63d8db941c87501296c0e8c73c7871541455571a,prody/dynamics/functions.py,,calcENM,#,411

Before Change

    else:
        trim = str(trim).lower().strip()

    if trim == "trim" and select is not None:
        if isinstance(select, AtomSubset):
            atoms = select
        else:
            atoms = atoms.select(str(select))
    
    enm = None
    if model == "anm":
        anm = ANM(title)
        anm.buildHessian(atoms, gamma=gamma, **kwargs)

After Change

                enm, atoms = reduceModel(enm, atoms, select)
            enm.calcModes(n_modes=n_modes, zeros=zeros, turbo=turbo)
        elif trim == "trim":
            if isinstance(select, np.ndarray):
                enm = trimModelByMask(enm, select)
                atoms = select
            else:
                enm, atoms = trimModel(enm, atoms, select)
            enm.calcModes(n_modes=n_modes, zeros=zeros, turbo=turbo)
        else:
            raise ValueError("trim can only be "trim", "reduce", or "slice"")
    

Instances