def add_com_to_pdb(mhc_com, vtcr_com, sample_structure):
"""
Function to add pseudoatoms at MHC-CoM, TCR-CoM, and XYZ axise to the output PDB file
"""
# mhc_com
mhc_com_chain = "X"
sample_structure.add(Chain.Chain(mhc_com_chain))
res_id = (" ", 1, " ")
new_residue = Residue.Residue(res_id, "MCM", " ")
new_atom = Atom.Atom("C", mhc_com, 0, 0.0, " ", "C", 1, "C")
new_residue.add(new_atom)
sample_structure.child_dict[mhc_com_chain].add(new_residue)
# tcr com
tcr_com_chain = "Y"
sample_structure.add(Chain.Chain(tcr_com_chain))
res_id = (" ", 1, " ")
new_residue = Residue.Residue(res_id, "TCM", " ")
new_atom = Atom.Atom("C", vtcr_com, 0, 0.0, " ", "C", 1, "C")
new_residue.add(new_atom)
sample_structure.child_dict[tcr_com_chain].add(new_residue)
# X,Y,Z atoms
pos = [[50, 0, 0], [0, 50, 0], [0, 0, 50]]
resn = ["X", "Y", "Z"]
xyz_chain = "Z"
sample_structure.add(Chain.Chain(xyz_chain))
for i in [0, 1, 2]:
res_id = (" ", i + 1, " ")
new_residue = Residue.Residue(res_id, resn[i], " ")
new_atom = Atom.Atom("O", pos[i], 0, 0.0, " ", "O", 1, "O")
new_residue.add(new_atom)
sample_structure.child_dict[xyz_chain].add(new_residue)
return sample_structure
def makeCys(segID, N, CA, C, O, geo):
'''Creates a Cysteine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_SG_length = geo.CB_SG_length
CA_CB_SG_angle = geo.CA_CB_SG_angle
N_CA_CB_SG_diangle = geo.N_CA_CB_SG_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
sulfur_g = calculateCoordinates(N, CA, CB, CB_SG_length, CA_CB_SG_angle,
N_CA_CB_SG_diangle)
SG = Atom("SG", sulfur_g, 0.0, 1.0, " ", " SG", 0, "S")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "CYS", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(SG)
return res
def makeSer(segID, N, CA, C, O, geo):
'''Creates a Serine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_OG_length = geo.CB_OG_length
CA_CB_OG_angle = geo.CA_CB_OG_angle
N_CA_CB_OG_diangle = geo.N_CA_CB_OG_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
oxygen_g = calculateCoordinates(N, CA, CB, CB_OG_length, CA_CB_OG_angle,
N_CA_CB_OG_diangle)
OG = Atom("OG", oxygen_g, 0.0, 1.0, " ", " OG", 0, "O")
##Create Reside Data Structure
res = Residue((' ', segID, ' '), "SER", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(OG)
##print res
return res
def makeThr(segID, N, CA, C, O, geo):
'''Creates a Threonine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_OG1_length = geo.CB_OG1_length
CA_CB_OG1_angle = geo.CA_CB_OG1_angle
N_CA_CB_OG1_diangle = geo.N_CA_CB_OG1_diangle
CB_CG2_length = geo.CB_CG2_length
CA_CB_CG2_angle = geo.CA_CB_CG2_angle
N_CA_CB_CG2_diangle = geo.N_CA_CB_CG2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
oxygen_g1 = calculateCoordinates(N, CA, CB, CB_OG1_length, CA_CB_OG1_angle,
N_CA_CB_OG1_diangle)
OG1 = Atom("OG1", oxygen_g1, 0.0, 1.0, " ", " OG1", 0, "O")
carbon_g2 = calculateCoordinates(N, CA, CB, CB_CG2_length, CA_CB_CG2_angle,
