def main(number : int = 10, double : bool = False): # Add Strand 1 - ssDNA n = number nucleotides = [] print("Creating a nucleotide:") nucleotides.append( Nucleotide( random.choice(['A', 'T', 'C', 'G']), np.array([0., -10., 0.]), a1 = np.array([1., 0., 0.]), a3 = np.array([0., 1., 0.]) ) ) print(f"Nucleotide #0: {nucleotides[0]}") print("Creating more nucleotides...\n") for i in range(n): nucleotides.append(get_5p(nucleotides[-1], base=random.choice(['A', 'T', 'C', 'G']))) strand = Strand(nucleotides=nucleotides) print(f"Strand: {strand}") system = System(np.array([20., 20., 20.])) system.add_strand(strand) # Add Strand 2 - complementary ssDNA -> dsDNA if double: nucleotides = [] for nucleotide in strand.nucleotides[::-1]: nucleotides.append(get_across(nucleotide)) # for i in range(10): # nucleotides.append(get_5p(nucleotides[-1])) strand = Strand(nucleotides=nucleotides) print(f"Adding double: {strand}") system.add_strand(strand) system.write_oxDNA('local') return
def with_strands(N : int = 10): a1 = np.array([1., 0., 0.]) start = np.array([0., 0., 0.]) + a1 * 0.6 direction = np.array([0., 1., 0.]) strands = generate_helix( n=N, start_position=start, direction=direction, a1=a1, initial_rotation=0.0, ) new_position = start + (N) * 0.39 * direction new_direction = np.array([0.0, 1.0, 1.0]) / 2 ** 0.5 new_a1 = np.array([0.0, -1.0, 1.0]) / 2 ** 0.5 #print(np.dot(new_a1, new_direction)) rotation = -0.06 #rotation = 0.0 strands += generate_helix( n=N, start_position=new_position, direction=new_direction, a1=new_a1, initial_rotation=rotation, ) strand = Strand(strands[0].nucleotides + strands[1].nucleotides) return [strand]
def generate_system( n : int, double_strand_length : int, single_strand_length : int, box : float = None, ) -> System: """ Generates an oxDNA system containing a single piece of DNA which has blocks of equal size of double-stranded portions and single-stranded portions. Parameters: n - number of nucleotides e.g. 100 fraction_ds - fraction of double-strand DNA e.g. 0.5 Returns: system - oxDNA system """ # initialise system to comply with minimum image convention if not box: box = 2. * n * FENE_EPS print(f'Creating simulation system with box size: {box}') system = System(np.array([box, box, box])) # create a list of strands, our main strand which we will use # and our complementary strand strands = generate_helix(n, double=True) # make a copy of the complementary strand and remove it # from the main list of strands second_strand = strands[1].copy() strands = strands[:1] # calculate how many portions there should be portion_size = double_strand_length + single_strand_length portions = n // portion_size print(f'Creating {portions} portions of total size: {portion_size}') # iterate over all portions, adding a new complementary # strand to the list of strands we will use for i in range(portions): # take the nucleotides from each portion and # create a new strand for each double-stranded part # of the portion start = portion_size * i end = start + double_strand_length nucleotides = second_strand.nucleotides[start:end] new_strand = Strand(nucleotides=nucleotides) strands.append(new_strand) # finally add the strands to the system and return # the system system.add_strands(strands) return system
def add_strand(self, addition: Strand, index: int = None): """ Method to add strand(s) to the system Parameters: addition - accepted as Strand objects or a List of Strands index (default = None) - Strand will append to current system, otherwise Strand inserted at location given """ try: assert isinstance(addition, Strand) except TypeError: raise TypeError(f"addition must be Strand but is {type(addition)}") try: if index == None: self._strands.append(addition.copy()) else: self._strands.insert(index, addition.copy()) except TypeError: raise TypeError("Index must an an integer")
def test_strand(): strand = Strand([ Nucleotide( "A", np.array([1.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([2.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([3.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([4.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([5.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([6.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), ]) print(strand.lammps) return
