molsysmt.thirds.nglview package#
Submodules#
molsysmt.thirds.nglview.add_arrows module#
- molsysmt.thirds.nglview.add_arrows.add_arrows(view, origin=None, end=None, vectors=None, color='#808080', radius='0.2 angstroms')[source]#
Adding arrows to a view.
A list of arrows can be added to an NGL view (NGLWidget).
- Parameters:
view (nglview.NGLWidget) – A view of the molecular system as an nglview.NGLWidget native object.
coordinates (Quantity (value:numpy.ndarray, dimensionality:['L']=1)) – Positions of the points of origin for the set of arrows. A quantity with length dimensions is required ([‘L’]=1), the value must be a numpy ndarray with shape [n_arrows, 3] (n_arrows is the number of arrows to be added).
arrows (Quantity (value:numpy.ndarray, dimensionality:['L']=1)) – Vectors to be added as arrows. A quantity with length dimensions is required ([‘L’]=1), the value must be a numpy ndarray with shape [n_arrows, 3] (n_arrows is the number of arrows to be added).
color (list, tuple, string default='#808080') – HEX or RGB color code of the arrows.
radius (Quantity (value:float, dimensionality:['L']=1), default='0.2 angstroms') – Radius of the arrows.
- Returns:
The method modifies an nglview.NGLWidget object to add a list of arrows.
- Return type:
None
Examples
>>> import molsysmt as msm >>> from molsysmt import pyunitwizard as puw >>> import numpy as np >>> molecular_system = msm.convert('181L', selection='molecule_type=="protein"') >>> coordinates = msm.get(molecular_system, element='atom', selection='atom_name=="CA"', coordinates=True) >>> vectors = puw.quantity(np.ones([coordinates.shape[0],3]), 'angstroms') >>> view = msm.view(molecular_system) >>> msm.thirds.add_arrows(view, origin=coordinates, vectors=arrows) >>> view
See also
Notes
Have a look to the `YYY`_.
molsysmt.thirds.nglview.add_contacts module#
- molsysmt.thirds.nglview.add_contacts.add_contacts(view, selection=None, center_of_atoms=False, weights=None, structure_indices='all', selection_2=None, center_of_atoms_2=False, weights_2=None, structure_indices_2=None, threshold=None, pbc=False, atom_pairs=None, color='#808080', color_2=None, radius='0.1 angstroms', color_values=None, min_color_value=None, mid_color_value=None, max_color_value=None, color_values_scale='linear', colormap='bwr', color_values_2=None, min_color_value_2=None, mid_color_value_2=None, max_color_value_2=None, color_values_scale_2=None, colormap_2=None, syntax='MolSysMT', skip_digestion=False)[source]#
molsysmt.thirds.nglview.add_cylinders module#
- molsysmt.thirds.nglview.add_cylinders.add_cylinders(view, bottom=None, top=None, vectors=None, color='#808080', color_2=None, radius='0.1 angstroms', color_values=None, min_color_value=None, mid_color_value=None, max_color_value=None, color_values_scale='linear', colormap='bwr', color_values_2=None, min_color_value_2=None, mid_color_value_2=None, max_color_value_2=None, color_values_scale_2=None, colormap_2=None, skip_digestion=False)[source]#
Adding cylinders to a view.
Cylinders can be added to an NGL view (NGLWidget).
- Parameters:
view (nglview.NGLWidget) – A view of the molecular system as an nglview.NGLWidget native object.
start (Quantity (value:numpy.ndarray, dimensionality:['L']=1)) – Positions of the origin points for the set of cylinders. A quantity with length dimensions is required ([‘L’]=1), the value must be a numpy ndarray with shape [n_cylinders, 3] (n_cylinders is the number of arrows to be added).
end (Quantity (value:numpy.ndarray, dimensionality:['L']=1)) – Positions of the end points for the set of cylinders. A quantity with length dimensions is required ([‘L’]=1), the value must be a numpy ndarray with shape [n_cylinders, 3] (n_cylinders is the number of arrows to be added).
color (list, tuple, string default='#808080') – HEX or RGB color code of the first half of the cylinder.
color2 (list, tuple, string default='#808080') – HEX or RGB color code of the first half of the cylinder.
radius (Quantity (value:float, dimensionality:['L']=1), default='0.2 angstroms') – Radius of the cylinder.
- Returns:
The method modifies an nglview.NGLWidget object to add a list of arrows.
- Return type:
None
Examples
>>> import molsysmt as msm >>> from molsysmt import pyunitwizard as puw >>> import nglview as nv >>> view = nv.NGLWidget() >>> start = puw.quantity([[0,0,0], [0,5,0]], 'angstroms') >>> end = puw.quantity([[10,0,0], [0,10,0]], 'angstroms') >>> msm.thirds.nglview.add_cylinders(view, start, end, color='#ff0000', color_2='#0000ff', radius='0.2 angstroms') >>> view
See also
Notes
Have a look to the `YYY`_.
molsysmt.thirds.nglview.add_hbonds module#
molsysmt.thirds.nglview.clear module#
molsysmt.thirds.nglview.load_html_in_jupyter_notebook module#
molsysmt.thirds.nglview.patching_nglview module#
molsysmt.thirds.nglview.set_color module#
molsysmt.thirds.nglview.set_color_by_value module#
- molsysmt.thirds.nglview.set_color_by_value.set_color_by_value(view, values, element='group', selection='all', cmap='bwr_r', min_value=None, mid_value=None, max_value=None, representation='cartoon', syntax='MolSysMT')[source]#
Adding a new representation colored by a color scale.
A new representation can be added to an NGL view (NGLWidget) with elements colored by a list of values and a color map.
- Parameters:
view (nglview.NGLWidget) – A view of the molecular system as an nglview.NGLWidget native object.
values (list, tuple or numpy.ndarray) – List of values or magnitudes corresponding to each element to be encoded as a color.
element (str, default='group') – Element to be colored according to its value in the input argument values.
selection (str, list, tuple or numpy.ndarray, default='all') – Selection over which this method applies. The selection can be given by a list, tuple or numpy array of integers (0-based), or by means of a string following any of the selection syntax parsable by MolSysMT (see:
molsysmt.select()).cmap (str, matplotlib.colors.LinearSegmentedColormap, default:'rwb') – The name of the matplotlib colormap or a LineraSegemendedColormap native Python object of the MatPlotLib library.
min_value (float, Quantity, default='None') – Minimum value of the color scale. By default (‘None’), the minimum of the input argument values is taken.
mid_value (float, Quantity, default='None') – Middle value of the color scale. By default (‘None’), the center between of the range [min_value, max_value] is taken.
max_value (float, Quantity, default='None') – Maximum value of the color scale. By default (‘None’), the maximum of the input argument values is taken.
representation (str, default='cartoon') – Representation type supported by NGLView: ‘cartoon’, ‘licorice’, ‘surface’, ‘ball_and_stick’…
syntax (str, default='MolSysMT') – Syntaxis used in the argument selection (in case it is a string). The current options supported by MolSysMt can be found in section XXX (see:
molsysmt.basic.select()).
- Returns:
The method modifies an nglview.NGLWidget object including the new representation.
- Return type:
None
Examples
>>> import molsysmt as msm >>> from matplotlib.pyplot import colormaps >>> molecular_system = msm.convert('181L', selection='molecule_type=="protein"') >>> charge_residues = msm.physchem.charge(molecular_system, element='group', definition='physical_pH7')  >>> view = msm.view(molecular_system) >>> view.clear() >>> msm.thirds.nglview.color_by_value(view, charge_residues) >>> viewSee also
Notes
Have a look to the `YYY`_.