def get_all_interaction_pairs(pdb_filename, print_files=True):
"""
Takes a pdb file path and generates a folder with all the pairs of interacting chains without checking if
there is redundant content. This simulates the user input
:param pdb_filename: pdb file with the structure we want to break into interactions
:param print_files: parameter indicating if we want to output the interaction pairs to a directory.
:return: a directory with pdb files of the interactions and a list with the first element being the list of all
interactions, ... to finish this with adri
"""
parser = PDBParser(PERMISSIVE=1)
# Load pdb structure to a pdb file
structure_id = get_structure_name(pdb_filename)
filename = pdb_filename
structure = parser.get_structure(structure_id, filename)
neighbor_chains = get_neighbor_chains(structure)
# Create a new directory with the interaction pdb files
if print_files:
if not os.path.exists('%s_all_interactions' % structure_id):
os.makedirs('%s_all_interactions' % structure_id)
else:
for the_file in os.listdir('%s_all_interactions' % structure_id):
file_path = os.path.join('%s_all_interactions' % structure_id,
the_file)
if os.path.isfile(file_path):
os.unlink(file_path)
io = PDBIO()
io.set_structure(structure)
for chain in neighbor_chains:
for other_chain in neighbor_chains[chain]:
io.save(
'%s_all_interactions/%s_%s%s.pdb' %
(structure_id, structure_id, chain.get_id(),
other_chain.get_id()), ChainSelect(chain, other_chain))
else:
interaction_list = []
structure_counter = 0
for chain, neighbor in neighbor_chains.items():
for chain2 in neighbor:
new_str = Structure.Structure(
'%s_%s' % (structure_id, structure_counter))
structure_counter += 1
new_str.add(Model.Model(0))
new_str[0].add(chain)
new_str[0].add(chain2)
interaction_list.append(new_str)
return [interaction_list, 's%s_all_interactions' % structure_id]
def set_new_positions(self, positions):
self.positions = positions
new_model = Model.Model(len(self.structure.child_list), len(self.structure.child_list) + 1)
chain = self.structure[0].child_list[0].copy()
new_model.add(chain)
self.structure.add(new_model)
chain = new_model.child_list[0]
counter = 0
for residue in chain.get_residues():
for atom in residue.get_atoms():
atom.set_coord(positions[counter])
counter += 1
def dump_pdb(self, filename):
'''
If the BulgeGraph has a chain created for it, dump that as well.
@param filename: The filename of the pdb file to which the chain
coordinates will be written.
'''
if self.chain is None:
return
self.chain.child_list.sort()
mod = bpm.Model(' ')
s = bps.Structure(' ')
mod.add(self.chain)
s.add(mod)
io = bp.PDBIO()
io.set_structure(s)
io.save(filename)
def get_structure_slice_by_residues(struct: Structure, domain_name: str,
chain_order: int, start: int,
finish: int) -> Structure:
"""
Return new structure that contains new model (id=1), new chain (id=1) with residues
from 'start' to 'finish' of specified chain of input structure
:param struct: input structure to slice
:param chain_order: order of chain to extract residues
:param start: start residue
:param finish: finish residues
:param domain_name: new structure name
:return: new structure
"""
new_chain = Chain.Chain(1)
chain = list(struct.get_chains())[chain_order]
for i in range(start, finish + 1):
new_chain.add(chain[i])
model = Model.Model(1)
model.add(new_chain)
domain = Structure.Structure(domain_name)
domain.add(model)
return domain
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
invalid = True
if invalid:
continue
num_items = {"O": 0, "T": 0}
for hit in item:
num_items[hit[5]] += 1
for hit in item:
if len(hit[1]) > 1:
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
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 compare_interactions(interaction1, interaction2):
structure1 = Structure.Structure('1')
structure2 = Structure.Structure('2')
structure1.add(Model.Model(0))
structure2.add(Model.Model(0))
homodimer = False
for chain in interaction1:
if len(list(structure1[0].get_chains())) == 1 and compare_chains(
chain,
list(structure1[0].get_chains())[0]):
homodimer = True
structure1[0].add(Chain.Chain(chain.get_id()))
res_counter = 0
for residue in chain:
if 'CA' in [x.get_id() for x in residue.get_atoms()]:
atom = residue['CA']
structure1[0][chain.get_id()].add(
Residue.Residue(
('', res_counter, ''), residue.get_resname(),
residue.get_segid()))
structure1[0][chain.get_id()][('', res_counter,
'')].add(atom.copy())
res_counter += 1
for chain in interaction2:
structure2[0].add(Chain.Chain(chain.get_id()))
res_counter = 0
for residue in chain:
if 'CA' in [x.get_id() for x in residue.get_atoms()]:
atom = residue['CA']
structure2[0][chain.get_id()].add(
Residue.Residue(
('', res_counter, ''), residue.get_resname(),
residue.get_segid()))
structure2[0][chain.get_id()][('', res_counter,
'')].add(atom.copy())
res_counter += 1
if homodimer:
for int in [structure1[0], structure2[0]]:
trim_to_superimpose(
list(int.get_chains())[0],
list(int.get_chains())[1])
for chain1 in structure1[0]:
for chain2 in structure2[0]:
if chain1.get_id() != chain2.get_id():
continue
trim_to_superimpose(chain1, chain2)
# print(list(chain1.get_residues())[0])
# print(list(chain2.get_residues())[0])
# print(list(structure1.get_chains()))
# print(list(structure2.get_chains()))
result = str_comparison_superimpose(structure1, structure2)
return result
def get_chain_ids(model: Model):
chains = model.get_chains()
chain_list = []
for chain in chains:
chain_list.append(chain.get_id())
return chain_list
def assemble_multiscale_visualization(topology_fn, rmf_fn, pdb_dir,
outprefix=None, chimerax=True,
xl_fn=None):
"""
Render multiscale versions of rigid bodies from PDB files + flexible
beads from RMF files w/o mapped crosslinks.