N_CA_CB_CG2_diangle)
CG2 = Atom("CG2", carbon_g2, 0.0, 1.0, " ", " CG2", 0, "C")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "THR", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(OG1)
res.add(CG2)
return res
def calc_rms(ref_coords, alt_coords):
# print ref_coords, alt_coords
assert( len(ref_coords) == len(alt_coords) )
if pyRMSD:
calculator = pyRMSD.RMSDCalculator.RMSDCalculator(pyrmsd_calc, np.array([ref_coords, alt_coords]))
return calculator.pairwiseRMSDMatrix()[0]
else:
super_imposer = Bio.PDB.Superimposer()
ref_atoms = [Atom.Atom('CA', coords, 0.0, 1.0, '', ' CA ', i+1, element='C') for i, coords in enumerate(ref_coords)]
alt_atoms = [Atom.Atom('CA', coords, 0.0, 1.0, '', ' CA ', i+1, element='C') for i, coords in enumerate(alt_coords)]
super_imposer.set_atoms(ref_atoms, alt_atoms)
return super_imposer.rms
def place_line(element, position1, position2, resname, chain):
global runtime_mark_id
res_temp = Residue((" ", runtime_mark_id, " "), resname, " ")
runtime_mark_id += 1
atom_temp1 = Atom("X1", position1, 0.0, 1, " ", "X", runtime_mark_id,
element)
atom_temp2 = Atom("X2", position2, 0.0, 1, " ", "X", runtime_mark_id,
element)
res_temp.add(atom_temp1)
res_temp.add(atom_temp2)
chain.add(res_temp)
def makeGln(segID, N, CA, C, O, geo):
'''Creates a Glutamine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD_length = geo.CG_CD_length
CB_CG_CD_angle = geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle = geo.CA_CB_CG_CD_diangle
CD_OE1_length = geo.CD_OE1_length
CG_CD_OE1_angle = geo.CG_CD_OE1_angle
CB_CG_CD_OE1_diangle = geo.CB_CG_CD_OE1_diangle
CD_NE2_length = geo.CD_NE2_length
CG_CD_NE2_angle = geo.CG_CD_NE2_angle
CB_CG_CD_NE2_diangle = geo.CB_CG_CD_NE2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d = calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle,
CA_CB_CG_CD_diangle)
CD = Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
oxygen_e1 = calculateCoordinates(CB, CG, CD, CD_OE1_length,
CG_CD_OE1_angle, CB_CG_CD_OE1_diangle)
OE1 = Atom("OE1", oxygen_e1, 0.0, 1.0, " ", " OE1", 0, "O")
nitrogen_e2 = calculateCoordinates(CB, CG, CD, CD_NE2_length,
CG_CD_NE2_angle, CB_CG_CD_NE2_diangle)
NE2 = Atom("NE2", nitrogen_e2, 0.0, 1.0, " ", " NE2", 0, "N")
##Create Residue DS
res = Residue((' ', segID, ' '), "GLN", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
res.add(OE1)
res.add(NE2)
return res
def makeLys(segID, N, CA, C, O, geo):
'''Creates a Lysine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD_length = geo.CG_CD_length
CB_CG_CD_angle = geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle = geo.CA_CB_CG_CD_diangle
CD_CE_length = geo.CD_CE_length
CG_CD_CE_angle = geo.CG_CD_CE_angle
CB_CG_CD_CE_diangle = geo.CB_CG_CD_CE_diangle
CE_NZ_length = geo.CE_NZ_length
CD_CE_NZ_angle = geo.CD_CE_NZ_angle
CG_CD_CE_NZ_diangle = geo.CG_CD_CE_NZ_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d = calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle,
