.all_residues) - 1 and self.connected_to_next(i):
res_plus_one = self.all_residues[i + 1]
next_n = res_plus_one['N'].get_vector()
next_ca = res_plus_one['CA'].get_vector()
omega = calc_dihedral(ca, c, next_n, next_ca)
return omega
elif not rosetta_definitions and i > 1 and self.connected_to_previous(
i):
res_minus_one = self.all_residues[i - 1]
pre_c = res_minus_one['C'].get_vector()
pre_ca = res_minus_one['CA'].get_vector()
omega = calc_dihedral(pre_ca, pre_c, n, ca)
return omega
else:
return 0.0
except BaseException:
print "Could not get omega for " + repr(i)
raise LookupError
def test_Vector(self):
"""Test Vector object."""
v1 = Vector(0, 0, 1)
v2 = Vector(0, 0, 0)
v3 = Vector(0, 1, 0)
v4 = Vector(1, 1, 0)
self.assertEqual(calc_angle(v1, v2, v3), 1.5707963267948966)
self.assertEqual(calc_dihedral(v1, v2, v3, v4), 1.5707963267948966)
self.assertTrue(
numpy.array_equal((v1 - v2).get_array(), numpy.array([0.0, 0.0, 1.0]))
)
self.assertTrue(
numpy.array_equal((v1 - 1).get_array(), numpy.array([-1.0, -1.0, 0.0]))
)
self.assertTrue(
numpy.array_equal(
(v1 - (1, 2, 3)).get_array(), numpy.array([-1.0, -2.0, -2.0])
)
)
self.assertTrue(
numpy.array_equal((v1 + v2).get_array(), numpy.array([0.0, 0.0, 1.0]))
)
self.assertTrue(
numpy.array_equal((v1 + 3).get_array(), numpy.array([3.0, 3.0, 4.0]))
)
self.assertTrue(
numpy.array_equal(
(v1 + (1, 2, 3)).get_array(), numpy.array([1.0, 2.0, 4.0])
)
)
self.assertTrue(numpy.array_equal(v1.get_array() / 2, numpy.array([0, 0, 0.5])))
self.assertTrue(numpy.array_equal(v1.get_array() / 2, numpy.array([0, 0, 0.5])))
self.assertEqual(v1 * v2, 0.0)
self.assertTrue(
numpy.array_equal((v1 ** v2).get_array(), numpy.array([0.0, -0.0, 0.0]))
)
self.assertTrue(
numpy.array_equal((v1 ** 2).get_array(), numpy.array([0.0, 0.0, 2.0]))
)
self.assertTrue(
numpy.array_equal(
(v1 ** (1, 2, 3)).get_array(), numpy.array([0.0, 0.0, 3.0])
)
)
self.assertEqual(v1.norm(), 1.0)
self.assertEqual(v1.normsq(), 1.0)
v1[2] = 10
self.assertEqual(v1.__getitem__(2), 10)
def parse(structure, aa):
# Solo consideramos el 1er modelo
model = structure[0]
num_chains = len(structure[0])
print('Number of chains ' + str(num_chains))
df = DataFrame([])
res = 0
for chain in model:
for residue in chain:
if residue.get_id()[0] == ' ': #ignore all hetero atoms
name = residue.get_resname()
if not isin(name, aa):
print('Non recognized residue ' + name)
return DataFrame([])
N_xyz = residue['N'].get_vector()
df = df.append({'chain':chain.id, 'aa': name, 'atom': 'N', 'res': res, 'coord': N_xyz}, ignore_index=True)
CA_xyz = residue['CA'].get_vector()
df = df.append({'chain':chain.id, 'aa': name, 'atom': 'CA', 'res': res, 'coord': CA_xyz}, ignore_index=True)
C_xyz = residue['C'].get_vector()
df = df.append({'chain':chain.id, 'aa': name, 'atom': 'C', 'res': res, 'coord': C_xyz}, ignore_index=True)
res = res + 1
bond_length = [(df.iloc[1].coord - df.iloc[0].coord).norm(), (df.iloc[2].coord - df.iloc[1].coord).norm()]
bond_angle = [0, calc_angle(df.iloc[0].coord, df.iloc[1].coord, df.iloc[2].coord)*180/pi]
torsion_angle = [0, 0]
coord = [df.iloc[0].coord.get_array(), df.iloc[1].coord.get_array()]
for ij in range(2, len(df)-1):
bond_length.append((df.iloc[ij+1].coord - df.iloc[ij].coord).norm())
bond_angle.append(calc_angle(df.iloc[ij-1].coord, df.iloc[ij].coord, df.iloc[ij+1].coord)*180/pi)
torsion_angle.append(calc_dihedral(df.iloc[ij-2].coord, df.iloc[ij-1].coord, df.iloc[ij].coord, df.iloc[ij+1].coord)*180/pi)
coord.append(df.iloc[ij].coord.get_array())
bond_length.append(0)
bond_angle.append(0)
torsion_angle.append(0)
coord.append(df.iloc[len(df)-1].coord.get_array())
coord = array(coord)
df_new = df.drop('coord', axis=1)
df_new['x'] = coord[:, 0]
df_new['y'] = coord[:, 1]
df_new['z'] = coord[:, 2]
