smc_lammps.generate.structures.smc package¶

Submodules¶

smc_lammps.generate.structures.smc.smc module¶

class smc_lammps.generate.structures.smc.smc.SMC(use_rigid_hinge: bool, pos: SMC_Pos, t_arms_heads: AtomType, t_kleisin: AtomType, t_shield: AtomType, t_hinge: AtomType, t_atp: AtomType, t_upper_site: AtomType, t_middle_site: AtomType, t_lower_site: AtomType, t_ref_site: AtomType, t_side_site: AtomType, k_bond: float, k_hinge: float, max_bond_length: float, k_elbow: float, k_arm: float, k_align_site: float, k_fold: float, k_asymmetry: float, bridge_width: float, arm_length: float, _hinge_radius: float, arms_angle_ATP: float, folding_angle_ATP: float, folding_angle_APO: float, elbow_attraction: float, elbow_spacing: float)¶

Bases: object

Stores an SMC with its bonds, pair interactions, etc.

__init__(use_rigid_hinge: bool, pos: SMC_Pos, t_arms_heads: AtomType, t_kleisin: AtomType, t_shield: AtomType, t_hinge: AtomType, t_atp: AtomType, t_upper_site: AtomType, t_middle_site: AtomType, t_lower_site: AtomType, t_ref_site: AtomType, t_side_site: AtomType, k_bond: float, k_hinge: float, max_bond_length: float, k_elbow: float, k_arm: float, k_align_site: float, k_fold: float, k_asymmetry: float, bridge_width: float, arm_length: float, _hinge_radius: float, arms_angle_ATP: float, folding_angle_ATP: float, folding_angle_APO: float, elbow_attraction: float, elbow_spacing: float) → None¶

add_repel_interactions(pair_inter: PairWise, eps: float, sigma: float, r_cut: float) → None¶

arm_length: float¶: Length of one arm (nm).

arms_angle_ATP: float¶: Angle between arms in the ATP state (degrees).

bridge_width: float¶: ATP bridge width (nm).

elbow_attraction: float¶

elbow_spacing: float¶

folding_angle_APO: float¶

folding_angle_ATP: float¶

get_angles() → list[BAI]¶

get_bonds(hinge_opening: float | None = None) → list[BAI]¶

get_groups() → list[AtomGroup]¶

get_impropers() → list[BAI]¶

get_molecule_ids() → list[int]¶

get_repulsive_groups() → list[AtomGroup]¶: Returns a list of groups that should have a repulsive LJ interaction with other (inert) beads such as obstacles.

has_side_site() → bool¶

has_toroidal_hinge() → bool¶

property hinge_radius: float¶

k_align_site: float¶: Improper strength used to maintain site orientation, should be stiff (pN * nm / rad^2).

k_arm: float¶: Angular strength of arms relative to bridge, typically stiff (pN * nm / rad^2).

k_asymmetry: float¶: Improper strength used to induce asymmetric folding, should be stiff (pN * nm / rad^2).

k_bond: float¶: Bond strength for general connections (e.g. arms connected at elbow) (pN/nm = mN/m).

k_elbow: float¶: Angular strength at elbows, typically soft to allow bending (pN * nm / rad^2).

k_fold: float¶: Improper folding strength of Kleisin relative to arms, should be stiff (pN * nm / rad^2).

k_hinge: float¶: Hinge bond strength (pN/nm = 1e-3 N/m).

max_bond_length: float¶: Max bond length for connected parts (nm).

pos: SMC_Pos¶: The positions of the beads comprising the SMC.

t_arms_heads: AtomType¶: Type of arms.

t_atp: AtomType¶: Type of ATP bridge.

t_hinge: AtomType¶: Type of hinge.

t_kleisin: AtomType¶: Type of Kleisin.

t_lower_site: AtomType¶: Type of attractive atoms at lower (Kleisin) site.

t_middle_site: AtomType¶: Type of attractive atoms at middle (bridge) site.

t_ref_site: AtomType¶: Type of extra reference bead near middle site (used for asymmetric folding).

t_shield: AtomType¶: Type of repusilve shield atoms in interaction sites.

t_side_site: AtomType¶: Type of attractive atoms at optional side site (when strand swapping is desired).

t_upper_site: AtomType¶: Type of attractive atoms at upper (hinge) site.

use_rigid_hinge: bool¶: If True, the hinge is one rigid molecule. Otherwise, the two parts of the hinge are connected by bonds.

smc_lammps.generate.structures.smc.smc_creator module¶

class smc_lammps.generate.structures.smc.smc_creator.SMC_Creator(SMC_spacing: float, upper_site_h: float, upper_site_v: float, middle_site_h: float, middle_site_v: float, lower_site_h: float, lower_site_v: float, arm_length: float, bridge_width: float, use_toroidal_hinge: bool, hinge_radius: float, hinge_opening: float, add_side_site: bool, kleisin_radius: float, folding_angle_APO: float, seed: int = 5894302289572, small_noise: float = 1e-05)¶

Bases: object

Generates the positions of all SMC beads.

