def test_geometry_P():
g = Geometry.geometry("P")
assert isinstance(g, ProGeo)
assert g.CA_CB_CG_CD_diangle == -34.8
assert g.CA_CB_CG_angle == 104.21
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.2945
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD_angle == 105.03
assert g.CB_CG_length == 1.49
assert g.CG_CD_length == 1.5
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == 29.6
assert g.N_CA_C_O_diangle == -45.0
assert g.N_CA_C_angle == 112.7499
assert g.N_C_CA_CB_diangle == 115.2975
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "P"
def test_make_structure_from_geos():
"""Build a helix containing all 20 amino acids from list of geometries.
The structure should be identical to `extended.pdb`
"""
geos = [Geometry.geometry(aa) for aa in "ACDEFGHIKLMNPQRSTVWY"]
structure = PeptideBuilder.make_structure_from_geos(geos)
assert compare_to_reference(structure, "extended.pdb")
def test_geometry_M():
g = Geometry.geometry("M")
assert g.CA_CB_CG_SD_diangle == -179.6
assert g.CA_CB_CG_angle == 113.68
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.4816
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_SD_CE_diangle == 70.1
assert g.CB_CG_SD_angle == 112.69
assert g.CB_CG_length == 1.52
assert g.CG_SD_CE_angle == 100.61
assert g.CG_SD_length == 1.81
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -64.4
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.9416
assert g.N_C_CA_CB_diangle == 122.6733
assert g.SD_CE_length == 1.79
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "M"
def test_geometry_I():
g = Geometry.geometry("I")
assert g.CA_CB_CG1_CD1_diangle == 169.8
assert g.CA_CB_CG1_angle == 110.7
assert g.CA_CB_CG2_angle == 110.4
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5403
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG1_CD1_angle == 113.97
assert g.CB_CG1_length == 1.527
assert g.CB_CG2_length == 1.527
assert g.CG1_CD1_length == 1.52
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG1_diangle == 59.7
assert g.N_CA_CB_CG2_diangle == -61.6
assert g.N_CA_C_O_diangle == -60.0
assert g.N_CA_C_angle == 109.7202
assert g.N_C_CA_CB_diangle == 123.2347
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "I"
def test_geometry_N():
g = Geometry.geometry("N")
assert g.CA_CB_CG_ND2_diangle == 121.7
assert g.CA_CB_CG_OD1_diangle == -58.3
assert g.CA_CB_CG_angle == 112.62
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.4826
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_ND2_angle == 116.48
assert g.CB_CG_OD1_angle == 120.85
assert g.CB_CG_length == 1.52
assert g.CG_ND2_length == 1.33
assert g.CG_OD1_length == 1.23
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -65.5
assert g.N_CA_C_O_diangle == -60.0
assert g.N_CA_C_angle == 111.5
assert g.N_C_CA_CB_diangle == 123.2254
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "N"
def test_geometry_K():
g = Geometry.geometry("K")
assert g.CA_CB_CG_CD_diangle == -178.1
assert g.CA_CB_CG_angle == 113.83
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.54
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD_CE_diangle == -179.6
assert g.CB_CG_CD_angle == 111.79
assert g.CB_CG_length == 1.52
assert g.CD_CE_NZ_angle == 124.79
assert g.CD_CE_length == 1.46
assert g.CE_NZ_length == 1.33
assert g.CG_CD_CE_NZ_diangle == 179.6
assert g.CG_CD_CE_angle == 111.68
assert g.CG_CD_length == 1.52
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -64.5
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 111.08
assert g.N_C_CA_CB_diangle == 122.76
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "K"
def test_geometry_Q():