CA_CB_CG_CD_diangle)
CD = Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
carbon_e = calculateCoordinates(CB, CG, CD, CD_CE_length, CG_CD_CE_angle,
CB_CG_CD_CE_diangle)
CE = Atom("CE", carbon_e, 0.0, 1.0, " ", " CE", 0, "C")
nitrogen_z = calculateCoordinates(CG, CD, CE, CE_NZ_length, CD_CE_NZ_angle,
CG_CD_CE_NZ_diangle)
NZ = Atom("NZ", nitrogen_z, 0.0, 1.0, " ", " NZ", 0, "N")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "LYS", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
res.add(CE)
res.add(NZ)
return res
def construct_initial_atoms(self):
"""Finds positions in between the O3' and C5'"""
vec = self.c5.coord - self.o3.coord
coord_p = self.o3.coord + vec * 0.333333
coord_o5 = self.o3.coord + vec * 0.666666
self.p = Atom.Atom("P", coord_p, 0.0, 1.0, ' ', " P", 1, element="P")
self.o5 = Atom.Atom("O5'",
coord_o5,
0.0,
1.0,
' ',
" O5'",
1,
element="O")
self.r2.add(self.p)
self.r2.add(self.o5)
def generate_plus_atom_matches(self, next_pattern_atom: Atom,
inspecting_atoms: list,
distance_error_coefficient: float) -> list:
pattern_atoms = self.matched_pattern_atoms + [next_pattern_atom]
pattern_atoms_distances = [
numpy.linalg.norm(atom.coord - next_pattern_atom.coord)
for atom in self.matched_pattern_atoms
]
matches = list()
for atom in inspecting_atoms:
# skip atom that is already presented in matched atoms
if atom in self.matched_inspecting_atoms:
continue
# skip non-compatible atoms
if atom.get_id()[0] != next_pattern_atom.get_id()[0]:
continue
# skip atoms if they do not fit by distance
all_distances_are_acceptable = True
for atom_index in range(len(pattern_atoms_distances)):
acceptable_distance = pattern_atoms_distances[atom_index]
if not distance_is_acceptable(
self.matched_inspecting_atoms[atom_index], atom,
acceptable_distance, distance_error_coefficient):
all_distances_are_acceptable = False
break
if all_distances_are_acceptable:
matches.append(
Match(pattern_atoms,
self.matched_inspecting_atoms + [atom]))
return matches
def test_pdbio_write_custom_residue(self):
"""Write a chainless residue using PDBIO."""
res = Residue.Residue((" ", 1, " "), "DUM", "")
atm = Atom.Atom("CA", [0.1, 0.1, 0.1], 1.0, 1.0, " ", "CA", 1, "C")
res.add(atm)
# Ensure that set_structure doesn't alter parent
parent = res.parent
# Write full model to temp file
self.io.set_structure(res)
self.assertIs(parent, res.parent)
filenumber, filename = tempfile.mkstemp()
os.close(filenumber)
try:
self.io.save(filename)
struct2 = self.parser.get_structure("res", filename)
latoms = list(struct2.get_atoms())
self.assertEqual(len(latoms), 1)
self.assertEqual(latoms[0].name, "CA")
self.assertEqual(latoms[0].parent.resname, "DUM")
self.assertEqual(latoms[0].parent.parent.id, "A")
finally:
os.remove(filename)
def check_clash(str_name, v=False):
"""check_clash, fract of clashes!
