def get_chain(structure: Structure, return_a_chain: bool = False) -> ChainDesc:
if return_a_chain:
for chain in structure.get_chains():
if chain.get_id() == 'A':
return chain
chains = [ChainDesc(chain=c) for c in structure.get_chains()]
# fast return if structure contains a single chain
if len(chains) == 1:
print('structure contains a single chain')
return chains[0]
print(f'structure contains {len(chains)} chains')
chains_with_ligands = [c for c in chains if c.if_has_ligands()]
print(f'chains with ligands: {len(chains_with_ligands)}')
shortened_chain_sequences = [c.get_shortened_seq() for c in chains_with_ligands]
# - check all pair alignments
# - if at least one pair has equality score less than threshold,
# ask user for which chain to choose (by its letter)
# - otherwise (that means that all chains are similar) choose longest one
equality_threshold = 0.95
for first_index in range(len(shortened_chain_sequences)):
for second_index in range(first_index+1, len(shortened_chain_sequences)):
first_sequence = shortened_chain_sequences[first_index]
second_sequence = shortened_chain_sequences[second_index]
alignments = pairwise2.align.globalds(first_sequence, second_sequence, blosum62, -10, -0.5)
first_aligned, second_aligned, score, begin, end = alignments[0]
if score < equality_threshold:
print(f'two different sequences found (score={score})')
print('please enter a letter of chain to work with: ', end='')
chain_letter = input()[0]
chain_index = int(chain_letter) - int('A')
return chains[chain_index]
# as we are here, then no different chains were found -
# so choose longest one
def get_chain_length(chain: ChainDesc) -> int:
sequence = chain.get_shortened_seq()
return len(sequence)
sorted_chains = sorted(chains_with_ligands, key=get_chain_length, reverse=True)
longest_chain = sorted_chains[0]
print(f'chain selected: {longest_chain.chain.get_id()}')
return longest_chain
class PyRyStructure(object):
"""
class represents structure as entity (very wide definition)
used for storing information about structures,
creating BIO.pdb structures,
saving structure files etc.
"""
def __init__(self, structure=None):
if structure: self.struct = structure
else: self.struct = None
self.sequence = '' # sequence taken from structure
#----------------will decide on one of these 3 ----------------------------
self.center_of_mass = [] # [x,y,z] coords of center of mass
self.geometric_center = [] # geometric centre
self.center = None # actual center of given complex component
#--------------------------------------------------------------------------
self.chain = '' # chain name from structure file
self.moltype = '' # protein, DNA, RNA
def __str__(self):
return "%s %s %s %s %s"%(self.struct, self.chain, self.center_of_mass,\
self.moltype, self.sequence)
def add_chain_to_struct(self, chain_id):
"""
adds another model to BIO.pdb structure object
Parameters:
-----------
chain_id : chain name
Returns:
---------
self.struct : Bio.PDB structure with new chain
"""
chain = Chain(chain_id)
self.struct[0].add(chain)
def add_residues_to_structure(self, struct, chain_id, chain2_id):
"""
adds residues from struct to a given structure (self.structure)
Parameters:
-----------
struct : template structure object with residues which will
be added to self.structure object
chain_id : name of template chain
chain2_id : name of new chain in self.struct
Returns:
---------
self.stuct : with extra residues
"""
residues = struct[0][chain_id].child_list
[self.struct[0][chain2_id].add(res) for res in residues]
def calculate_atom_atom_distance(self, atom1, atom2):
"""
calculates distance between two atoms
Parameters:
-----------
atom1, atom2 : Bio.PDB.Atom entities
Returns:
---------
distance from atom1 to atom2 in 3D space
Raises:
-------
PyRyStructureError if parameters are not Bio.PDB.Atom entities
"""
if is_structure(): return atom1 - atom2
def calculate_centre_of_mass(self, entity=None, geometric=False):
"""
calculates centre of mass for given structure
Returns gravitic or geometric center of mass of an Entity.
Geometric assumes all masses are equal (geometric=True)
Defaults to Gravitic.
