def test_PeptideBuilder(pdb_code):
# retrieve pdb file
pdb_file = "%s_clean.pdb" % (pdb_code)
# build backbone model from all angles and bond lengths
structure_backbone= PeptideBuilder.make_structure_from_geos(build_backbone_model(pdb_file))
# build backbone model from all angles
structure_all_angles= PeptideBuilder.make_structure_from_geos(build_all_angles_model(pdb_file))
# build models from dihedral angles only
structure_omega, structure_phi_psi=build_phi_psi_model(pdb_file)
# compare models to original structure
RMS_backbone_50, RMS_backbone_150, RMS_backbone, size= compare_structure(pdb_file, make_pdb_file(structure_backbone, "Backbone_" + pdb_file))
RMS_phi_psi_50, RMS_phi_psi_150, RMS_phi_psi, size= compare_structure(pdb_file, make_pdb_file(structure_phi_psi, "PhiPsi_" + pdb_file))
RMS_omega_50, RMS_omega_150, RMS_omega, size= compare_structure(pdb_file, make_pdb_file(structure_omega, "PhiPsiOmega_" + pdb_file))
RMS_all_angles_50, RMS_all_angles_150, RMS_all_angles, size= compare_structure(pdb_file, make_pdb_file(structure_all_angles, "AllAngles_" + pdb_file))
output_line= "%s\t%i\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\n" % \
(pdb_code, \
size, \
RMS_phi_psi_50, \
RMS_phi_psi_150, \
RMS_phi_psi, \
RMS_omega_50, \
RMS_omega_150, \
RMS_omega, \
RMS_all_angles_50, \
RMS_all_angles_150, \
RMS_all_angles, \
RMS_backbone_50, \
RMS_backbone_150, \
RMS_backbone )
return output_line
def test_PeptideBuilder(pdb_code):
# retrieve pdb file
pdb_file = "%s_clean.pdb" % (pdb_code)
# build backbone model from all angles and bond lengths
structure_backbone = PeptideBuilder.make_structure_from_geos(
build_backbone_model(pdb_file)
)
# build backbone model from all angles
structure_all_angles = PeptideBuilder.make_structure_from_geos(
build_all_angles_model(pdb_file)
)
# build models from dihedral angles only
structure_omega, structure_phi_psi = build_phi_psi_model(pdb_file)
# compare models to original structure
RMS_backbone_50, RMS_backbone_150, RMS_backbone, size = compare_structure(
pdb_file, make_pdb_file(structure_backbone, "Backbone_" + pdb_file)
)
RMS_phi_psi_50, RMS_phi_psi_150, RMS_phi_psi, size = compare_structure(
pdb_file, make_pdb_file(structure_phi_psi, "PhiPsi_" + pdb_file)
)
RMS_omega_50, RMS_omega_150, RMS_omega, size = compare_structure(
pdb_file, make_pdb_file(structure_omega, "PhiPsiOmega_" + pdb_file)
)
RMS_all_angles_50, RMS_all_angles_150, RMS_all_angles, size = compare_structure(
pdb_file, make_pdb_file(structure_all_angles, "AllAngles_" + pdb_file)
)
output_line = (
"%s\t%i\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\n"
% (
pdb_code,
size,
RMS_phi_psi_50,
RMS_phi_psi_150,
RMS_phi_psi,
RMS_omega_50,
RMS_omega_150,
RMS_omega,
RMS_all_angles_50,
RMS_all_angles_150,
RMS_all_angles,
RMS_backbone_50,
RMS_backbone_150,
RMS_backbone,
)
)
return output_line
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")
out.set_structure(structure)
out.save("test2.pdb")
# Print out all geometries
outfile = open("test3.txt", 'w')
for aa in "ACDEFGHIKLMNPQRSTVWY":
print(outfile, Geometry.geometry(aa))
# Build a helix containing all 20 amino acids from list of geometries.
# The structure should be identical to test1.pdb
geos = []
for aa in "ACDEFGHIKLMNPQRSTVWY":
geos.append(Geometry.geometry(aa))
structure = PeptideBuilder.make_structure_from_geos(geos)
out.set_structure(structure)
out.save("test4.pdb")