if zero contacts then error -> fix ->
Problem, contacts, str_name: 311 505 na-prot_13536.pdb
Sterical clashes 0.615841584158
c is counter
"""
if v: print('fn:', str_name)
structure = open(str_name)
#model = structure[0]
atoms_A = []
atoms_B = []
for line in structure.readlines():
if line[:4] == "ATOM":
#print line
at_nam = line[12:16].strip()
coor = [float(line[30:38]), float(line[38:46]), float(line[46:54])]
at = Atom.Atom(at_nam, coor, 0.0, 1.0, ' ', at_nam, 1, at_nam[0])
if line[21] == "A":
atoms_A.append(at)
elif line[21] == "B":
atoms_B.append(at)
else:
pass
#atoms_B = Selection.unfold_entities(structure[0]['B'], 'A')
#print len(atoms_A), len(atoms_B)
if len(atoms_A) > len(atoms_B):
less = atoms_B
more = atoms_A
else:
less = atoms_A
more = atoms_B
problem = 0
contacts = 0
ns = NeighborSearch(more)
for at in less:
neighbors = ns.search(array(at.get_coord()), 2.0, 'A')
if neighbors != []:
problem += 1
contacts += 1
else:
neighbors1 = ns.search(array(at.get_coord()), 4.0, 'A')
if neighbors1 != []:
contacts += 1
if v:
print('problem:', float(problem))
print('contacts:', float(contacts))
try:
fract = float(problem) / float(contacts)
except ZeroDivisionError:
fract = problem # or skip this structure
if v: print('ZeroDivison -- skip:', problem, contacts, str_name)
return fract
#print 'Contacts, str_name:', problem, contacts, str_name, "Sterical clashes ", fract
return fract
def create_cobalt(v):
global runtime_mark_id
#res_co = Residue((" ", runtime_mark_id, " "), "Co3", " ")
co = Atom("CO", v, 0.0, 1, " ", "X", runtime_mark_id, "CO")
#runtime_mark_id += 1
#res_co.add(co)
#new_chain_mark.add(res_co)
return co
def makeHis(N, CA, CB, chi1, chi2):
'''Creates a Histidine residue'''
CB_CG_length = 1.49
CA_CB_CG_angle = 113.74
N_CA_CB_CG_diangle = chi1
CG_ND1_length = 1.38
CB_CG_ND1_angle = 122.85
CA_CB_CG_ND1_diangle = chi2
CG_CD2_length = 1.35
CB_CG_CD2_angle = 130.61
CA_CB_CG_CD2_diangle = 180.0 + CA_CB_CG_ND1_diangle
ND1_CE1_length = 1.32
CG_ND1_CE1_angle = 108.5
CB_CG_ND1_CE1_diangle = 180.0
CD2_NE2_length = 1.35
CG_CD2_NE2_angle = 108.5
CB_CG_CD2_NE2_diangle = 180.0
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
nitrogen_d1 = calculateCoordinates(CA, CB, CG, CG_ND1_length,
CB_CG_ND1_angle, CA_CB_CG_ND1_diangle)
ND1 = Atom("ND1", nitrogen_d1, 0.0, 1.0, " ", " ND1", 0, "N")
carbon_d2 = calculateCoordinates(CA, CB, CG, CG_CD2_length,
CB_CG_CD2_angle, CA_CB_CG_CD2_diangle)
CD2 = Atom("CD2", carbon_d2, 0.0, 1.0, " ", " CD2", 0, "C")
carbon_e1 = calculateCoordinates(CB, CG, ND1, ND1_CE1_length,
CG_ND1_CE1_angle, CB_CG_ND1_CE1_diangle)
CE1 = Atom("CE1", carbon_e1, 0.0, 1.0, " ", " CE1", 0, "C")
nitrogen_e2 = calculateCoordinates(CB, CG, CD2, CD2_NE2_length,
CG_CD2_NE2_angle, CB_CG_CD2_NE2_diangle)
NE2 = Atom("NE2", nitrogen_e2, 0.0, 1.0, " ", " OE1", 0, "N")
_dict = {
'cg': (carbon_g, CG),
'nd1': (nitrogen_d1, ND1),
'cd2': (carbon_d2, CD2),
'ce1': (carbon_e1, CE1),
'ne2': (nitrogen_e2, NE2)
}
return _dict
def place_atom(element, position, resname, chain):
global runtime_mark_id
res_temp = Residue((" ", runtime_mark_id, " "), resname, " ")
runtime_mark_id += 1