Parameters:
-----------
geometric : optional
Returns:
---------
centre of mass coordinates as [x,y,z] list
Raises:
-------
ValueError : if wrong object is given as a target
PyRyStructureError : no PyRyStructure object
"""
#if self.struct == None: raise PyRyStructureError("You haven't provided \
# any structure to PyRyStructure class")
if isinstance(self.struct,
Entity.Entity): # Structure, Model, Chain, Residue
atom_list = self.struct.get_atoms()
elif hasattr(entity, '__iter__') and filter(lambda x: x.level ==\
'A', entity): # List of Atoms
atom_list = entity
else: # Some other weirdo object
raise ValueError('Center of Mass can only be calculated from \n\
the following objects:Structure, Model, Chain, Residue, list of Atoms.'
)
new_centre = [0., 0., 0.]
whole_mass = 0
for atom in atom_list:
atom_centre = array([
float(atom.coord[0]),
float(atom.coord[1]),
float(atom.coord[2])
])
whole_mass += atom.molweight
new_centre += atom_centre * atom.molweight
new_centre /= whole_mass
self.center_of_mass = new_centre
return self.center_of_mass
def create_PDB_obj(self, id, filename):
"""
creates Bio.PDB object from pdb file
Parameters:
-----------
id : name of structure
filename : file name
"""
parser = PDBParser()
self.struct = parser.get_structure(str(id), filename)
def create_new_structure(self, name, chain_id):
"""
creates new Bio.PDB structure object
Parameters:
-----------
name : structure name
chain_id : chain name (e.g. A, B, C)
Returns:
---------
self.struct : Bio.PDB object with model and chain inside
"""
self.struct = Structure(name)
my_model = Model(0)
my_chain = Chain(chain_id)
self.struct.add(my_model)
self.struct[0].add(my_chain)
def get_chainname(self):
"""
returns name of given structures chain
"""
self.chain = list(self.struct.get_chains())[0].id
def get_mol_sequence(self):
"""
retrieves struct sequence as one letter code
Parameters:
-----------
self.struct : structure object
Returns:
---------
self.sequence : sequence of given structure in one letter code
"""
##----must be included in tests!!!--------------------
for resi in self.struct.get_residues():
resi_name = resi.resname.strip().upper()
#add one letter nucleotide names
if len(resi_name) == 1 and resi_name in RESNAMES.values():
self.sequence += resi_name
#add hetatms with modifications
elif resi_name in to_one_letter_code:
self.sequence += to_one_letter_code[resi_name]
#do not add ions and ligands into sequence
elif resi_name in LIGANDS:
pass
#if antyhing else appeared include as X
else:
self.sequence += "X"
return self.sequence
def get_moltype(self):
"""
based on component's sequence determines if a certain
component is DNA, RNA or protein
Raises:
-------
PyRyStructureError if resnames are incorrect
"""
res = list(self.struct.get_residues())[0]
if len(res.resname.strip()) == 3:
if res.resname.strip() in AMINOACIDS.values():
self.moltype = 'protein'
else:
if res.resname.strip() in RESNAMES.keys(): pass
else:
raise PyRyStructureError("Wrong 3letter name",
res.resname.strip())
else:
for at in res:
if at.fullname.strip() == "CA":
self.moltype = 'protein'
break
elif at.fullname.strip() == "C4'" or at.fullname.strip(
) == "C4*":
for atom in res.child_list:
if atom.fullname.strip() == "O2'":
self.moltype = "RNA"
break
if self.moltype == "":
self.moltype = "DNA"
return self.moltype
def is_structure(self):
"""
checks if a given structure is Bio.PDB structure object
Raises:
------
PyRyStructureError : if self.struct is not Bio.PDB object
"""
if isinstance(self.struct,
Entity.Entity): # Structure, Model, Chain, Residue
return True
else:
raise PyRyStructureError('%s should be one of\n\
the following objects:Structure, Model, Chain, Residue, \n\
list of Atoms.' %
(self.struct))
def set_chain_name(self, chain):
self.chain = chain
def set_moltype(self, moltype):
"""
"""
self.moltype = moltype
def set_structure(self, struct):
self.struct = struct
def set_pyrystructure(self, structure=None):
"""
sets structure as PyRyStructure atrribute
Parameters:
-----------
structure : Bio.PDB structure object
"""
if self.struct == None: self.struct = structure
if self.sequence == '': self.get_mol_sequence()
self.get_chainname()
self.get_moltype()
def set_sequence(self, seq):
"""
"""
self.sequence = seq
def write_structure(self, filename):
"""
Writting structure to the pdb_file, saving changed coordinated
Parameters:
-----------
filename : final name of structure file
"""
out = PDBIO()
out.set_structure(self.struct)
out.save(filename)