The final SMC is oriented towards the +x direction (movement direction), is oriented in the +y direction the bottom-to-top (Kleisin to hinge). The z direction is symmetric.

The interactions are added in smc_lammps.generate.structures.smc.smc.SMC.

SMC_spacing: float¶: The spacing between coarse-grained beads (nm).

__init__(SMC_spacing: float, upper_site_h: float, upper_site_v: float, middle_site_h: float, middle_site_v: float, lower_site_h: float, lower_site_v: float, arm_length: float, bridge_width: float, use_toroidal_hinge: bool, hinge_radius: float, hinge_opening: float, add_side_site: bool, kleisin_radius: float, folding_angle_APO: float, seed: int = 5894302289572, small_noise: float = 1e-05) → None¶

add_side_site: bool¶: Whether to add an additional binding site on the lower right arm or not. This is used for strand swapping.

arm_length: float¶: Length of one SMC arm (nm). This includes both (lower and upper) segments connected by the elbow.

bridge_width: float¶: Width of the ATP bridge, which is the distance between the bottom-most arm beads (nm).

folding_angle_APO: float¶: The angle between the arms and Kleisin in the APO state (degrees).

get_arms() → tuple[ndarray[tuple[Any, ...], dtype[float32]], ndarray[tuple[Any, ...], dtype[float32]], ndarray[tuple[Any, ...], dtype[float32]], ndarray[tuple[Any, ...], dtype[float32]]]¶

Generates the positions of the two arms in four segments.

Each of the two arms is split between the upper (u, between elbow and hinge), and the lower (d, between ATP bridge and elbow) segments. This makes 4 total segments, which are all straight lines.

Returns:: Tuple of (lower left dl, upper left ul, upper right ur, lower right dr).

get_bridge() → ndarray[tuple[Any, ...], dtype[float32]]¶

Generates the positions of the ATP bridge.

The bridge is a single straight segment.

Returns:: Positions of the bridge.

get_heads_kleisin() → ndarray[tuple[Any, ...], dtype[float32]]¶

Generates the positions of the Kleisin compartment.

The Kleisin is a segment of a circle, with a cut-out at the bridge location.

Returns:: Positions of the Kleisin ring.
Raises:: ValueError – The kleisin radius is incompatible with the bridge width.

get_interaction_sites(lower_site_points_down: bool) → tuple[ndarray[tuple[Any, ...], dtype[float32]], ndarray[tuple[Any, ...], dtype[float32]], ndarray[tuple[Any, ...], dtype[float32]]]¶

get_mass_per_atom(total_mass: float) → float¶

Returns the mass that should be assigned to each atom.

Parameters:: total_mass – The total mass of the SMC.
Returns:: Mass of one bead.

get_smc(lower_site_points_down: bool, extra_rotation=None) → SMC_Pos¶

get_toroidal_hinge() → ndarray[tuple[Any, ...], dtype[float32]]¶

hinge_opening: float¶

hinge_radius: float¶

kleisin_radius: float¶: The radius of the (semi-circular) Kleisin (nm).

lower_site_h: float¶: Horizontal distance between bottom binding sites (units bead spacing).

lower_site_v: float¶: Distance of bottom binding sites from kleisin (units of bead spacing).

middle_site_h: float¶: Horizontal distance between middle binding sites (units bead spacing).

middle_site_v: float¶: Vertical distance of middle binding sites from bridge (units of bead spacing).

seed: int = 5894302289572¶: A random seed. This is used when applying random shifts between the different segments to prevent exact overlap which can cause issues in LAMMPS.

static shielded_site_template(n_inner_beads: int, n_outer_beads_per_inner_bead: int, inner_spacing: float, outer_spacing: float) → ndarray[tuple[Any, ...], dtype[float32]]¶

Generates a line of beads surrounded by a protective shell/shield.

