How to use the nglview.show_ase function in nglview

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github pyiron / pyiron / pyiron / atomistics / job / atomistic.py View on Github external
def view_structure(self, snapshot=-1, spacefill=True, show_cell=True):
        """

        Args:
            snapshot (int): Snapshot of the trajectory one wants
            spacefill (bool):
            show_cell (bool):

        Returns:
            view: nglview IPython widget

        """
        import nglview

        atoms = self.get_structure(snapshot)
        picture = nglview.show_ase(atoms)
        if spacefill:
            picture.add_spacefill(radius_type="vdw", scale=0.5)
            picture.remove_ball_and_stick()
        else:
            picture.add_ball_and_stick()
        if show_cell:
            if atoms.cell is not None:
                picture.add_unitcell()
        return picture
github pyiron / pyiron / pyiron / atomistics / job / atomistic.py View on Github external
def view_structure(self, snapshot=-1, spacefill=True, show_cell=True):
        """

        Args:
            snapshot (int): Snapshot of the trajectory one wants
            spacefill (bool):
            show_cell (bool):

        Returns:
            view: nglview IPython widget

        """
        import nglview
        atoms = self.get_structure(snapshot)
        picture = nglview.show_ase(atoms)
        if spacefill:
            picture.add_spacefill(radius_type='vdw', scale=0.5)
            picture.remove_ball_and_stick()
        else:
            picture.add_ball_and_stick()
        if show_cell:
            if atoms.cell is not None:
                picture.add_unitcell()
        return picture
github pyiron / pyiron / pyiron / atomistics / structure / atoms.py View on Github external
def plot3d_ase(self, spacefill=True, show_cell=True, camera='perspective', particle_size=0.5, background='white', color_scheme='element', show_axes=True):
        """
        Possible color schemes: 
          " ", "picking", "random", "uniform", "atomindex", "residueindex",
          "chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
          "hydrophobicity", "value", "volume", "occupancy"
        Returns:
        """
        try:  # If the graphical packages are not available, the GUI will not work.
            import nglview
        except ImportError:
            raise ImportError("The package nglview needs to be installed for the plot3d() function!")
        # Always visualize the parent basis
        parent_basis = self.get_parent_basis()
        view = nglview.show_ase(parent_basis)
        if spacefill:
            view.add_spacefill(radius_type='vdw', color_scheme=color_scheme, radius=particle_size)
            # view.add_spacefill(radius=1.0)
            view.remove_ball_and_stick()
        else:
            view.add_ball_and_stick()
        if show_cell:
            if parent_basis.cell is not None:
                view.add_unitcell()
        if show_axes:
            view.shape.add_arrow([-2, -2, -2], [2, -2, -2], [1, 0, 0], 0.5)
            view.shape.add_arrow([-2, -2, -2], [-2, 2, -2], [0, 1, 0], 0.5)
            view.shape.add_arrow([-2, -2, -2], [-2, -2, 2], [0, 0, 1], 0.5)
        if camera!='perspective' and camera!='orthographic':
            print('Only perspective or orthographic is permitted')
            return None
github rosswhitfield / ase / ase / visualize / ngl.py View on Github external
def __init__(self, atoms, xsize=500, ysize=500):
        import nglview
        import nglview.color

        from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox
        self.atoms = atoms
        if isinstance(atoms[0], Atoms):
            # Assume this is a trajectory or struct list
            self.view = nglview.show_asetraj(atoms)
            self.frm = IntSlider(value=0, min=0, max=len(atoms) - 1)
            self.frm.observe(self._update_frame)
            self.struct = atoms[0]
        else:
            # Assume this is just a single structure
            self.view = nglview.show_ase(atoms)
            self.struct = atoms
            self.frm = None

        self.colors = {}
        self.view._remote_call('setSize', target='Widget',
                               args=['%dpx' % (xsize,), '%dpx' % (ysize,)])
        self.view.add_unitcell()
        self.view.add_spacefill()
        self.view.remove_ball_and_stick()
        self.view.camera = 'orthographic'
        self.view.parameters = { "clipDist": 0 }

        self.view.center()

        self.asel = Dropdown(options=['All'] +
                             list(set(self.struct.get_chemical_symbols())),
github pyiron / pyiron / pyiron / atomistics / structure / atoms.py View on Github external
def plot3d_ase(self, spacefill=True, show_cell=True, camera='perspective', particle_size=0.5, background='white', color_scheme='element', show_axes=True):
        """
        Possible color schemes: 
          " ", "picking", "random", "uniform", "atomindex", "residueindex",
          "chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
          "hydrophobicity", "value", "volume", "occupancy"
        Returns:
        """
        try:  # If the graphical packages are not available, the GUI will not work.
            import nglview
        except ImportError:
            raise ImportError("The package nglview needs to be installed for the plot3d() function!")
        # Always visualize the parent basis
        parent_basis = self.get_parent_basis()
        view = nglview.show_ase(parent_basis)
        if spacefill:
            view.add_spacefill(radius_type='vdw', color_scheme=color_scheme, radius=particle_size)
            # view.add_spacefill(radius=1.0)
            view.remove_ball_and_stick()
        else:
            view.add_ball_and_stick()
        if show_cell:
            if parent_basis.cell is not None:
                view.add_unitcell()
        if show_axes:
            view.shape.add_arrow([-2, -2, -2], [2, -2, -2], [1, 0, 0], 0.5)
            view.shape.add_arrow([-2, -2, -2], [-2, 2, -2], [0, 1, 0], 0.5)
            view.shape.add_arrow([-2, -2, -2], [-2, -2, 2], [0, 0, 1], 0.5)
        if camera!='perspective' and camera!='orthographic':
            print('Only perspective or orthographic is permitted')
            return None

nglview

IPython widget to interactively view molecular structures and trajectories.

MIT
Latest version published 27 days ago

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84 / 100
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