def test_add_struture_then_trajectory():
view = nv.show_structure_file(get_fn('tz2.pdb'))
view.loaded = True
traj = pt.datafiles.load_trpcage()
view.add_trajectory(traj)
view.frame = 3
coords = view.coordinates_dict[1].copy()
aa_eq(coords, traj[3].xyz)
view.loaded = False
view.add_trajectory(traj)
def demo(*args, **kwargs):
'''
Examples
--------
>>> import nglview as nv
>>> view = nv.demo()
>>> view # doctest: +SKIP
'''
from nglview import show_structure_file
return show_structure_file(datafiles.PDB, *args, **kwargs)
def show(*args, camera='perspective', move='auto', div=5, distance=(-10, -10), axis=0, caps=True, save=None, group=True, rotate=None):
"""
Show given structure(s) using nglview
- save: file_path -> save pdb file to given path
- camera: 'perspective' / 'orthographic'
- move: 'auto' / 'single' / None -> separate multiple structures equally distant from each other
- distance: tuple (x, y) -> separation distance
- axis: 0 / 1 / 2 -> separation direction (0:x, 1:y, 2:z)
- caps: bool -> capitalize atom names so they show true colors in nglview+
- group: bool -> group molecules in pdb file (to show bonds properly in nglview)
- rotate: 0 / 1 / 2 -> rotate 90 degrees in (0:x, 1:y, 2:z) axis (view in xy plane)
"""
if move is 'auto':
translation_vectors = arrange_structure_positions(len(args), div=div, distance=distance)
elif move is 'single':
translation_vectors = axis_translation(len(args), distance=distance[0], axis=axis)
else:
translation_vectors = [[0, 0, 0]] * len(args)
atom_names = []
atom_coors = []
group_numbers = []
for mol_index, (molecule, vec) in enumerate(zip(args, translation_vectors), start=1):
atom_names += molecule.atom_names
coordinates = molecule.atom_coors
if rotate is not None:
coordinates = rotate_90(coordinates, axis=rotate)
coordinates = translate(coordinates, vector=vec)
atom_coors += coordinates
group_numbers += [mol_index] * len(molecule.atom_names)
# nglview require atom names in all caps to color them properly
if caps:
atom_names = [name.upper() for name in atom_names]
# nglview requires molecules to be grouped separately to show proper bonding
if not group:
group_numbers = [1] * len(atom_names)
temp_pdb_file = tempfile.NamedTemporaryFile(mode='w+', suffix='.pdb')
write_pdb(temp_pdb_file, atom_names, atom_coors, group=group_numbers)
view = nglview.show_structure_file(temp_pdb_file.name)
view.camera = camera
temp_pdb_file.close()
if save is not None:
with open(save, 'w') as save_file:
write_pdb(save_file, atom_names, atom_coors, group=group_numbers)
return view
def view_structure(self, only_chains=None, opacity=1.0, recolor=False, gui=False):
"""Use NGLviewer to display a structure in a Jupyter notebook
Args:
only_chains (str, list): Chain ID or IDs to display
opacity (float): Opacity of the structure
recolor (bool): If structure should be cleaned and recolored to silver
gui (bool): If the NGLview GUI should show up
Returns:
NGLviewer object
"""
# TODO: show_structure_file does not work for MMTF files - need to check for that and load accordingly
if ssbio.utils.is_ipynb():
import nglview as nv
else:
raise EnvironmentError('Unable to display structure - not running in a Jupyter notebook environment')
if not self.structure_file:
raise ValueError("Structure file not loaded")
only_chains = ssbio.utils.force_list(only_chains)
to_show_chains = '( '
for c in only_chains:
to_show_chains += ':{} or'.format(c)
to_show_chains = to_show_chains.strip(' or ')
to_show_chains += ' )'
if self.file_type == 'mmtf' or self.file_type == 'mmtf.gz':
view = nv.NGLWidget()
view.add_component(self.structure_path)
else:
view = nv.show_structure_file(self.structure_path, gui=gui)
if recolor:
view.clear_representations()
if only_chains:
view.add_cartoon(selection='{} and (not hydrogen)'.format(to_show_chains), color='silver', opacity=opacity)
else:
view.add_cartoon(selection='protein', color='silver', opacity=opacity)
elif only_chains:
view.clear_representations()
view.add_cartoon(selection='{} and (not hydrogen)'.format(to_show_chains), color='silver', opacity=opacity)
return view
def test_show_structure_file():
view = nv.show_structure_file(nv.datafiles.PDB)
def test_show_structure_file():
view = nv.show_structure_file(nv.datafiles.PDB)
def view_ball_stick(structfile):
"""Return a nglview object to view structfile as a ball+stick model"""
v = nv.show_structure_file(structfile)
v.representations = [{'type': 'ball+stick', 'params': {}}]
v.parameters = {'backgroundColor': 'black'}
return v
def demo(*args, **kwargs):
from nglview import show_structure_file
return show_structure_file(datafiles.PDB, *args, **kwargs)
def colored_struct(
*,
pdb,
prop_df,
chain_col='chain',
site_col='site',
color_col='color',
representation='cartoon',
highlight_col=None,
highlight_representation='spacefill',
show_other=False,
other_color='#FFFFFF',
orientation=None,
):
"""Create widget showing a colored structure.