g = Geometry.geometry("Q")
assert g.CA_CB_CG_CD_diangle == -69.6
assert g.CA_CB_CG_angle == 113.75
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5029
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD_NE2_diangle == 129.5
assert g.CB_CG_CD_OE1_diangle == -50.5
assert g.CB_CG_CD_angle == 112.78
assert g.CB_CG_length == 1.52
assert g.CD_NE2_length == 1.33
assert g.CD_OE1_length == 1.24
assert g.CG_CD_NE2_angle == 116.5
assert g.CG_CD_OE1_angle == 120.86
assert g.CG_CD_length == 1.52
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -60.2
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 111.0849
assert g.N_C_CA_CB_diangle == 122.8134
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "Q"
def test_geometry_H():
g = Geometry.geometry("H")
assert g.CA_CB_CG_CD2_diangle == 104.3
assert g.CA_CB_CG_ND1_diangle == -75.7
assert g.CA_CB_CG_angle == 113.74
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.4732
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD2_NE2_diangle == 180.0
assert g.CB_CG_CD2_angle == 130.61
assert g.CB_CG_ND1_CE1_diangle == 180.0
assert g.CB_CG_ND1_angle == 122.85
assert g.CB_CG_length == 1.49
assert g.CD2_NE2_length == 1.35
assert g.CG_CD2_NE2_angle == 108.5
assert g.CG_CD2_length == 1.35
assert g.CG_ND1_CE1_angle == 108.5
assert g.CG_ND1_length == 1.38
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.ND1_CE1_length == 1.32
assert g.N_CA_CB_CG_diangle == -63.2
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 111.0859
assert g.N_C_CA_CB_diangle == 122.6711
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "H"
def create_PDB(seq, phi, psi, output):
try:
import Bio.PDB
except ImportError:
raise ImportError(
"You need to have BioPython installed to convert peptide sequences to structures"
)
try:
from PeptideBuilder import Geometry
import PeptideBuilder
except ImportError:
try:
import Geometry
import PeptideBuilder
except ImportError:
raise ImportError(
"You need to have the Python module PeptideBuilder installed to convert peptide sequences to structures"
)
geo = Geometry.geometry(seq[0])
struc = PeptideBuilder.initialize_res(geo)
for aa in seq[1:]:
struc = PeptideBuilder.add_residue(struc, aa, phi, psi)
out = Bio.PDB.PDBIO()
out.set_structure(struc)
out.save(output)
def test_geometry_D():
g = Geometry.geometry("D")
assert g.CA_CB_CG_OD1_diangle == -46.7
assert g.CA_CB_CG_OD2_diangle == 133.3
assert g.CA_CB_CG_angle == 113.06
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.51
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_OD1_angle == 119.22
assert g.CB_CG_OD2_angle == 118.218
assert g.CB_CG_length == 1.52
assert g.CG_OD1_length == 1.25
assert g.CG_OD2_length == 1.25
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -66.4
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 111.03
assert g.N_C_CA_CB_diangle == 122.82
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "D"
def test_geometry_E():
g = Geometry.geometry("E")
assert g.CA_CB_CG_CD_diangle == -179.8
assert g.CA_CB_CG_angle == 113.82
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.511
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD_OE1_diangle == -6.2
assert g.CB_CG_CD_OE2_diangle == 173.8
assert g.CB_CG_CD_angle == 113.31
assert g.CB_CG_length == 1.52
assert g.CD_OE1_length == 1.25
assert g.CD_OE2_length == 1.25
assert g.CG_CD_OE1_angle == 119.02
assert g.CG_CD_OE2_angle == 118.08
assert g.CG_CD_length == 1.52
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -63.8
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 111.1703
assert g.N_C_CA_CB_diangle == 122.8702
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "E"
