helixmc.pose.HelixPose¶
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class
helixmc.pose.
HelixPose
(params, frame0=None, compute_tw_wr=False)¶ Pose object storing the state info of the helix.
Parameters: params : ndarray of (N,6)
List of all bp-step parameters. A N bp helix has (N-1)*6 parameters.
frame0 : ndarray of (3,3), optional
The frame of the first base-pair, default is np.eye(3) (overlaps with global coordinate).
compute_tw_wr : bool, optional
Whether to compute twist and writhe (Fuller writhe) during system update. Should be set to True for link-constrained simulations.
Attributes
compute_tw_wr (bool) See Parameters section above. writhe_exact (float) Exact writhe of the helix. writhe_fuller (float) Fuller’s writhe of the helix. twist (float) Supercoiling twist of the helix. coord_terminal (1d array of (3)) Coordinate (x,y,z) of the center of last base-pair. frame_terminal (ndarray of (3,3)) Coordinate frame of the last base-pair. Each column represent the cooresponding axis (frame[:,0] is the x-axis etc.) z_terminal (float) Z-component of coord_terminal link_fuller (float) Link of the helix computed using Fuller’s approximation. link_exact (float) Exact link of the helix. n_bp (int) Number of base-pairs in the helix. coord (ndarray of (N,3)) Coordinates of all base-pairs in the helix (n_bp entries). dr (ndarray of (N,3)) Delta-r vectors of the entire helix (n_bp-1 entries). frames (ndarray of (N,3,3)) Frames of all base-pairs in the helix (n_bp entries). params (ndarray of (N,6)) List of all bp-step parameters in the helix (n_bp-1 entries). rb_vec (ndarray of (N,3)) Ribbon vectors of all base-pairs in the helix (n_bp entries). -
__init__
(params, frame0=None, compute_tw_wr=False)¶
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accept_update
()¶ Accept a trial update.
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copy
()¶ Return a copy of the current pose.
Returns: pose_copy : HelixPose
Copy of the current pose.
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classmethod
from_file
(input_file, compute_tw_wr=False)¶ Load pose data from an input file.
Parameters: input_file : str
Input file (.npz) that stores the helix pose data.
compute_tw_wr : bool, optional
Whether to compute twist and writhe (Fuller writhe) during system update. Should be set to True for link-constrained simulations.
Raises: ValueError
If n_bp < 2 in the input file.
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guess_twist_center
()¶ Attempt to guess the twist center value. Use circmean of the current twists.
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plot_centerline
(color='k', show=True, fig_ax=None)¶ Plot the helix center-line using matplotlib + mplot3d.
Parameters: color : str, optional
Colors of the centerline (matplotlib color codes).
show : bool, optional
Whether to invoke pyplot.show() method at the end.
fig_ax : mplot3d.Axes3D, optional
Input mplot3d.Axes3D object. For ploting multiple helix on the same graph.
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plot_helix
(rb_width=5.0, color='kb', show=True, fig_ax=None)¶ Plot the helix using matplotlib + mplot3d.
Parameters: rb_width : float, optional
Width of the helix ribbon in Å.
color : str, optional
Colors of the plot (matplotlib color codes), first letter for backbond and second letter for base-pair.
show : bool, optional
Whether to invoke pyplot.show() method at the end.
fig_ax : mplot3d.Axes3D, optional
Input mplot3d.Axes3D object. For ploting multiple helix on the same graph.
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reject_update
()¶ Reject a trial update.
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set_params
(params, frame0=None)¶ Set the bp-step params of the HelixPose.
Parameters: params : ndarray of (N,6), optional
List of all bp-step parameters. Number of params should equal to n_bp - 1.
frame0 : ndarray of (3,3)
The frame of the first base-pair, default is np.eye(3).
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update
(i, params, o=None, R=None)¶ Full update of the i-th bp-step.
Parameters: i : int
The index of the bp-step to be updated.
params : ndarray
Input base-pair step parameter set.
o : ndarray, optional
Coordiantes for the bp-centers of the 2nd base-pair.
R : ndarray, optional
Rotational matrix for the transformation.
Raises: ValueError
If i < 0 or i >= n_bp.
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update_trial
(i, params, o=None, R=None)¶ Trial update of the i-th bp-step. Following accept_update or reject_update is required.
Parameters: i : int
The index of the bp-step to be updated.
params : ndarray
Input base-pair step parameter set.
o : ndarray, optional
Coordiantes for the bp-centers of the 2nd base-pair.
R : ndarray, optional
Rotational matrix for the transformation.
Raises: ValueError
If i < 0 or i >= n_bp.
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write2disk
(filename)¶ Write the current pose to disk.
Parameters: filename : str
Name of the output file.
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