a902ddf5be91cb738efb1746847f74bb0f756ae2,prody/dynamics/perturb.py,,calcDynamicCouplingIndex,#Any#Any#Any#Any#,173

Before Change

       *Biophys J.* **2015** 109(6):1273-81.

    
    if not isinstance(prs_matrix, np.ndarray):
        raise TypeError("prs_matrix should be a numpy array")

    if prs_matrix.ndim != 2:
        raise ValueError("prs_matrix should be 2-dimensional")

    if not isinstance(atoms, Atomic):
        raise TypeError("atoms should be an Atomic object")

    if not isinstance(select, (str, Selection)):

After Change

       *Biophys J.* **2015** 109(6):1273-81.

    
    if not isinstance(model, NMA) or not model.is3d():
        raise TypeError("model must be of type ANM or PCA, not {0}"
                        .format(type(model)))

    if not isinstance(atoms, Atomic):
        raise TypeError("atoms should be an Atomic object")

    norm = kwargs.get("norm", False)
    if norm:
        prs_matrix, _, _ = calcPerturbResponse(model, atoms=atoms, **kwargs)
    else:
        prs_matrix = model.getCovariance()

    if not isinstance(select, (str, Selection)):
        raise TypeError("select should be a Selection or selection string")
    
    if not isinstance(func_sel, (str, Selection)):

Instances