smc_lammps.generate.structures.dna package¶

Submodules¶

smc_lammps.generate.structures.dna.dna module¶

class smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety(dna_strands: list[Polymer], dna_parameters: DnaParameters, tether: Tether, dna_safety_belt_index: int)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, tether: Tether, dna_safety_belt_index: int)¶

add_interactions(**kwargs)¶

get_all_groups(**kwargs)¶

get_angles(**kwargs)¶

get_bonds(**kwargs)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → AdvancedObstacleSafety¶

get_post_process_parameters(**kwargs)¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.DnaConfiguration(dna_strands: list[Polymer], dna_parameters: DnaParameters)¶

Bases: object

class PostProcessParameters(end_points: 'list[AtomIdentifier]', freeze_indices: 'list[AtomIdentifier]', stretching_forces_array: 'dict[tuple[float, float, float], list[AtomIdentifier]]', dna_indices_list: 'dict[int, list[tuple[AtomIdentifier, AtomIdentifier]]]')¶

Bases: object

__init__(end_points: list[tuple[AtomGroup, int]], freeze_indices: list[tuple[AtomGroup, int]], stretching_forces_array: dict[tuple[float, float, float], list[tuple[AtomGroup, int]]], dna_indices_list: dict[int, list[tuple[tuple[AtomGroup, int], tuple[AtomGroup, int]]]]) → None¶

dna_indices_list: dict[int, list[tuple[tuple[AtomGroup, int], tuple[AtomGroup, int]]]]¶

end_points: list[tuple[AtomGroup, int]]¶

freeze_indices: list[tuple[AtomGroup, int]]¶

stretching_forces_array: dict[tuple[float, float, float], list[tuple[AtomGroup, int]]]¶

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters) → None¶

add_bead_to_dna(bead_type: AtomType, mol_index: int, strand_index: int, dna_id: int, bond: None | BAI_Type, angle: None | BAI_Type, bead_size: float) → tuple[AtomGroup, int]¶

add_interactions(pair_inter: PairWise) → None¶

property all_dna_groups: list[AtomGroup]¶

change_dna_stiffness(strand_index: int, from_id: int, to_id: int, bond: BAI_Type, angle: BAI_Type) → None¶

dna_indices_list_get_all_dna(strand_index: int) → list[tuple[tuple[AtomGroup, int], tuple[AtomGroup, int]]]¶

dna_indices_list_get_dna_from_to(strand_index: int, from_ratio: float, to_ratio: float) → list[tuple[tuple[AtomGroup, int], tuple[AtomGroup, int]]]¶

dna_indices_list_get_dna_to(strand_index: int, ratio: float) → list[tuple[tuple[AtomGroup, int], tuple[AtomGroup, int]]]¶

get_all_groups() → list[AtomGroup]¶

get_angles() → list[BAI]¶

get_bonds() → list[BAI]¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → DnaConfiguration¶

get_post_process_parameters() → PostProcessParameters¶

get_stopper_ids() → list[StrandId]¶

map_to_atom_id(strnd: StrandId | tuple[AtomGroup, int]) → tuple[AtomGroup, int]¶

classmethod set_parameters(par: Parameters, inter_par: InteractionParameters) → None¶

classmethod set_smc(smc: SMC) → None¶

static str_to_config(string: str) → DnaConfiguration¶

static strand_concat(lst: Sequence[tuple[int, int]]) → list[tuple[int, int]]¶

update_tether_bond(old_id: tuple[AtomGroup, int], bead: None | tuple[AtomGroup, int]) → None¶

class smc_lammps.generate.structures.dna.dna.DnaParameters(nDNA: 'int', DNA_bond_length: 'float', DNA_mass: 'float', type: 'AtomType', mol_DNA: 'int', bond: 'BAI_Type', angle: 'BAI_Type', ssangle: 'BAI_Type')¶

Bases: object

DNA_bond_length: float¶

DNA_mass: float¶

__init__(nDNA: int, DNA_bond_length: float, DNA_mass: float, type: AtomType, mol_DNA: int, bond: BAI_Type, angle: BAI_Type, ssangle: BAI_Type) → None¶

angle: BAI_Type¶

bond: BAI_Type¶

create_dna_polymer(dna_positions: Sequence[ndarray[tuple[Any, ...], dtype[float32]]]) → Polymer¶

mol_DNA: int¶

nDNA: int¶

ssangle: BAI_Type¶

type: AtomType¶

class smc_lammps.generate.structures.dna.dna.Doubled(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_center)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_center)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → Doubled¶

get_post_process_parameters() → PostProcessParameters¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.Folded(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_center)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_center)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → Folded¶

get_post_process_parameters() → PostProcessParameters¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.InteractionParameters(sigma_DNA_DNA: 'float', epsilon_DNA_DNA: 'float', rcut_DNA_DNA: 'float', k_bond_DNA_DNA: 'float', sigma_SMC_DNA: 'float', epsilon_SMC_DNA: 'float', rcut_SMC_DNA: 'float', sigma_upper_site_DNA: 'float', rcut_lower_site_DNA: 'float', epsilon_upper_site_DNA: 'float')¶

Bases: object

__init__(sigma_DNA_DNA: float, epsilon_DNA_DNA: float, rcut_DNA_DNA: float, k_bond_DNA_DNA: float, sigma_SMC_DNA: float, epsilon_SMC_DNA: float, rcut_SMC_DNA: float, sigma_upper_site_DNA: float, rcut_lower_site_DNA: float, epsilon_upper_site_DNA: float) → None¶

epsilon_DNA_DNA: float¶

epsilon_SMC_DNA: float¶

epsilon_upper_site_DNA: float¶

k_bond_DNA_DNA: float¶

rcut_DNA_DNA: float¶

rcut_SMC_DNA: float¶

rcut_lower_site_DNA: float¶

sigma_DNA_DNA: float¶

sigma_SMC_DNA: float¶

sigma_upper_site_DNA: float¶

class smc_lammps.generate.structures.dna.dna.Line(dna_strands: list[Polymer], dna_parameters: DnaParameters)¶