atom_temp = Atom("X", position, 0.0, 1, " ", "X", runtime_mark_id, element)
res_temp.add(atom_temp)
chain.add(res_temp)
def makeIle(segID, N, CA, C, O, geo):
'''Creates an Isoleucine residue'''
##R-group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG1_length = geo.CB_CG1_length
CA_CB_CG1_angle = geo.CA_CB_CG1_angle
N_CA_CB_CG1_diangle = geo.N_CA_CB_CG1_diangle
CB_CG2_length = geo.CB_CG2_length
CA_CB_CG2_angle = geo.CA_CB_CG2_angle
N_CA_CB_CG2_diangle = geo.N_CA_CB_CG2_diangle
CG1_CD1_length = geo.CG1_CD1_length
CB_CG1_CD1_angle = geo.CB_CG1_CD1_angle
CA_CB_CG1_CD1_diangle = geo.CA_CB_CG1_CD1_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g1 = calculateCoordinates(N, CA, CB, CB_CG1_length, CA_CB_CG1_angle,
N_CA_CB_CG1_diangle)
CG1 = Atom("CG1", carbon_g1, 0.0, 1.0, " ", " CG1", 0, "C")
carbon_g2 = calculateCoordinates(N, CA, CB, CB_CG2_length, CA_CB_CG2_angle,
N_CA_CB_CG2_diangle)
CG2 = Atom("CG2", carbon_g2, 0.0, 1.0, " ", " CG2", 0, "C")
carbon_d1 = calculateCoordinates(CA, CB, CG1, CG1_CD1_length,
CB_CG1_CD1_angle, CA_CB_CG1_CD1_diangle)
CD1 = Atom("CD1", carbon_d1, 0.0, 1.0, " ", " CD1", 0, "C")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "ILE", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG1)
res.add(CG2)
res.add(CD1)
return res
def makeLeu(segID, N, CA, C, O, geo):
'''Creates a Leucine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD1_length = geo.CG_CD1_length
CB_CG_CD1_angle = geo.CB_CG_CD1_angle
CA_CB_CG_CD1_diangle = geo.CA_CB_CG_CD1_diangle
CG_CD2_length = geo.CG_CD2_length
CB_CG_CD2_angle = geo.CB_CG_CD2_angle
CA_CB_CG_CD2_diangle = geo.CA_CB_CG_CD2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g1 = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g1, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d1 = calculateCoordinates(CA, CB, CG, CG_CD1_length,
CB_CG_CD1_angle, CA_CB_CG_CD1_diangle)
CD1 = Atom("CD1", carbon_d1, 0.0, 1.0, " ", " CD1", 0, "C")
carbon_d2 = calculateCoordinates(CA, CB, CG, CG_CD2_length,
CB_CG_CD2_angle, CA_CB_CG_CD2_diangle)
CD2 = Atom("CD2", carbon_d2, 0.0, 1.0, " ", " CD2", 0, "C")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "LEU", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD1)
res.add(CD2)
return res
def makeAsn(segID, N, CA, C, O, geo):
'''Creates an Asparagine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_OD1_length = geo.CG_OD1_length
CB_CG_OD1_angle = geo.CB_CG_OD1_angle
CA_CB_CG_OD1_diangle = geo.CA_CB_CG_OD1_diangle
CG_ND2_length = geo.CG_ND2_length
CB_CG_ND2_angle = geo.CB_CG_ND2_angle
CA_CB_CG_ND2_diangle = geo.CA_CB_CG_ND2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
oxygen_d1 = calculateCoordinates(CA, CB, CG, CG_OD1_length,
CB_CG_OD1_angle, CA_CB_CG_OD1_diangle)
OD1 = Atom("OD1", oxygen_d1, 0.0, 1.0, " ", " OD1", 0, "O")
nitrogen_d2 = calculateCoordinates(CA, CB, CG, CG_ND2_length,
CB_CG_ND2_angle, CA_CB_CG_ND2_diangle)
ND2 = Atom("ND2", nitrogen_d2, 0.0, 1.0, " ", " ND2", 0, "N")
res = Residue((' ', segID, ' '), "ASN", ' ')
##Create Residue Data Structure
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(OD1)
res.add(ND2)
return res
def makeMet(segID, N, CA, C, O, geo):