Args:
topology_fn (str): Topolgy file in pipe-separated-value (PSV) format
as required in integrative modeling using IMP. For details on how
to write a topology file, see:
https://integrativemodeling.org/2.13.0/doc/ref/classIMP_1_1pmi_1_1topology_1_1TopologyReader.html
rmf_fn (str): Name of the RMF file.
pdb_dir (str): Directory containing all the PDB files for the rigid
bodies used in modeling.
outprefix (str, optional): Prefix for output files. Defaults to None.
chimerax (bool, optional): If true, a Chimerax script will be written (extension ".cxc"). Defaults to True.
xl_fn (str, optional): A file containing a XL dataset. Defaults to None.
If this dataset is supplied, then it will be mapped on to the overall
structure with satisfied XLs drawn in blue and violated XLs drawn in red.
A XL dataset should be supplied in a comma-separated-value (CSV) format
containing at least the following fields
protein1, residue1, protein2, residue2, sat
where the last field <sat> is a boolean 1 or 0 depending on whether
the particular XL is satisfied (in the ensemble sense) as a result of the
integrative modeling exercise.
"""
# -------------------------------------------
# read the RMF file and extract all particles
# -------------------------------------------
of = RMF.open_rmf_file_read_only(rmf_fn)
rmf_model = IMP.Model()
hier = IMP.rmf.create_hierarchies(of, rmf_model)[0]
IMP.rmf.load_frame(of, 0)
particles = IMP.core.get_leaves(hier)
rmf_ps = {}
for p in particles:
molname = p.get_parent().get_parent().get_parent().get_name().strip()
name = p.get_name().strip()
coord = IMP.core.XYZ(p).get_coordinates()
rmf_ps[(molname, name)] = coord
# --------------------------------------------------------------
# map pdb residues to rmf particles for each rigid body pdb file
# --------------------------------------------------------------
# read the topology file
t = TopologyReader(topology_fn, pdb_dir=pdb_dir)
components = t.get_components()
map_pdb2rmf = {}
rigid_body_models = {}
rigid_body_residues = {}
chain_ids = {} # these are matched to the chimerax rmf plugin
chain_id_count = 0
for c in components:
# ignore unstructured residues
if c.pdb_file == "BEADS": continue
mol = c.molname
pdb_prefix = os.path.basename(c.pdb_file).split(".pdb")[0]
chain_id = c.chain
resrange = c.residue_range
offset = c.pdb_offset
r0 = resrange[0] + offset
r1 = resrange[1] + 1 + offset
if mol not in chain_ids:
chain_ids[mol] = string.ascii_uppercase[chain_id_count]
chain_id_count += 1
if pdb_prefix not in map_pdb2rmf:
map_pdb2rmf[pdb_prefix] = {}
this_rigid_body_model = PDBParser().get_structure("x", c.pdb_file)[0]
this_rigid_body_residues = {(r.full_id[2], r.id[1]): r for r in this_rigid_body_model.get_residues()}
rigid_body_models[pdb_prefix] = this_rigid_body_model
rigid_body_residues[pdb_prefix] = this_rigid_body_residues
for r in range(r0, r1):
key = (chain_id, r)
val = (mol, r)
if key in rigid_body_residues[pdb_prefix]:
map_pdb2rmf[pdb_prefix][key] = val
# --------------------------------
# align all pdb files with the rmf
# --------------------------------
print("\nAligning all rigid body structures...")