def test_geometry_L():
g = Geometry.geometry("L")
assert g.CA_CB_CG_CD1_diangle == 174.9
assert g.CA_CB_CG_CD2_diangle == 66.7
assert g.CA_CB_CG_angle == 116.1
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.4647
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD1_angle == 110.27
assert g.CB_CG_CD2_angle == 110.58
assert g.CB_CG_length == 1.53
assert g.CG_CD1_length == 1.524
assert g.CG_CD2_length == 1.525
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -60.1
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.8652
assert g.N_C_CA_CB_diangle == 122.4948
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "L"
def generateAA(aaName):
geo = Geometry.geometry(aaName)
geo.phi = 0
geo.psi_im1 = 0
structure = PeptideBuilder.initialize_res(geo)
tx = -np.pi / 2.0
Rx = np.array([[1, 0, 0], [0, cos(tx), -sin(tx)], [0, sin(tx), cos(tx)]])
for atom in structure.get_atoms():
atom.transform(Rx, np.array([0, 0, 0]))
nAtom = list(structure.get_atoms())[0]
nV = nAtom.get_coord()
I = np.identity(3)
for atom in structure.get_atoms():
atom.transform(I, -nV)
R = rotaxis(np.pi, list(structure.get_atoms())[1].get_vector())
for atom in structure.get_atoms():
atom.transform(R, np.array([0, 0, 0]))
# print(list(structure.get_atoms())[1].get_coord(), list(structure.get_atoms())[1])
out = Bio.PDB.PDBIO()
out.set_structure(structure)
out.save("example.pdb")
return structure[0]['A'][1]
def test_geometry_V():
g = Geometry.geometry("V")
assert isinstance(g, ValGeo)
assert g.CA_CB_CG1_angle == 110.7
assert g.CA_CB_CG2_angle == 110.4
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5686
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG1_length == 1.527
assert g.CB_CG2_length == 1.527
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG1_diangle == 177.2
assert g.N_CA_CB_CG2_diangle == -63.3
assert g.N_CA_C_O_diangle == -60.0
assert g.N_CA_C_angle == 109.7698
assert g.N_C_CA_CB_diangle == 123.2347
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "V"
def test_geometry_T():
g = Geometry.geometry("T")
assert isinstance(g, ThrGeo)
assert g.CA_CB_CG2_angle == 111.13
assert g.CA_CB_OG1_angle == 109.18
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5359
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG2_length == 1.53
assert g.CB_OG1_length == 1.43
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG2_diangle == -60.3
assert g.N_CA_CB_OG1_diangle == 60.0
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.7014
assert g.N_C_CA_CB_diangle == 123.0953
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "T"
def build_fullatom_from_distance(p, aa, X, text):
geos = []
for a in aa:
geos.append(Geometry.geometry(a))
structure = PeptideBuilderCoords.make_structure_from_geos_coords(geos, X)
out = Bio.PDB.PDBIO()
out.set_structure(structure)
out.save('{}_'.format(p)+text+'.pdb')
def new_cuckoo(aminoacid):
'''
A cuckoo is born
'''
cuckoo = Geometry.geometry(aminoacid)
cuckoo.phi = random.uniform(-180.0, 180.0)
cuckoo.psi_im1 = random.uniform(-180.0, 180.0)
return cuckoo
def build_all_angles_model(pdb_filename):
parser=PDBParser()
structure=parser.get_structure('sample', \
path.join(PDBdir, pdb_filename))
model=structure[0]
chain=model['A']
model_structure_geo=[]
prev="0"
N_prev="0"
CA_prev="0"
CO_prev="0"
prev_res=""
rad=180.0/math.pi
for res in chain:
if(res.get_resname() in resdict.keys()):
geo=Geometry.geometry(resdict[res.get_resname()])
if(prev=="0"):
N_prev=res['N']
CA_prev=res['CA']
C_prev=res['C']
prev="1"
else:
n1=N_prev.get_vector()
ca1=CA_prev.get_vector()
c1=C_prev.get_vector()
C_curr=res['C']
N_curr=res['N']
CA_curr=res['CA']