def main(length=16, n_strands=10): # generate a strand strands = [] strand = generate_helix(n=length, enforce_180=True)[0] strands.append(strand.copy()) for i in range(n_strands - 1): last_nuc = strands[-1].nucleotides[-1] direction = -last_nuc._a3 a1 = -last_nuc._a1 # ensure the backbone position is FENE_LENGTH away from # the backbone position of the previous nucleotide start = last_nuc.pos_back + (FENE_LENGTH - POS_BACK) * a1 # generate strand above that's going in opposite direction strand = generate_helix( n=length, start_position=start, direction=direction, a1=a1, enforce_180=True, )[0] strands.append(strand) # using the two previously created strands create a new strand that # we will add to the system nucleotides = [] for strand in strands: nucleotides += strand.nucleotides strand = Strand(nucleotides=nucleotides) # create system and add the final completed strand system = System(np.array([50., 50., 50.])) system.add_strand(strand) system.write_oxDNA('turns_18nt') return system
def generate_helix( n: int = None, sequence: str = None, start_position: np.ndarray = np.array([0., 0., 0.]), direction: np.ndarray = np.array([0., 1., 0.]), a1: np.ndarray = np.array([1., 0., 0.]), initial_rotation: float = None, double: bool = False, enforce_180: bool = False, bp_per_turn: float = 10.45, ) -> List[Strand]: # handle sequence/n arguments if sequence and n: if len(sequence) != n: difference = len(sequence) - n # sequence longer than n if difference > 0: sequence = sequence[:n] # n longer than sequence else: sequence += ''.join([ random.choice(['A', 'T', 'C', 'G']) for i in range(-difference) ]) elif sequence: n = len(sequence) elif n: sequence = ''.join( [random.choice(['A', 'T', 'C', 'G']) for i in range(n)]) else: raise TypeError( 'Please provide either the number of base-pairs or a sequence') # handle a1/angle arguments if initial_rotation: a1 = get_rotation_matrix(direction, initial_rotation) if enforce_180: half_turns = round_to_multiple(n / bp_per_turn, 0.5, 1) angle = np.radians(360 * half_turns / (n - 1)) else: angle = 0.626 # initialise strand list strands = [] # create main strand strand = Strand() strand.add_nucleotide( Nucleotide(sequence[0], start_position, a1=a1, a3=direction)) for base in sequence[1:]: strand.add_nucleotide(strand.nucleotides[-1].make_5p(base, angle)) # add to strand list which will be returned strands.append(strand.copy()) # create across strand if double: strand = Strand() # iterate over nucleotides from original strand but in reverse for nucleotide in strands[0].nucleotides[::-1]: strand.add_nucleotide(nucleotide.make_across()) strands.append(strand.copy()) return strands
def test_System(): system = System(np.array([50.0, 50.0, 50.0])) strand_1 = Strand( [ Nucleotide( "A", np.array([1.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([2.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([3.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([4.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([5.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "A", np.array([6.0, 0.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), ] ) strand_2 = Strand( [ Nucleotide( "T", np.array([1.0, 2.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "T", np.array([2.0, 2.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "T", np.array([3.0, 2.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "T", np.array([4.0, 2.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "T", np.array([5.0, 2.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), Nucleotide( "T", np.array([6.0, 2.0, 0.0]), np.array([1.0, 0.0, 0.0]), np.array([0, 0.0, 1.0]), ), ] ) system.add_strands([strand_1, strand_2]) assert isinstance(system, System) assert system.E_tot == 0.0 assert len(system.dataframe.count()) == 10 assert len(system.configuration.count()) == 5 assert len(system.topology.count()) == 4 assert len(system.strands) == 2 assert len(system.nucleotides) == 12 system.strands[0].sequence = "AGAGAG" system.add_strand(system.strands[0].copy()) system.strands[0].sequence = "TATATA" assert len(system.strands) == 3 assert len(system.nucleotides) == 18 assert system.strands[0].sequence == "TATATA" assert system.strands[2].sequence == "AGAGAG" strand_3 = system.strands[1].copy() strand_3.sequence = "CCCGGG" strand_4 = strand_3.copy() strand_4.sequence = "AAATTT" system.add_strands({ 0 : strand_3, 1 : strand_4 }) assert len(system.strands) == 5 assert len(system.nucleotides) == 30 print(system.strands) assert system.strands[0].sequence == "CCCGGG" assert system.strands[1].sequence == "AAATTT" assert system.strands[2].sequence == "TATATA" print(system) print(system.dataframe) # system.write_oxDNA() return