align = SVDSuperimposer()
for pdb_prefix, mapper in map_pdb2rmf.items():
pdb_coords = []
pdb_atoms = []
rmf_coords = []
residues = rigid_body_residues[pdb_prefix]
for (chain, pdb_res), (mol, rmf_res) in mapper.items():
r = residues[(chain, pdb_res)]
pdb_coords.append(r["CA"].coord)
pdb_atoms.extend([a for a in r.get_atoms()])
rmf_coords.append(rmf_ps[(mol, str(rmf_res))])
pdb_coords = np.array(pdb_coords)
rmf_coords = np.array(rmf_coords)
align.set(rmf_coords, pdb_coords)
align.run()
rotmat, vec = align.get_rotran()
[a.transform(rotmat, vec) for a in pdb_atoms]
# --------------------------
# assemble the composite pdb
# --------------------------
mols = set(sorted([c.molname for c in components]))
print("\nChain IDs by molecule:")
for k, v in chain_ids.items():
print("molecule %s, chain ID %s" % (k, v))
reslists = {mol: [] for mol in mols}
for pdb_prefix, mapper in map_pdb2rmf.items():
residues = rigid_body_residues[pdb_prefix]
for (chain, pdb_res), (mol, rmf_res) in mapper.items():
r = residues[(chain, pdb_res)] ; resid = rmf_res
new_id = (r.id[0], resid, r.id[2])
new_resname = r.resname
new_segid = r.segid
new_atoms = r.get_atoms()
new_residue = Residue.Residue(id=new_id, resname=new_resname, segid=new_segid)
[new_residue.add(a) for a in new_atoms]
reslists[mol].append(new_residue)
composite_model = Model.Model(0)
for mol, chain_id in chain_ids.items():
this_residues = sorted(reslists[mol], key=lambda r: r.id[1])
this_chain = Chain.Chain(chain_id)
[this_chain.add(r) for r in this_residues]
composite_model.add(this_chain)
# save the composite pdb to file
io = PDBIO()
io.set_structure(composite_model)
if outprefix is None:
outprefix = "centroid_model"
io.save(outprefix + ".pdb")
# -------------------------------------------------------------------
# chimerax rendering (hide most of the rmf except unstructured beads)
# -------------------------------------------------------------------
if not chimerax: exit()
print("\nWriting UCSF Chimerax script...")
s = ""
s += "open %s\n" % (outprefix + ".pdb")
s += "open %s\n" % rmf_fn
s += "hide\n"
s += "show cartoon\n"
s += "color #%d %s\n" % (CHIMERAX_PDB_MODEL_NUM, STRUCT_COLOR)
s += "color #%d %s\n" % (CHIMERAX_RMF_MODEL_NUM, UNSTRUCT_COLOR)
s += "hide #%d\n" % CHIMERAX_RMF_MODEL_NUM
struct_residues = []
for key, val in map_pdb2rmf.items():
struct_residues.extend(list(val.values()))
unstruct_atomspec = {}
for p in rmf_ps:
molname, particle_name = p
rmf_chain_id = chain_ids[molname]
if "bead" in particle_name:
r0, r1 = particle_name.split("_")[0].split("-")
r0 = int(r0) ; r1 = int(r1)
this_atomspec = "#%d/%s:%d-%d" % \
(CHIMERAX_RMF_MODEL_NUM, rmf_chain_id, r0, r1)
for r in range(r0, r1+1):
unstruct_atomspec[(molname, r)] = this_atomspec
else:
if (molname, int(particle_name)) not in struct_residues:
r = int(particle_name)
this_atomspec = "#%d/%s:%d" % \
(CHIMERAX_RMF_MODEL_NUM, rmf_chain_id, r)
unstruct_atomspec[(molname, r)] = this_atomspec
s += "show %s\n" % (" ".join(set(unstruct_atomspec.values())))
# ----------------------------------------------------------
# if crosslink data is supplied, write out a pseudobond file
# ----------------------------------------------------------
if xl_fn is not None:
# parse XL data
df = pd.read_csv(os.path.abspath(xl_fn))
xls = []
for i in range(len(df)):
this_df = df.iloc[i]
p1 = this_df["protein1"] ; r1 = this_df["residue1"]
p2 = this_df["protein2"] ; r2 = this_df["residue2"]
sat = this_df["sat"]
xls.append((p1, r1, p2, r2, sat))
# get lists of struct atomspecs
atomspec = {}
for (mol, particle_name) in rmf_ps:
if "bead" in particle_name: continue
if (mol, int(particle_name)) in unstruct_atomspec: continue
chain_id = chain_ids[mol]
resid = int(particle_name)
atomspec[(mol, resid)] = "#%d/%s:%d@CA" % \
(CHIMERAX_PDB_MODEL_NUM, chain_id, resid)
# now add in all the unstruct atomspecs
atomspec.update(unstruct_atomspec)
# write pseudobond script
s_pb = ""
s_pb += "; radius = %2.2f\n" % XL_RADIUS
s_pb += "; dashes = 0\n"
for xl in xls:
p1, r1, p2, r2, sat = xl
atomspec_1 = atomspec[(p1, r1)]
atomspec_2 = atomspec[(p2, r2)]
if atomspec_1 == atomspec_2:
continue
color = SAT_XL_COLOR if sat else VIOL_XL_COLOR
s_pb += "%s %s %s\n" % (atomspec_1, atomspec_2, color)
s_pb += "\n"
pb_fn = outprefix + "_XLs.pb"
with open(pb_fn, "w") as of:
of.write(s_pb)
s += "open %s\n" % pb_fn
s += "preset 'overall look' publication\n"
chimerax_out_fn = outprefix + ".cxc"
with open(chimerax_out_fn, "w") as of:
of.write(s)
def generate_pairwise_subunits_from_pdb(pdb_file_path, templates_path,
file_type, verbose):
"""Take an existing complex and fragment it into each of the pairwise interactions between subunits.