c=C_curr.get_vector()
n=N_curr.get_vector()
ca=CA_curr.get_vector()
geo.CA_C_N_angle=calc_angle(ca1, c1, n)*rad
geo.C_N_CA_angle=calc_angle(c1, n, ca)*rad
psi= calc_dihedral(n1, ca1, c1, n) ##goes to current res
omega= calc_dihedral(ca1, c1, n, ca) ##goes to current res
phi= calc_dihedral(c1, n, ca, c) ##goes to current res
geo.psi_im1=psi*rad
geo.omega=omega*rad
geo.phi=phi*rad
geo.N_CA_C_angle= calc_angle(n, ca, c)*rad
##geo.CA_C_O_angle= calc_angle(ca, c, o)*rad
##geo.N_CA_C_O= calc_dihedral(n, ca, c, o)*rad
N_prev=res['N']
CA_prev=res['CA']
C_prev=res['C']
##O_prev=res['O']
model_structure_geo.append(geo)
return model_structure_geo
def build_all_angles_model(pdb_filename):
parser = PDBParser()
structure=parser.get_structure('sample', \
path.join(PDBdir, pdb_filename))
model = structure[0]
chain = model['A']
model_structure_geo = []
prev = "0"
N_prev = "0"
CA_prev = "0"
CO_prev = "0"
prev_res = ""
rad = 180.0 / math.pi
for res in chain:
if (res.get_resname() in resdict.keys()):
geo = Geometry.geometry(resdict[res.get_resname()])
if (prev == "0"):
N_prev = res['N']
CA_prev = res['CA']
C_prev = res['C']
prev = "1"
else:
n1 = N_prev.get_vector()
ca1 = CA_prev.get_vector()
c1 = C_prev.get_vector()
C_curr = res['C']
N_curr = res['N']
CA_curr = res['CA']
c = C_curr.get_vector()
n = N_curr.get_vector()
ca = CA_curr.get_vector()
geo.CA_C_N_angle = calc_angle(ca1, c1, n) * rad
geo.C_N_CA_angle = calc_angle(c1, n, ca) * rad
psi = calc_dihedral(n1, ca1, c1, n) ##goes to current res
omega = calc_dihedral(ca1, c1, n, ca) ##goes to current res
phi = calc_dihedral(c1, n, ca, c) ##goes to current res
geo.psi_im1 = psi * rad
geo.omega = omega * rad
geo.phi = phi * rad
geo.N_CA_C_angle = calc_angle(n, ca, c) * rad
##geo.CA_C_O_angle= calc_angle(ca, c, o)*rad
##geo.N_CA_C_O= calc_dihedral(n, ca, c, o)*rad
N_prev = res['N']
CA_prev = res['CA']
C_prev = res['C']
##O_prev=res['O']
model_structure_geo.append(geo)
return model_structure_geo
def test_add_residue2():
phi = -60
psi_im1 = -40
geo = Geometry.geometry("A")
geo.phi = phi
geo.psi_im1 = psi_im1
structure = PeptideBuilder.initialize_res(geo)
for aa in "CDEFGHIKLMNPQRSTVWY":
phi += 1
psi_im1 -= 1
geo = Geometry.geometry(aa)
geo.phi = phi
geo.psi_im1 = psi_im1
structure = PeptideBuilder.add_residue(structure, geo)
# now compare to saved reference structure
assert compare_to_reference(structure, "helix.pdb")
def generateSeq(seq):
structure = None
for aa in seq:
geo = Geometry.geometry(aa)
if structure is None:
structure = PeptideBuilder.initialize_res(geo)
else:
structure = PeptideBuilder.add_residue(structure, geo)
return structure
def build_fullatom_from_torsion(p, aa, X, text):
#phis, psis = compute_torsion_angles(X_fullatom)
#print(n, len(phis), len(psis), phis)
#structure = PeptideBuilder.make_structure(aa, phis, psis)
geos = []
for a in aa:
geos.append(Geometry.geometry(a))
structure = PeptideBuilderCoords.make_structure_from_geos_coords(geos, X)
out = Bio.PDB.PDBIO()
out.set_structure(structure)
out.save('{}_'.format(p)+text+'.pdb')
def test_add_residue2():
"""
Build a helix containing all 20 amino acids, with slowly varying backbone angles
"""
phi = -60
psi_im1 = -40
geo = Geometry.geometry("A")
geo.phi = phi
geo.psi_im1 = psi_im1
structure = PeptideBuilder.initialize_res(geo)
for aa in "CDEFGHIKLMNPQRSTVWY":
phi += 1
psi_im1 -= 1
geo = Geometry.geometry(aa)
geo.phi = phi
geo.psi_im1 = psi_im1
PeptideBuilder.add_residue(structure, geo)
assert compare_to_reference(structure, "helix.pdb")
def test_geometry_G():
g = Geometry.geometry("G")
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5117