# Build a peptide containing all 20 amino acids in extended conformation.
# The structure should be identical to test1.pdb
structure = PeptideBuilder.make_extended_structure("ACDEFGHIKLMNPQRSTVWY")
out.set_structure(structure)
out.save("test4.pdb")
# Build a peptide containing all 20 amino acids from list of geometries.
# The structure should be identical to test1.pdb
geos = []
for aa in "ACDEFGHIKLMNPQRSTVWY":
def build_exact_model(structure, chain_index):
model=structure[0]
chain=model[chain_index]
model_structure_geo=[]
prev="0"
N_prev="0"
CA_prev="0"
C_prev="0"
O_prev="0"
prev_res=""
rad=180.0/math.pi
for res in chain:
name=res.get_resname()
if(name !="HOH"):
geo=Geometry.geometry(resdict[name])
if(prev=="0"):
N_prev= res['N']
CA_prev= res['CA']
C_prev= res['C']
O_prev= res['O']
prev="1"
else:
n1=N_prev.get_vector()
ca1=CA_prev.get_vector()
c1=C_prev.get_vector()
o1=O_prev.get_vector()
O_curr=res['O']
C_curr=res['C']
N_curr=res['N']
CA_curr=res['CA']
o=O_curr.get_vector()
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
geo.peptide= N_curr-C_prev
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.CA_N_length= CA_curr - N_curr
geo.CA_C_length= CA_curr - C_curr
geo.C_O_length= C_curr - O_curr
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']
if(name=='ALA'):
geo.CA_CB_length=CA_curr-res['CB']
geo.C_CA_CB_angle= calc_angle(c, ca, res['CB'].get_vector())*rad
geo.N_C_CA_CB_diangle= calc_dihedral(n, c, ca, res['CB'].get_vector())*rad
elif(name=='GLU'):
geo.CA_CB_length=CA_curr-res['CB']
geo.C_CA_CB_angle=calc_angle(c, ca, res['CB'].get_vector())*rad
geo.N_C_CA_CB_diangle=calc_dihedral(n, c, ca, res['CB'].get_vector() )*rad
geo.CB_CG_length=res['CB']-res['CG']
geo.CA_CB_CG_angle=calc_angle(ca, res['CB'].get_vector(), res['CG'].get_vector())*rad
geo.N_CA_CB_CG_diangle=calc_dihedral(n, ca, res['CB'].get_vector(), res['CG'].get_vector())*rad
geo.CG_CD_length=res['CG']-res['CD']
geo.CB_CG_CD_angle=calc_angle(res['CB'].get_vector(), res['CG'].get_vector(), res['CD'].get_vector() )*rad
geo.CA_CB_CG_CD_diangle=calc_dihedral(ca, res['CB'].get_vector(), res['CG'].get_vector(), res['CD'].get_vector())*rad
geo.CD_OE1_length=res['CD']-res['OE1']
geo.CG_CD_OE1_angle=calc_angle(res['CG'].get_vector(), res['CD'].get_vector(), res['OE1'].get_vector() )*rad
geo.CB_CG_CD_OE1_diangle= calc_dihedral(res['CB'].get_vector(), res['CG'].get_vector(),res['CD'].get_vector(), res['OE1'].get_vector())*rad
geo.CD_OE2_length=res['CD']-res['OE2']
geo.CG_CD_OE2_angle=calc_angle(res['CG'].get_vector(), res['CD'].get_vector(), res['OE2'].get_vector() )*rad
geo.CB_CG_CD_OE2_diangle= calc_dihedral(res['CB'].get_vector(), res['CG'].get_vector(),res['CD'].get_vector(), res['OE2'].get_vector())*rad
elif(name=='HIS'):
geo.CA_CB_length=CA_curr-res['CB']
geo.CB_CG_length=(res['CB']-res['CG'])
geo.CG_ND1_length=(res['CG']-res['ND1'])
geo.CG_CD2_length=(res['CG']-res['CD2'])
geo.ND1_CE1_length=(res['ND1']-res['CE1'])
geo.CD2_NE2_length=(res['CD2']-res['NE2'])