'''Creates a Methionine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_SD_length = geo.CG_SD_length
CB_CG_SD_angle = geo.CB_CG_SD_angle
CA_CB_CG_SD_diangle = geo.CA_CB_CG_SD_diangle
SD_CE_length = geo.SD_CE_length
CG_SD_CE_angle = geo.CG_SD_CE_angle
CB_CG_SD_CE_diangle = geo.CB_CG_SD_CE_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
sulfur_d = calculateCoordinates(CA, CB, CG, CG_SD_length, CB_CG_SD_angle,
CA_CB_CG_SD_diangle)
SD = Atom("SD", sulfur_d, 0.0, 1.0, " ", " SD", 0, "S")
carbon_e = calculateCoordinates(CB, CG, SD, SD_CE_length, CG_SD_CE_angle,
CB_CG_SD_CE_diangle)
CE = Atom("CE", carbon_e, 0.0, 1.0, " ", " CE", 0, "C")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "MET", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(SD)
res.add(CE)
return res
def makeSer(N, CA, CB, chi1):
_dict = {}
CB_OG_length = 1.417
CA_CB_OG_angle = 110.773
N_CA_CB_OG_diangle = chi1
oxygen_g = calculateCoordinates(N, CA, CB, CB_OG_length, CA_CB_OG_angle,
N_CA_CB_OG_diangle)
OG = Atom("OG", oxygen_g, 0.0, 1.0, " ", " OG", 0, "O")
_dict['og'] = (oxygen_g, OG)
return _dict
def create_atom(self, name, elem, coord):
"""Finds positions in between the O3' and C5'"""
atom = Atom.Atom(name,
coord,
0.0,
1.0,
' ',
" " + name,
1,
element=elem)
return atom
def makeHis(segID, N, CA, C, O, geo):
'''Creates a Histidine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_ND1_length = geo.CG_ND1_length
CB_CG_ND1_angle = geo.CB_CG_ND1_angle
CA_CB_CG_ND1_diangle = geo.CA_CB_CG_ND1_diangle
CG_CD2_length = geo.CG_CD2_length
CB_CG_CD2_angle = geo.CB_CG_CD2_angle
CA_CB_CG_CD2_diangle = geo.CA_CB_CG_CD2_diangle
ND1_CE1_length = geo.ND1_CE1_length
CG_ND1_CE1_angle = geo.CG_ND1_CE1_angle
CB_CG_ND1_CE1_diangle = geo.CB_CG_ND1_CE1_diangle
CD2_NE2_length = geo.CD2_NE2_length
CG_CD2_NE2_angle = geo.CG_CD2_NE2_angle
CB_CG_CD2_NE2_diangle = geo.CB_CG_CD2_NE2_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
nitrogen_d1 = calculateCoordinates(CA, CB, CG, CG_ND1_length,
CB_CG_ND1_angle, CA_CB_CG_ND1_diangle)
ND1 = Atom("ND1", nitrogen_d1, 0.0, 1.0, " ", " ND1", 0, "N")
carbon_d2 = calculateCoordinates(CA, CB, CG, CG_CD2_length,
CB_CG_CD2_angle, CA_CB_CG_CD2_diangle)
CD2 = Atom("CD2", carbon_d2, 0.0, 1.0, " ", " CD2", 0, "C")
carbon_e1 = calculateCoordinates(CB, CG, ND1, ND1_CE1_length,
CG_ND1_CE1_angle, CB_CG_ND1_CE1_diangle)
CE1 = Atom("CE1", carbon_e1, 0.0, 1.0, " ", " CE1", 0, "C")
nitrogen_e2 = calculateCoordinates(CB, CG, CD2, CD2_NE2_length,
CG_CD2_NE2_angle, CB_CG_CD2_NE2_diangle)
NE2 = Atom("NE2", nitrogen_e2, 0.0, 1.0, " ", " NE2", 0, "N")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "HIS", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(ND1)
res.add(CD2)
res.add(CE1)
res.add(NE2)
return res
def place_atoms(atoms, element, resname, chain):
global runtime_mark_id
res_temp = Residue((" ", runtime_mark_id, " "), resname, " ")
runtime_mark_id += 3
n = 0
for a in atoms:
n += 1
atom_temp = Atom("X" + str(n), a.get_coord(), 0.0, 1, " ", "X",
runtime_mark_id, element)
res_temp.add(atom_temp)
chain.add(res_temp)
def test_assign_unknown_element(self):
"""Unknown element is assigned 'X'."""