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_C_O_diangle == 180.0
assert g.N_CA_C_angle == 110.8914
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "G"
def build_linear_model(pdb_filename):
parser = PDBParser()
structure = parser.get_structure("sample", path.join(PDBdir, pdb_filename))
model = structure[0]
chain = model["A"]
model_structure_geo = []
for res in chain:
if res.get_resname() in resdict.keys():
tempgeo = Geometry.geometry(resdict[res.get_resname()])
model_structure_geo.append(tempgeo)
model_structure = PeptideBuilder.initialize_res(model_structure_geo[0])
for i in range(1, len(model_structure_geo)):
model_structure = PeptideBuilder.add_residue(model_structure,
model_structure_geo[i])
return model_structure
def build_linear_model(pdb_filename):
parser=PDBParser()
structure=parser.get_structure('sample', \
path.join(PDBdir, pdb_filename) )
model=structure[0]
chain=model['A']
model_structure_geo=[]
for res in chain:
if(res.get_resname() in resdict.keys()):
tempgeo=Geometry.geometry(resdict[res.get_resname()])
model_structure_geo.append(tempgeo)
model_structure=PeptideBuilder.initialize_res(model_structure_geo[0])
for i in range(1,len(model_structure_geo)):
model_structure=PeptideBuilder.add_residue(model_structure, model_structure_geo[i])
return model_structure
def test_geometry_W():
g = Geometry.geometry("W")
assert isinstance(g, TrpGeo)
assert g.CA_CB_CG_CD1_diangle == 96.3
assert g.CA_CB_CG_CD2_diangle == -83.7
assert g.CA_CB_CG_angle == 114.1
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5117
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD1_NE1_diangle == 180.0
assert g.CB_CG_CD1_angle == 127.07
assert g.CB_CG_CD2_CE2_diangle == 180.0
assert g.CB_CG_CD2_CE3_diangle == 0.0
assert g.CB_CG_CD2_angle == 126.66
assert g.CB_CG_length == 1.5
assert g.CD1_NE1_length == 1.38
assert g.CD2_CE2_CZ2_CH2_diangle == 0.0
assert g.CD2_CE2_CZ2_angle == 120.0
assert g.CD2_CE2_length == 1.4
assert g.CD2_CE3_CZ3_angle == 120.0
assert g.CD2_CE3_length == 1.4
assert g.CE2_CZ2_CH2_angle == 120.0
assert g.CE2_CZ2_length == 1.4
assert g.CE3_CZ3_length == 1.4
assert g.CG_CD1_NE1_angle == 108.5
assert g.CG_CD1_length == 1.37
assert g.CG_CD2_CE2_CZ2_diangle == 180.0
assert g.CG_CD2_CE2_angle == 108.5
assert g.CG_CD2_CE3_CZ3_diangle == 180.0
assert g.CG_CD2_CE3_angle == 133.83
assert g.CG_CD2_length == 1.43
assert g.CZ2_CH2_length == 1.4
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -66.4
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.8914
assert g.N_C_CA_CB_diangle == 122.6112
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "W"
def test_geometry_A():
g = Geometry.geometry("A")
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_C_O_diangle == -60.5
assert g.N_CA_C_angle == 111.068
assert g.N_C_CA_CB_diangle == 122.686
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "A"
def test_geometry_Y():
g = Geometry.geometry("Y")
assert isinstance(g, TyrGeo)
assert g.CA_CB_CG_CD1_diangle == 93.1
assert g.CA_CB_CG_CD2_diangle == 273.1
assert g.CA_CB_CG_angle == 113.8
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5434
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD1_CE1_diangle == 180.0
assert g.CB_CG_CD1_angle == 120.98
assert g.CB_CG_CD2_CE2_diangle == 180.0
assert g.CB_CG_CD2_angle == 120.82
assert g.CB_CG_length == 1.51
assert g.CD1_CE1_CZ_OH_diangle == 180.0
assert g.CD1_CE1_CZ_angle == 120.0
assert g.CD1_CE1_length == 1.39
assert g.CD2_CE2_length == 1.39
assert g.CE1_CZ_OH_angle == 119.78
assert g.CE1_CZ_length == 1.39
assert g.CG_CD1_CE1_CZ_diangle == 0.0
assert g.CG_CD1_CE1_angle == 120.0
assert g.CG_CD1_length == 1.39