geo.C_CA_CB_angle=(calc_angle(c, ca, res['CB'].get_vector()))*rad
geo.CA_CB_CG_angle=(calc_angle(ca, res['CB'].get_vector(), res['CG'].get_vector() ) )*rad
geo.CB_CG_ND1_angle= (calc_angle(res['CB'].get_vector(), res['CG'].get_vector(), res['ND1'].get_vector() ) )*rad
geo.CB_CG_CD2_angle=(calc_angle(res['CB'].get_vector(), res['CG'].get_vector(), res['CD2'].get_vector() ) )*rad
geo.CG_ND1_CE1_angle=(calc_angle(res['CG'].get_vector(), res['ND1'].get_vector(), res['CE1'].get_vector() ) )*rad
geo.CG_CD2_NE2_angle=(calc_angle(res['CG'].get_vector(), res['CD2'].get_vector(), res['NE2'].get_vector() ) )*rad
geo.N_C_CA_CB_diangle=(calc_dihedral(n, c, ca, res['CB'].get_vector()))*rad
geo.N_CA_CB_CG_diangle=(calc_dihedral(n, ca, res['CB'].get_vector(), res['CG'].get_vector()))*rad
geo.CA_CB_CG_ND1_diangle=(calc_dihedral(ca, res['CB'].get_vector(), res['CG'].get_vector(), res['ND1'].get_vector()))*rad
geo.CA_CB_CG_CD2_diangle=(calc_dihedral(ca, res['CB'].get_vector(), res['CG'].get_vector(), res['CD2'].get_vector()))*rad
geo.CB_CG_ND1_CE1_diangle=(calc_dihedral(res['CB'].get_vector(), res['CG'].get_vector(), res['ND1'].get_vector(), res['CE1'].get_vector()))*rad
geo.CB_CG_CD2_NE2_diangle=(calc_dihedral(res['CB'].get_vector(), res['CG'].get_vector(), res['CD2'].get_vector(), res['NE2'].get_vector()))*rad
model_structure_geo.append(geo)
model_structure=PeptideBuilder.make_structure_from_geos(model_structure_geo)
return model_structure
def build_exact_model(structure, chain_index):
model = structure[0]
chain = model[chain_index]
model_structure_geo = []
prev = "0"
N_prev = "0"
CA_prev = "0"
C_prev = "0"
O_prev = "0"
prev_res = ""
rad = 180.0 / math.pi
for res in chain:
name = res.get_resname()
if (name != "HOH"):
geo = Geometry.geometry(resdict[name])
if (prev == "0"):
N_prev = res['N']
CA_prev = res['CA']
C_prev = res['C']
O_prev = res['O']
prev = "1"
else:
n1 = N_prev.get_vector()
ca1 = CA_prev.get_vector()
c1 = C_prev.get_vector()
o1 = O_prev.get_vector()
O_curr = res['O']
C_curr = res['C']
N_curr = res['N']
CA_curr = res['CA']
o = O_curr.get_vector()
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
geo.peptide = N_curr - C_prev
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.CA_N_length = CA_curr - N_curr
geo.CA_C_length = CA_curr - C_curr
geo.C_O_length = C_curr - O_curr
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']
if (name == 'ALA'):
geo.CA_CB_length = CA_curr - res['CB']
geo.C_CA_CB_angle = calc_angle(
c, ca, res['CB'].get_vector()) * rad
geo.N_C_CA_CB_diangle = calc_dihedral(
n, c, ca, res['CB'].get_vector()) * rad
elif (name == 'GLU'):
geo.CA_CB_length = CA_curr - res['CB']
geo.C_CA_CB_angle = calc_angle(
c, ca, res['CB'].get_vector()) * rad
geo.N_C_CA_CB_diangle = calc_dihedral(
n, c, ca, res['CB'].get_vector()) * rad
geo.CB_CG_length = res['CB'] - res['CG']
geo.CA_CB_CG_angle = calc_angle(
ca, res['CB'].get_vector(),
res['CG'].get_vector()) * rad
geo.N_CA_CB_CG_diangle = calc_dihedral(