Keyword arguments:
pdb_file_path -- path where the complex PDB is
templates_path -- folder where the resulting folders will be saved
file_type -- type of file
verbose -- if a log of the program execution is saved
Considerations:
Does not consider nucleic acid sequences, it is only for testing the program on different complexes"""
num_file = 0
if file_type == 'PDB':
parser = pdb.PDBParser(PERMISSIVE=1)
else:
parser = pdb.MMCIFParser()
structure = parser.get_structure('pdb_name', pdb_file_path)
# give unique chain identifiers to a structure, it has to be similar to the ids of the chains used in build_complex, to be able to use further the structure_in_created_structures() function
id_nch = 0
for chain in structure.get_chains():
actual_id = chain.id
chain.id = (complete_chain_alphabet[id_nch] + '_', actual_id)
id_nch += 1
# free the ./templates_path/
os.system('rm -rf ' + templates_path + '*')
# initialize the saved pairs and structures
saved_pairs = set()
saved_structures = []
# loop through all possible pairwise files
for chain1 in structure.get_chains():
for chain2 in structure.get_chains():
# the following strings define the pairs already saved
comb = tuple(list(chain1.id) + list(chain2.id))
comb_rev = tuple(list(chain2.id) + list(chain1.id))
if chain1 is not chain2 and comb not in saved_pairs:
# save the combination
saved_pairs.add(comb)
saved_pairs.add(comb_rev)
# ask if any of the residues is interacting, if so save the PDB
chains_interacting = False
for residue1 in chain1:
if chains_interacting is True:
break
for residue2 in chain2:
if residue1 != residue2:
# define which is the important residue of each chain:
atoms1 = [x.id for x in residue1.get_atoms()]
atoms2 = [x.id for x in residue2.get_atoms()]
important_atom1 = None
if 'CA' in atoms1:
important_atom1 = residue1['CA']
elif 'P' in atoms1:
important_atom1 = residue1['P']
important_atom2 = None
if 'CA' in atoms2:
important_atom2 = residue2['CA']
elif 'P' in atoms2:
important_atom2 = residue2['P']
# compute the distance:
if important_atom1 is not None and important_atom2 is not None:
distance = important_atom1 - important_atom2
else:
continue
if distance < 7:
chains_interacting = True
break
if chains_interacting is True:
# create a structure object
ID = str(num_file)
num_file += 1
new_structure = pdb_struct.Structure(ID)
new_model = pdb_model.Model(0)
new_model.add(chain1.copy())
new_model.add(chain2.copy())
new_structure.add(new_model)
# move the coordinates of the structure to simulate what would happen if they were coming from different files
rotation = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
translation = np.array((0, 0, 1), 'f')
for atom in new_structure.get_atoms():
atom.transform(rotation, translation)
# write to new pdb:
if structure_in_created_structures(
new_structure, saved_structures) is False:
# record as a saved structure:
saved_structures.append(new_structure.copy())
# give unique chains to a structure (A and B)
id_nch = 0
for chain in new_structure.get_chains():
chain.id = chain_alphabet[id_nch]
id_nch += 1
if verbose:
print(
'writing PDB file with the interaction of %s and %s into %s.pdb'
% (chain1.id[1], chain2.id[1], ID))
# write using our customized writer
io = pdb.PDBIO()
io.set_structure(new_structure)
io.save(templates_path + ID + '.pdb')