structure = PDBParser(QUIET=False).get_structure(
"dimer", path_structure + "dimer.pdb")
new_model = Model(2)
new_chain = Chain("C")
new_model.add(new_chain)
new_chain_mark = Chain("M")
add_markers(new_chain_mark)
new_model.add(new_chain_mark)
structure.add(new_model)
# mutations = {} [sorted IDs] : [cobalt], [residues], num_HIS, clash_info_list, num, type, coords
res_co = Residue((" ", runtime_mark_id, " "), "Co3",
" ")
res_co.add(hit[0])
new_chain.add(res_co) # Add cobalt in its own residue
for res in hit[1]: # Add rotamers
if res not in new_chain:
new_chain.add(res)
if hit[2] > 0:
directory = path_output + "/HIS/" + str(
hit[2]) + "/" + mut_name_full + "/"
if not os.path.exists(directory):
os.makedirs(directory)
count = len(glob.glob1(directory, "*.pdb"))
io = PDBIO()
def initialize_res(residue):
'''Creates a new structure containing a single amino acid. The type and
geometry of the amino acid are determined by the argument, which has to be
either a geometry object or a single-letter amino acid code.
The amino acid will be placed into chain A of model 0.'''
if isinstance(residue, Geo):
geo = residue
else:
geo = geometry(residue)
segID = 1
AA = geo.residue_name
CA_N_length = geo.CA_N_length
CA_C_length = geo.CA_C_length
N_CA_C_angle = geo.N_CA_C_angle
CA_coord = [0., 0., 0.]
C_coord = [CA_C_length, 0, 0]
N_coord = [
CA_N_length * math.cos(N_CA_C_angle * (math.pi / 180.0)),
CA_N_length * math.sin(N_CA_C_angle * (math.pi / 180.0)), 0
]
N = Atom("N", N_coord, 0.0, 1.0, " ", " N", 0, "N")
CA = Atom("CA", CA_coord, 0.0, 1.0, " ", " CA", 0, "C")
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)
elif (AA == 'A'):
res = makeAla(segID, N, CA, C, O, geo)
elif (AA == 'S'):
res = makeSer(segID, N, CA, C, O, geo)
elif (AA == 'C'):
res = makeCys(segID, N, CA, C, O, geo)
elif (AA == 'V'):
res = makeVal(segID, N, CA, C, O, geo)
elif (AA == 'I'):
res = makeIle(segID, N, CA, C, O, geo)
elif (AA == 'L'):
res = makeLeu(segID, N, CA, C, O, geo)
elif (AA == 'T'):
res = makeThr(segID, N, CA, C, O, geo)
elif (AA == 'R'):
res = makeArg(segID, N, CA, C, O, geo)
elif (AA == 'K'):
res = makeLys(segID, N, CA, C, O, geo)
elif (AA == 'D'):
res = makeAsp(segID, N, CA, C, O, geo)
elif (AA == 'E'):
res = makeGlu(segID, N, CA, C, O, geo)
elif (AA == 'N'):
res = makeAsn(segID, N, CA, C, O, geo)
elif (AA == 'Q'):
res = makeGln(segID, N, CA, C, O, geo)
elif (AA == 'M'):
res = makeMet(segID, N, CA, C, O, geo)
elif (AA == 'H'):
res = makeHis(segID, N, CA, C, O, geo)
elif (AA == 'P'):
res = makePro(segID, N, CA, C, O, geo)
elif (AA == 'F'):
res = makePhe(segID, N, CA, C, O, geo)
elif (AA == 'Y'):
res = makeTyr(segID, N, CA, C, O, geo)
elif (AA == 'W'):
res = makeTrp(segID, N, CA, C, O, geo)
else:
res = makeGly(segID, N, CA, C, O, geo)
cha = Chain('A')
cha.add(res)
mod = Model(0)
mod.add(cha)
struc = Structure('X')
struc.add(mod)
return struc
def initialize_res(residue):
'''Creates a new structure containing a single amino acid. The type and
geometry of the amino acid are determined by the argument, which has to be
either a geometry object or a single-letter amino acid code.
The amino acid will be placed into chain A of model 0.'''
if isinstance( residue, Geo ):
geo = residue
else:
geo=geometry(residue)
segID=1
AA= geo.residue_name
CA_N_length=geo.CA_N_length
CA_C_length=geo.CA_C_length
N_CA_C_angle=geo.N_CA_C_angle
CA_coord= [0.,0.,0.]
C_coord= [CA_C_length,0,0]
N_coord = [CA_N_length*math.cos(N_CA_C_angle*(math.pi/180.0)),CA_N_length*math.sin(N_CA_C_angle*(math.pi/180.0)),0]
N= Atom("N", N_coord, 0.0 , 1.0, " "," N", 0, "N")
CA=Atom("CA", CA_coord, 0.0 , 1.0, " "," CA", 0,"C")
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)
elif(AA=='A'):
res=makeAla(segID, N, CA, C, O, geo)
elif(AA=='S'):
res=makeSer(segID, N, CA, C, O, geo)
elif(AA=='C'):
res=makeCys(segID, N, CA, C, O, geo)
elif(AA=='V'):
res=makeVal(segID, N, CA, C, O, geo)
elif(AA=='I'):
res=makeIle(segID, N, CA, C, O, geo)
elif(AA=='L'):
res=makeLeu(segID, N, CA, C, O, geo)
elif(AA=='T'):
res=makeThr(segID, N, CA, C, O, geo)
elif(AA=='R'):
res=makeArg(segID, N, CA, C, O, geo)
elif(AA=='K'):
res=makeLys(segID, N, CA, C, O, geo)
elif(AA=='D'):
res=makeAsp(segID, N, CA, C, O, geo)
elif(AA=='E'):
res=makeGlu(segID, N, CA, C, O, geo)
elif(AA=='N'):
res=makeAsn(segID, N, CA, C, O, geo)
elif(AA=='Q'):
res=makeGln(segID, N, CA, C, O, geo)
elif(AA=='M'):
res=makeMet(segID, N, CA, C, O, geo)
elif(AA=='H'):
res=makeHis(segID, N, CA, C, O, geo)
elif(AA=='P'):
res=makePro(segID, N, CA, C, O, geo)
elif(AA=='F'):
res=makePhe(segID, N, CA, C, O, geo)
elif(AA=='Y'):
res=makeTyr(segID, N, CA, C, O, geo)
elif(AA=='W'):
res=makeTrp(segID, N, CA, C, O, geo)
else:
res=makeGly(segID, N, CA, C, O, geo)
cha= Chain('A')
cha.add(res)
mod= Model(0)
mod.add(cha)
struc= Structure('X')
struc.add(mod)
return struc