assert g.CG_CD2_CE2_angle == 120.0
assert g.CG_CD2_length == 1.39
assert g.CZ_OH_length == 1.39
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -64.3
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.9288
assert g.N_C_CA_CB_diangle == 122.6023
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "Y"
def test_geometry_C():
g = Geometry.geometry("C")
assert g.CA_CB_SG_angle == 113.8169
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_SG_length == 1.808
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_SG_diangle == -62.2
assert g.N_CA_C_O_diangle == -60.0
assert g.N_CA_C_angle == 110.8856
assert g.N_C_CA_CB_diangle == 122.5037
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "C"
def test_geometry_R():
g = Geometry.geometry("R")
assert isinstance(g, ArgGeo)
assert g.CA_CB_CG_CD_diangle == -179.2
assert g.CA_CB_CG_angle == 113.83
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.54
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD_NE_diangle == -179.3
assert g.CB_CG_CD_angle == 111.79
assert g.CB_CG_length == 1.52
assert g.CD_NE_CZ_NH1_diangle == 0.0
assert g.CD_NE_CZ_NH2_diangle == 180.0
assert g.CD_NE_CZ_angle == 124.79
assert g.CD_NE_length == 1.46
assert g.CG_CD_NE_CZ_diangle == -178.7
assert g.CG_CD_NE_angle == 111.68
assert g.CG_CD_length == 1.52
assert g.CZ_NH1_length == 1.33
assert g.CZ_NH2_length == 1.33
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.NE_CZ_NH1_angle == 120.64
assert g.NE_CZ_NH2_angle == 119.63
assert g.NE_CZ_length == 1.33
assert g.N_CA_CB_CG_diangle == -65.2
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.98
assert g.N_C_CA_CB_diangle == 122.76
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "R"
def test_geometry_F():
g = Geometry.geometry("F")
assert isinstance(g, PheGeo)
assert g.CA_CB_CG_CD1_diangle == 93.3
assert g.CA_CB_CG_CD2_diangle == -86.7
assert g.CA_CB_CG_angle == 113.85
assert g.CA_CB_length == 1.52
assert g.CA_C_N_angle == 116.642992978143
assert g.CA_C_O_angle == 120.5316
assert g.CA_C_length == 1.52
assert g.CA_N_length == 1.46
assert g.CB_CG_CD1_CE1_diangle == 180.0
assert g.CB_CG_CD1_angle == 120.0
assert g.CB_CG_CD2_CE2_diangle == 180.0
assert g.CB_CG_CD2_angle == 120.0
assert g.CB_CG_length == 1.5
assert g.CD1_CE1_CZ_angle == 120.0
assert g.CD1_CE1_length == 1.39
assert g.CD2_CE2_length == 1.39
assert g.CE1_CZ_length == 1.39
assert g.CG_CD1_CE1_CZ_diangle == 0.0
assert g.CG_CD1_CE1_angle == 120.0
assert g.CG_CD1_length == 1.39
assert g.CG_CD2_CE2_angle == 120.0
assert g.CG_CD2_length == 1.39
assert g.C_CA_CB_angle == 109.5
assert g.C_N_CA_angle == 121.382215820277
assert g.C_O_length == 1.23
assert g.N_CA_CB_CG_diangle == -64.7
assert g.N_CA_C_O_diangle == 120.0
assert g.N_CA_C_angle == 110.7528
assert g.N_C_CA_CB_diangle == 122.6054
assert g.omega == 180.0
assert g.peptide_bond == 1.33
assert g.phi == -120
assert g.psi_im1 == 140
assert g.residue_name == "F"
# Build a peptide containing all 20 amino acids
structure = PeptideBuilder.initialize_res('A')
for aa in "CDEFGHIKLMNPQRSTVWY":
structure = PeptideBuilder.add_residue(structure, aa)
out = Bio.PDB.PDBIO()
out.set_structure(structure)
out.save("test1.pdb")
# Build a helix containing all 20 amino acids, with slowly varying backbone angles
phi = -60
psi_im1 = -40
geo = Geometry.geometry('A')
geo.phi = phi
geo.psi_im1 = psi_im1
structure = PeptideBuilder.initialize_res(geo)
for aa in "CDEFGHIKLMNPQRSTVWY":
phi += 1
psi_im1 -= 1
geo = Geometry.geometry(aa)
geo.phi = phi
geo.psi_im1 = psi_im1
structure = PeptideBuilder.add_residue(structure, geo)
out.set_structure(structure)
out.save("test2.pdb")