n, ca, res['CB'].get_vector(),
res['CG'].get_vector()) * rad
geo.CG_CD_length = res['CG'] - res['CD']
geo.CB_CG_CD_angle = calc_angle(
res['CB'].get_vector(), res['CG'].get_vector(),
res['CD'].get_vector()) * rad
geo.CA_CB_CG_CD_diangle = calc_dihedral(
ca, res['CB'].get_vector(), res['CG'].get_vector(),
res['CD'].get_vector()) * rad
geo.CD_OE1_length = res['CD'] - res['OE1']
geo.CG_CD_OE1_angle = calc_angle(
res['CG'].get_vector(), res['CD'].get_vector(),
res['OE1'].get_vector()) * rad
geo.CB_CG_CD_OE1_diangle = calc_dihedral(
res['CB'].get_vector(), res['CG'].get_vector(),
res['CD'].get_vector(), res['OE1'].get_vector()) * rad
geo.CD_OE2_length = res['CD'] - res['OE2']
geo.CG_CD_OE2_angle = calc_angle(
res['CG'].get_vector(), res['CD'].get_vector(),
res['OE2'].get_vector()) * rad
geo.CB_CG_CD_OE2_diangle = calc_dihedral(
res['CB'].get_vector(), res['CG'].get_vector(),
res['CD'].get_vector(), res['OE2'].get_vector()) * rad
elif (name == 'HIS'):
geo.CA_CB_length = CA_curr - res['CB']
geo.CB_CG_length = (res['CB'] - res['CG'])
geo.CG_ND1_length = (res['CG'] - res['ND1'])
geo.CG_CD2_length = (res['CG'] - res['CD2'])
geo.ND1_CE1_length = (res['ND1'] - res['CE1'])
geo.CD2_NE2_length = (res['CD2'] - res['NE2'])
geo.C_CA_CB_angle = (calc_angle(
c, ca, res['CB'].get_vector())) * rad
geo.CA_CB_CG_angle = (calc_angle(
ca, res['CB'].get_vector(),
res['CG'].get_vector())) * rad
geo.CB_CG_ND1_angle = (calc_angle(
res['CB'].get_vector(), res['CG'].get_vector(),
res['ND1'].get_vector())) * rad
geo.CB_CG_CD2_angle = (calc_angle(
res['CB'].get_vector(), res['CG'].get_vector(),
res['CD2'].get_vector())) * rad
geo.CG_ND1_CE1_angle = (calc_angle(
res['CG'].get_vector(), res['ND1'].get_vector(),
res['CE1'].get_vector())) * rad
geo.CG_CD2_NE2_angle = (calc_angle(
res['CG'].get_vector(), res['CD2'].get_vector(),
res['NE2'].get_vector())) * rad
geo.N_C_CA_CB_diangle = (calc_dihedral(
n, c, ca, res['CB'].get_vector())) * rad
geo.N_CA_CB_CG_diangle = (calc_dihedral(
n, ca, res['CB'].get_vector(),
res['CG'].get_vector())) * rad
geo.CA_CB_CG_ND1_diangle = (calc_dihedral(
ca, res['CB'].get_vector(), res['CG'].get_vector(),
res['ND1'].get_vector())) * rad
geo.CA_CB_CG_CD2_diangle = (calc_dihedral(
ca, res['CB'].get_vector(), res['CG'].get_vector(),
res['CD2'].get_vector())) * rad
geo.CB_CG_ND1_CE1_diangle = (calc_dihedral(
res['CB'].get_vector(), res['CG'].get_vector(),
res['ND1'].get_vector(),
res['CE1'].get_vector())) * rad
geo.CB_CG_CD2_NE2_diangle = (calc_dihedral(
res['CB'].get_vector(), res['CG'].get_vector(),
res['CD2'].get_vector(),
res['NE2'].get_vector())) * rad
model_structure_geo.append(geo)
model_structure = PeptideBuilder.make_structure_from_geos(
model_structure_geo)
return model_structure
def test_make_structure_from_geos2():
geos = []
for aa in "ACDEFGHIKLMNPQRSTVWY":
geos.append(Geometry.geometry(aa))
structure = PeptideBuilder.make_structure_from_geos(geos)
assert compare_to_reference(structure, "extended.pdb")