This is used to allow binding from a specific direction, where the inner beads are attractive and the outer beads repulsive.

Parameters:

n_inner_beads – Number of inner beads to generate.
n_outer_beads_per_inner_bead – Number of outer beads surrounding each inner bead in the main shell.
inner_spacing – The distance between neighboring inner beads.
outer_spacing – The distance between an inner bead and the nearest outer beads surrounding it.

Returns:

Positions of the beads in order of (inner beads, shell beads, shell left, shell right).

small_noise: float = 1e-05¶: Amount to shift overlapping segments by (units of bead spacing). See seed for more information.

static transpose_rotate_transpose(rotation, *arrays: ndarray[tuple[Any, ...], dtype[float32]]) → tuple[ndarray[tuple[Any, ...], dtype[float32]], ...]¶

Rotates the points in an (N, 3) array.

Parameters:

rotation – Rotation matrix.
arrays – Arrays to apply rotation to.

Returns:

Arrays of rotated 3D points.

upper_site_h: float¶: Horizontal distance between top binding sites (units bead spacing).

upper_site_v: float¶: Vertical distance of top binding sites from hinge (units of bead spacing).

use_toroidal_hinge: bool¶: Whether to use the toroidal hinge or the normal hinge. The toroidal hinge is used for tethered obstacle bypass.

class smc_lammps.generate.structures.smc.smc_creator.SMC_Pos(r_arm_dl: ndarray[tuple[Any, ...], dtype[float32]], r_arm_ul: ndarray[tuple[Any, ...], dtype[float32]], r_arm_ur: ndarray[tuple[Any, ...], dtype[float32]], r_arm_dr: ndarray[tuple[Any, ...], dtype[float32]], r_ATP: ndarray[tuple[Any, ...], dtype[float32]], r_kleisin: ndarray[tuple[Any, ...], dtype[float32]], r_upper_site: ndarray[tuple[Any, ...], dtype[float32]], r_middle_site: ndarray[tuple[Any, ...], dtype[float32]], r_lower_site: ndarray[tuple[Any, ...], dtype[float32]], r_hinge: ndarray[tuple[Any, ...], dtype[float32]], r_side_site: ndarray[tuple[Any, ...], dtype[float32]])¶

Bases: object

Stores all the positions of the beads of an SMC.

Note

Unused segments are stored as empty arrays.

__init__(r_arm_dl: ndarray[tuple[Any, ...], dtype[float32]], r_arm_ul: ndarray[tuple[Any, ...], dtype[float32]], r_arm_ur: ndarray[tuple[Any, ...], dtype[float32]], r_arm_dr: ndarray[tuple[Any, ...], dtype[float32]], r_ATP: ndarray[tuple[Any, ...], dtype[float32]], r_kleisin: ndarray[tuple[Any, ...], dtype[float32]], r_upper_site: ndarray[tuple[Any, ...], dtype[float32]], r_middle_site: ndarray[tuple[Any, ...], dtype[float32]], r_lower_site: ndarray[tuple[Any, ...], dtype[float32]], r_hinge: ndarray[tuple[Any, ...], dtype[float32]], r_side_site: ndarray[tuple[Any, ...], dtype[float32]]) → None¶

apply(func) → None¶: Update the object inplace by applying a function to every field

iter() → list[Any]¶: Returns a list of all fields

map(func) → list[Any]¶: Apply a function to every field and return the resulting list

r_ATP: ndarray[tuple[Any, ...], dtype[float32]]¶: ATP bridge.

r_arm_dl: ndarray[tuple[Any, ...], dtype[float32]]¶: Lower left arm.

r_arm_dr: ndarray[tuple[Any, ...], dtype[float32]]¶: Lower left arm.

r_arm_ul: ndarray[tuple[Any, ...], dtype[float32]]¶: Upper right arm.

r_arm_ur: ndarray[tuple[Any, ...], dtype[float32]]¶: Lower right arm.

r_hinge: ndarray[tuple[Any, ...], dtype[float32]]¶: TODO

r_kleisin: ndarray[tuple[Any, ...], dtype[float32]]¶: Kleisin ring.

r_lower_site: ndarray[tuple[Any, ...], dtype[float32]]¶: TODO

r_middle_site: ndarray[tuple[Any, ...], dtype[float32]]¶: TODO

r_side_site: ndarray[tuple[Any, ...], dtype[float32]]¶: TODO

r_upper_site: ndarray[tuple[Any, ...], dtype[float32]]¶: TODO