Bases: DnaConfiguration

Straight line of DNA

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → Line¶

get_post_process_parameters() → PostProcessParameters¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.Obstacle(dna_strands: list[Polymer], dna_parameters: DnaParameters, tether: Tether, dna_start_index: int)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, tether: Tether, dna_start_index: int)¶

add_interactions(**kwargs)¶

get_all_groups(**kwargs)¶

get_angles(**kwargs)¶

get_bonds(**kwargs)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → Obstacle¶

get_post_process_parameters(**kwargs)¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.ObstacleSafety(dna_strands: list[Polymer], dna_parameters: DnaParameters, tether: Tether, dna_safety_belt_index: int)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, tether: Tether, dna_safety_belt_index: int)¶

add_interactions(**kwargs)¶

get_all_groups(**kwargs)¶

get_angles(**kwargs)¶

get_bonds(**kwargs)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → ObstacleSafety¶

get_post_process_parameters(**kwargs)¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.RightAngle(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_center)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_center)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → RightAngle¶

get_post_process_parameters() → PostProcessParameters¶

get_stopper_ids() → list[StrandId]¶

class smc_lammps.generate.structures.dna.dna.Safety(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_safety_belt_index)¶

Bases: DnaConfiguration

__init__(dna_strands: list[Polymer], dna_parameters: DnaParameters, dna_safety_belt_index)¶

classmethod get_dna_config(dna_parameters: DnaParameters, r_lower_site, par) → Safety¶

get_post_process_parameters() → PostProcessParameters¶

get_stopper_ids() → list[StrandId]¶

type smc_lammps.generate.structures.dna.dna.StrandId = tuple[int, int]¶

class smc_lammps.generate.structures.dna.dna.Tether(polymer: 'Polymer', dna_tether_id: 'StrandId | AtomIdentifier', obstacle: 'Tether.Obstacle', bonds: 'list[BAI]', angles: 'list[BAI]')¶

Bases: object

class Gold(group: AtomGroup, radius: float, cut: float, tether_bond: BAI)¶

Bases: Obstacle

__init__(group: AtomGroup, radius: float, cut: float, tether_bond: BAI) → None¶

add_interactions(pair_inter: PairWise, dna_type: AtomType, ip: InteractionParameters, kBT: float, smc: SMC) → None¶

get_all_groups() → list[AtomGroup]¶

move(vector: ndarray[tuple[Any, ...], dtype[float32]]) → None¶

class Obstacle¶

Bases: object

add_interactions(pair_inter: PairWise, dna_type: AtomType, ip: InteractionParameters, kBT: float, smc: SMC) → None¶

get_all_groups() → list[AtomGroup]¶

move(vector: ndarray[tuple[Any, ...], dtype[float32]]) → None¶

class Wall(y_pos: float)¶

Bases: Obstacle

__init__(y_pos: float) → None¶

get_all_groups() → list[AtomGroup]¶

move(vector: ndarray[tuple[Any, ...], dtype[float32]]) → None¶

__init__(polymer: Polymer, dna_tether_id: StrandId | tuple[AtomGroup, int], obstacle: Obstacle, bonds: list[BAI], angles: list[BAI]) → None¶

add_interactions(pair_inter: PairWise, ip: InteractionParameters, dna_type: AtomType, smc: SMC, kBT: float) → None¶

add_tether_interactions(tether_type: AtomType, factor: float, pair_inter: PairWise, ip: InteractionParameters, dna_type: AtomType, smc: SMC, kBT: float) → None¶

angles: list[BAI]¶

bonds: list[BAI]¶

classmethod create_tether(dna_tether_id: StrandId, tether_length: int, bond_length: float, mass: float, bond_type: BAI_Type, angle_type: BAI_Type, obstacle: Obstacle) → Tether¶

dna_tether_id: StrandId | tuple[AtomGroup, int]¶

get_all_groups() → list[AtomGroup]¶

get_angles() → list[BAI]¶

get_bonds(bond_type: BAI_Type, dna_config: DnaConfiguration) → list[BAI]¶

static get_gold_mass(radius: float) → float¶: radius in nanometers, returns attograms

classmethod get_obstacle(real_obstacle: bool, ip: InteractionParameters, tether_group: AtomGroup) → Obstacle¶

handle_end_points(end_points: list[tuple[AtomGroup, int]]) → None¶

move(vector) → None¶

obstacle: Obstacle¶

polymer: Polymer¶

smc_lammps.generate.structures.dna.dna.class_decorator_factory(old_method)¶

smc_lammps.generate.structures.dna.dna.with_tether(cls)¶

smc_lammps.generate.structures.dna.dna_creator module¶

smc_lammps.generate.structures.dna.dna_creator.check_length(length: int)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates(nDNA: int, DNAbondLength: float, diameter: float, nArcStraight: int)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates_advanced_safety_belt(nDNA: int, DNAbondLength: float)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates_advanced_safety_belt_plus_loop(nDNA: int, DNAbondLength: float)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates_doubled(nDNA: int, DNAbondLength: float, diameter: float)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates_safety_belt(nDNA: int, DNAbondLength: float)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates_straight(nDNA: int, DNAbondLength: float)¶

smc_lammps.generate.structures.dna.dna_creator.get_dna_coordinates_twist(nDNA: int, DNAbondLength: float, diameter: float)¶