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import os
import math
from Bio.PDB import PDBIO
from Bio.PDB import PDBParser
from Bio.PDB import Superimposer
from Bio.PDB.vectors import calc_angle, calc_dihedral
from PeptideBuilder import Geometry
import PeptideBuilder
resdict = {
"ALA": "A",
"CYS": "C",
"ASP": "D",
"GLU": "E",
"PHE": "F",
"GLY": "G",
"HIS": "H",
"ILE": "I",
"LYS": "K",
"LEU": "L",
"MET": "M",
"ASN": "N",
"PRO": "P",
"GLN": "Q",
"ARG": "R",
"SER": "S",
"THR": "T",
"VAL": "V",
"TRP": "W",
"TYR": "Y",
}
PDBdir = "PDBs"
def build_linear_model(pdb_filename):
parser = PDBParser()
structure = parser.get_structure("sample", os.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 make_pdb_file(struct, file_nom):
outfile = PDBIO()
outfile.set_structure(struct)
outfile.save(os.path.join(PDBdir, file_nom))
return file_nom
def build_backbone_model(pdb_filename):
parser = PDBParser()
structure = parser.get_structure("sample", os.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"
##O_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"]
##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.CA_N_length = CA_curr - N_curr
geo.CA_C_length = CA_curr - C_curr
geo.peptide_bond = 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']
model_structure_geo.append(geo)
return model_structure_geo
def build_all_angles_model(pdb_filename):
parser = PDBParser()
structure = parser.get_structure("sample", os.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_phi_psi_model(pdb_filename):
parser = PDBParser()
structure = parser.get_structure("sample", os.path.join(PDBdir, pdb_filename))
model = structure[0]
chain = model["A"]
seq = ""
phi_diangle = []
psi_diangle = []
omega_diangle = []
for res in chain:
if res.get_resname() in resdict.keys():
seq += resdict[res.get_resname()]
if len(seq) == 1:
N_prev = res["N"]
CA_prev = res["CA"]
C_prev = res["C"]
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()
psi = calc_dihedral(n1, ca1, c1, n) ##goes to current res
omega = calc_dihedral(ca1, c1, n, ca)
phi = calc_dihedral(c1, n, ca, c) ##goes to current res
phi_diangle.append(phi * 180.0 / math.pi)
psi_diangle.append(psi * 180.0 / math.pi)
omega_diangle.append(omega * 180.0 / math.pi)
N_prev = res["N"]
CA_prev = res["CA"]
C_prev = res["C"]
model_structure_omega = PeptideBuilder.make_structure(
seq, phi_diangle, psi_diangle, omega_diangle
)
model_structure_phi_psi = PeptideBuilder.make_structure(
seq, phi_diangle, psi_diangle
)
return model_structure_omega, model_structure_phi_psi
def compare_structure(reference, alternate):
parser = PDBParser()
ref_struct = parser.get_structure("Reference", os.path.join(PDBdir, reference))
alt_struct = parser.get_structure("Alternate", os.path.join(PDBdir, alternate))
ref_model = ref_struct[0]
ref_chain = ref_model["A"]
alt_model = alt_struct[0]
alt_chain = alt_model["A"]
ref_atoms = []
alt_atoms = []
for ref_res in ref_chain:
if ref_res.get_resname() in resdict.keys():
ref_atoms.append(ref_res["CA"])
for alt_res in alt_chain:
if alt_res.get_resname() in resdict.keys():
alt_atoms.append(alt_res["CA"])
super_imposer = Superimposer()
super_imposer.set_atoms(ref_atoms, alt_atoms)
super_imposer.apply(alt_model.get_atoms())
make_pdb_file(alt_struct, "Aligned_" + alternate)
full = super_imposer.rms
super_imposer_50 = Superimposer()
super_imposer_50.set_atoms(ref_atoms[:50], alt_atoms[:50])
super_imposer_50.apply(alt_model.get_atoms())
make_pdb_file(alt_struct, "Aligned_50_" + alternate)
f_50 = super_imposer_50.rms
super_imposer_150 = Superimposer()
super_imposer_150.set_atoms(ref_atoms[:150], alt_atoms[:150])
super_imposer_150.apply(alt_model.get_atoms())
make_pdb_file(alt_struct, "Aligned_150_" + alternate)
f_150 = super_imposer_150.rms
return f_50, f_150, full, len(ref_atoms)
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
test_structures = [
"1aq7",
"1gfl",
"1nbw",
"1vca",
"2o6r",
"2r83",
"3cap",
"3cuq",
"3vni",
"7tim",
]
f_out = open("reconstructed_RMSDs.txt", "w")
f_out.write(
"PDB-ID\t\tlengthPhi-Psi-50\tPhi-Psi-150\tPhi-Psi\tPhi-Psi-Omega-50\tPhi-Psi-Omega-150\tPhi-Psi-Omega\tAll-Angles-50\tAll-Angles-150\tAll-Angles\tBackbone-50\tBackbone-150\tBackbone\n"
)
for i in test_structures:
print(i)
f_out.write(test_PeptideBuilder(i))
f_out.close()
|