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
a = Atom.Atom(
"XE1",
None,
None,
None,
None,
" XE1",
None # serial 5170 - 4CP4
)
self.assertEqual(a.element, "X")
def makePro(segID, N, CA, C, O, geo):
'''Creates a Proline residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
CB_CG_length = geo.CB_CG_length
CA_CB_CG_angle = geo.CA_CB_CG_angle
N_CA_CB_CG_diangle = geo.N_CA_CB_CG_diangle
CG_CD_length = geo.CG_CD_length
CB_CG_CD_angle = geo.CB_CG_CD_angle
CA_CB_CG_CD_diangle = geo.CA_CB_CG_CD_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d = calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle,
CA_CB_CG_CD_diangle)
CD = Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "PRO", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
res.add(CG)
res.add(CD)
return res
def add_residue_from_geo(structure, geo):
resRef= getReferenceResidue(structure)
AA=geo.residue_name
segID= resRef.get_id()[1]
segID+=1
##geometry to bring together residue
peptide_bond=geo.peptide_bond
CA_C_N_angle=geo.CA_C_N_angle
C_N_CA_angle=geo.C_N_CA_angle
##Backbone Coordinages
N_CA_C_angle=geo.N_CA_C_angle
CA_N_length=geo.CA_N_length
CA_C_length=geo.CA_C_length
phi= geo.phi
psi_im1=geo.psi_im1
omega=geo.omega
N_coord=calculateCoordinates(resRef['N'], resRef['CA'], resRef['C'], peptide_bond, CA_C_N_angle, psi_im1)
N= Atom("N", N_coord, 0.0 , 1.0, " "," N", 0, "N")
CA_coord=calculateCoordinates(resRef['CA'], resRef['C'], N, CA_N_length, C_N_CA_angle, omega)
CA=Atom("CA", CA_coord, 0.0 , 1.0, " "," CA", 0,"C")
C_coord=calculateCoordinates(resRef['C'], N, CA, CA_C_length, N_CA_C_angle, phi)
C= Atom("C", C_coord, 0.0, 1.0, " ", " C",0,"C")
##Create Carbonyl atom (to be moved later)
C_O_length=geo.C_O_length
CA_C_O_angle=geo.CA_C_O_angle
N_CA_C_O_diangle=geo.N_CA_C_O_diangle
carbonyl=calculateCoordinates(N, CA, C, C_O_length, CA_C_O_angle, N_CA_C_O_diangle)
O= Atom("O",carbonyl , 0.0 , 1.0, " "," O", 0, "O")
if(AA=='G'):
res=makeGly(segID, N, CA, C, O, geo)
else:
res=makeGly(segID, N, CA, C, O, geo)
resRef['O'].set_coord(calculateCoordinates(res['N'], resRef['CA'], resRef['C'], C_O_length, CA_C_O_angle, 180.0))
ghost= Atom("N", calculateCoordinates(res['N'], res['CA'], res['C'], peptide_bond, CA_C_N_angle, psi_im1), 0.0 , 0.0, " ","N", 0, "N")
res['O'].set_coord(calculateCoordinates( res['N'], res['CA'], res['C'], C_O_length, CA_C_O_angle, 180.0))
structure[0]['A'].add(res)
return structure
def build_residues(list_blueprints, list_names):
list_residues = []
resname = res_rev_name_dict[list_blueprints[0][0][2]]
rotamer_dict[resname] = []
for list_rotamer in list_blueprints:
new_res = Residue((" ", 279, " "), resname,
" ") # RESET TOTAL_RES_ID TO 1 ON SUBSEQUENT RUNS?