df_new['bond_length'] = bond_length
df_new['bond_angle'] = bond_angle
df_new['torsion_angle'] = torsion_angle
return df_new
def create_j_dict(self):
""" Description:
Given an JCalcPdb struct, create J dictioary with chosen 3JH,H
information to calc all J values
Usage:
JcalcPdb.create_j_dict()
"""
j_dict = {}
for j in self.j_list:
chosen_j = f"{j[0]},{j[3]}"
j_dict[chosen_j] = {}
j_dict[chosen_j]["HX"] = self.atom_dict[j[0]][0]
j_dict[chosen_j]["CX"] = self.atom_dict[j[1]][0]
j_dict[chosen_j]["CY"] = self.atom_dict[j[2]][0]
j_dict[chosen_j]["HY"] = self.atom_dict[j[3]][0]
j_dict[chosen_j]["dih"] = calc_dihedral(self.atom_dict[j[0]][0],
self.atom_dict[j[1]][0],
self.atom_dict[j[2]][0],
self.atom_dict[j[3]][0]
)
j_dict[chosen_j]["dih"] = math.degrees(j_dict[chosen_j]["dih"])
j_dict[chosen_j]["substituents"] = {}
self.j_dict = j_dict
# Search subs for CX and create subs dict
self.search_subs(hx_atom=j[0],
cx_atom=j[1],
cy_atom=j[2],
hy_atom=j[3],
j_atoms=j,
chosen_j=chosen_j
)
# Search subs for CY and create subs dict
self.search_subs(hx_atom=j[3],
cx_atom=j[2],
cy_atom=j[1],
hy_atom=j[0],
j_atoms=j,
chosen_j=chosen_j
)
def calc_subs_coupling(self, HX, CX, CY, SY, dihedral, element):
""" Description:
Given an JCalcPdb struct and atom vectors, calculate
J pertubation from substitute atoms
Usage:
JcalcPdb.calc_subs_coupling(vector_HX, vector_CX, vector_CY,
vector_SY, HX-CX-CY-XY_dih,
substitue_element
)
Parameters:
HX:
Atom coordinates vector, HX from HX-CX-CY-SY fragment
CX:
Atom coordinates vector, CX from HX-CX-CY-SY fragment
CY:
Atom coordinates vector, CY from HX-CX-CY-SY fragment
SY:
Atom coordinates vector, SY from HX-CX-CY-SY fragment
dihedral:
float, dihedral from JH,H fragment HX-CX-CY-XY in radians
element:
string, atom element from substitute atom (H, O, N)
"""
huggins_constant = HUGGINS_ELECTRO[element]
subs_dih = calc_dihedral(HX, CX, CY, SY)
if subs_dih >= 0:
return huggins_constant * \
(0.56 + (-2.32 * (math.cos(math.radians((dihedral * -1) +
(17.9 * huggins_constant))) ** 2)))
else:
return huggins_constant * \
(0.56 + (-2.32 * (math.cos(math.radians(dihedral +
(17.9 * huggins_constant))) ** 2)))
def psi(self, i):
"""
Get the Psi Angle of i in radians
:param i: int
:rtype: float
"""
res = self.all_residues[i]
if i == len(self.all_residues) or not self.connected_to_next(i):
return 0.0
try:
n = res['N'].get_vector()
ca = res['CA'].get_vector()
c = res['C'].get_vector()
res_plus_one = self.all_residues[i + 1]
nn = res_plus_one['N'].get_vector()
psi = calc_dihedral(n, ca, c, nn)
return psi
except Exception:
print "Could not get psi for " + repr(i)
raise LookupError
def phi(self, i):
"""
Get the Phi Angle of i in radians
:param i: int
:rtype: float
"""
if i == 1 or not self.connected_to_previous(i):
return 0.0
res = self.all_residues[i]
try:
n = res['N'].get_vector()
ca = res['CA'].get_vector()
c = res['C'].get_vector()
res_minus_one = self.all_residues[i - 1]
cp = res_minus_one['C'].get_vector()
phi = calc_dihedral(cp, n, ca, c)
return phi
except Exception:
print "Could not get phi for " + repr(i)
raise LookupError
from Bio.Alphabet import generic_protein
from Bio.PDB import calc_dihedral
seqs = [
Seq('HRFKVYNYMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVHHKCREKVANLC', generic_protein)
]
s = ds.Distructure('1ptq', seqs)
s.generate_primary_contacts()
s.run()
for r in s.get_residues():
if r.get_resname() != 'GLY':
v1 = r['CA'].get_vector()
v2 = r['N'].get_vector()
v3 = r['C'].get_vector()
v4 = r['CB'].get_vector()
theta = calc_dihedral(v1, v2, v3, v4)
if theta < 0.:
print("dihedral error at", r)
else:
print(r)
pass
pass
# NOTE write result to file
from Bio.PDB.mmcifio import MMCIFIO
io = MMCIFIO()
io.set_structure(s)
io.save('chirality_test.cif')
