Analysis Modules

mdna.nucleic

compute_rigid_parameters(traj, chainids=[0, 1], fit_reference=False)

Compute the rigid base parameters of the DNA structure.

Parameters:

Name	Type	Description	Default
traj	object	MDtraj trajectory containing the DNA structure.	required
chainids	list	List of chain IDs of the DNA structure. Default is [0, 1].	[0, 1]
fit_reference	bool	Fit each base to canonical reference bases before frame extraction. Default is False.	False

Returns:

Name	Type	Description
NucleicFrames	object	Object representing the rigid base parameters of the DNA structure.

Raises:

Type	Description
ValueError	If the traj argument is not provided.

Notes

• The returned NucleicFrames object contains information about the rigid base parameters of the DNA structure, such as the positions and orientations of the base steps.

Example

Compute the rigid base parameters of a DNA structure ```python traj = md.load('dna.pdb') rigid_params = mdna.compute_rigid_parameters(traj, chainids=[0, 1]) ````

Source code in mdna/nucleic.py

def compute_rigid_parameters(traj, chainids=[0,1], fit_reference=False):
    """Compute the rigid base parameters of the DNA structure.

    Args:
        traj (object): MDtraj trajectory containing the DNA structure.
        chainids (list, optional): List of chain IDs of the DNA structure. Default is [0, 1].
        fit_reference (bool, optional): Fit each base to canonical reference bases before
            frame extraction. Default is False.

    Returns:
        NucleicFrames (object): Object representing the rigid base parameters of the DNA structure.

    Raises:
        ValueError: If the traj argument is not provided.

    Notes:
        - The returned NucleicFrames object contains information about the rigid base parameters of the DNA structure, such as the positions and orientations of the base steps.

    Example:
        Compute the rigid base parameters of a DNA structure
        ```python
        traj = md.load('dna.pdb')
        rigid_params = mdna.compute_rigid_parameters(traj, chainids=[0, 1])
        ````
    """
    if traj is None:
        raise ValueError("The traj argument must be provided.")
    return NucleicFrames(traj, chainids, fit_reference=fit_reference)

compute_linking_number(traj, chainids=[0, 1])

Compute the linking number of the DNA structure

Source code in mdna/nucleic.py

def compute_linking_number(traj, chainids=[0,1]):
    """Compute the linking number of the DNA structure"""
    raise NotImplementedError

compute_curvature(traj, chainids=[0, 1])

Compute the curvature of the DNA structure

Source code in mdna/nucleic.py

def compute_curvature(traj, chainids=[0,1]):
    """Compute the curvature of the DNA structure"""
    raise NotImplementedError

compute_groove_width(traj, chainids=[0, 1])

Compute the groove width of the DNA structure

Source code in mdna/nucleic.py

def compute_groove_width(traj, chainids=[0,1]):
    """Compute the groove width of the DNA structure"""
    raise NotImplementedError