rotamer_dict[resname].append(list_rotamer[5][1])
for blueprint_atom in list_rotamer:
new_atom = Atom(blueprint_atom[0], blueprint_atom[6],
blueprint_atom[8], blueprint_atom[7],
blueprint_atom[1], blueprint_atom[0], 1,
blueprint_atom[10])
# INIT: NAME, COORDINATES, BFACTOR, OCCUPANCY, ALTLOC, FULL NAME, SERIAL NUMBER, ELEMENT
new_atom.set_parent(new_res)
new_res.add(new_atom)
list_residues.append(new_res)
return list_residues
def makeGlu(N, CA, CB, chi1, chi2, chi3):
CB_CG_length = 1.52
CA_CB_CG_angle = 113.82
N_CA_CB_CG_diangle = chi1
CG_CD_length = 1.52
CB_CG_CD_angle = 113.31
CA_CB_CG_CD_diangle = chi2
CD_OE1_length = 1.25
CG_CD_OE1_angle = 119.02
CB_CG_CD_OE1_diangle = chi3
CD_OE2_length = 1.25
CG_CD_OE2_angle = 118.08
CB_CG_CD_OE2_diangle = 180.0 + CB_CG_CD_OE1_diangle
carbon_g = calculateCoordinates(N, CA, CB, CB_CG_length, CA_CB_CG_angle,
N_CA_CB_CG_diangle)
CG = Atom("CG", carbon_g, 0.0, 1.0, " ", " CG", 0, "C")
carbon_d = calculateCoordinates(CA, CB, CG, CG_CD_length, CB_CG_CD_angle,
CA_CB_CG_CD_diangle)
CD = Atom("CD", carbon_d, 0.0, 1.0, " ", " CD", 0, "C")
oxygen_e1 = calculateCoordinates(CB, CG, CD, CD_OE1_length,
CG_CD_OE1_angle, CB_CG_CD_OE1_diangle)
OE1 = Atom("OE1", oxygen_e1, 0.0, 1.0, " ", " OE1", 0, "O")
oxygen_e2 = calculateCoordinates(CB, CG, CD, CD_OE2_length,
CG_CD_OE2_angle, CB_CG_CD_OE2_diangle)
OE2 = Atom("OE1", oxygen_e2, 0.0, 1.0, " ", " OE1", 0, "O")
_dict = {
'cg': (carbon_g, CG),
'cd': (carbon_d, CD),
'oe1': (oxygen_e1, OE1),
'oe2': (oxygen_e2, OE2)
}
return _dict
def makeAla(segID, N, CA, C, O, geo):
'''Creates an Alanine residue'''
##R-Group
CA_CB_length = geo.CA_CB_length
C_CA_CB_angle = geo.C_CA_CB_angle
N_C_CA_CB_diangle = geo.N_C_CA_CB_diangle
carbon_b = calculateCoordinates(N, C, CA, CA_CB_length, C_CA_CB_angle,
N_C_CA_CB_diangle)
CB = Atom("CB", carbon_b, 0.0, 1.0, " ", " CB", 0, "C")
##Create Residue Data Structure
res = Residue((' ', segID, ' '), "ALA", ' ')
res.add(N)
res.add(CA)
res.add(C)
res.add(O)
res.add(CB)
return res
def RemoveHydrogens(ProteinModel):
# Loop over entire structure
for Chain in list(ProteinModel.get_chains()):
for Residue in list(Chain.get_residues()):
if Residue.get_resname() not in ("HOH", "WAT"):
# And get rid of hydrogens
for Atom in list(Residue.get_atoms()):
if Atom.element == "H":
Residue.detach_child(Atom.get_id())
else:
Chain.detach_child(Residue.get_id())
if len(list(Chain.get_residues())) == 0:
ProteinModel.detach_child(Chain.get_id())
return