Parameters
------------
pdb : str
Existing PDB file, or ID to be downloaded from PDB.
prop_df : pandas DataFrame
Data on sites to show and how to color them. You are responsible for
ensuring that chaing / site labels are consistent with those in `pdb`,
no automatic checks of this are performed.
chain_col: str
Column in `prop_df` with PDB chain ID.
site_col : str
Column in `prop_df` with PDB site numbers.
color_col : str
Column in `prop_df` with color for each site.
representation : str or list
Protein representation (e.g., 'cartoon', 'surface', 'spacefill',
or other `nglview <https://github.com/arose/nglview>`_ representation;
or a list of such representations.
highlight_col : str or `None`
Optional column of boolean values in `prop_df` indicating
sites to also draw in `highlight_representation`.
highlight_representation : str
Additional representation for sites specified in `highlight_col`.
show_other : `False` or str
Show selections **not** listed as sites in `prop_df`? If so, specify
those selections. Can be 'all', 'protein', or other selection string
(`see here <https://github.com/arose/ngl/tree/master/doc/usage>`_).
other_color : str
Color for any sites not in `prop_df` but shown via `show_other`.
orientation : `None` or list of 16 numbers
Orientation to show the structure, can be obtained via the
`_camera_orientation` property of a structure widget
(https://github.com/arose/nglview/issues/785#issuecomment-487409212).
Returns
--------
nglview.widget.NGLWidget
The widget can be shown in a Jupyter notebook.
"""
# error checking on `prop_df` and its columns
cols = []
for colname, col, optional in [
('color_col', color_col, False),
('site_col', site_col, False),
('chain_col', chain_col, False),
('highlight_col', highlight_col, True),
]:
if col is None:
if not optional:
raise ValueError(f"must specify `{colname}`")
elif col not in prop_df.columns:
raise ValueError(f"`prop_df` lacks `{colname}` of {col}")
elif col in cols:
raise ValueError(f"duplicate column names of {col}")
else:
cols.append(col)
prop_df = (prop_df[cols].drop_duplicates())
if len(prop_df) != len(prop_df.groupby([chain_col, site_col])):
raise ValueError('Inconsistent duplicated rows for some sites in '
'`prop_df`. For each chain and site, entries must '
f"be the same for all rows in these columns: {cols}")
# get PDB into a widget; use `default_representation=False` as here:
# https://github.com/arose/nglview/issues/802#issuecomment-492760630
if os.path.isfile(pdb):
w = nglview.show_structure_file(
pdb,
default_representation=False,
)
else:
try:
w = nglview.show_pdbid(
pdb,
default_representation=False,
)
except HTTPError: # noqa: F821
raise ValueError(f"`pdb` {pdb} does not specify an existing "
'PDB file or an ID that can be downloaded')
# Set up color schemes as here:
# https://github.com/arose/nglview/pull/755
# For details on selection strings, see here:
# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
colorscheme = []
selectionlist = []
highlight_colorscheme = []
highlight_selectionlist = []
for row in prop_df.itertuples():
color = getattr(row, color_col)
sel_str = f":{getattr(row, chain_col)} and {getattr(row, site_col)}"
selectionlist.append(f"({sel_str})")
colorscheme.append([color, sel_str])
if highlight_col and getattr(row, highlight_col):
highlight_selectionlist.append(f"({sel_str})")
highlight_colorscheme.append([color, sel_str])
colorscheme.append([other_color, '*'])
selection = ', '.join(selectionlist)
if show_other:
selection = f"({show_other}) or ({selection})"
# uniquely label color schemes as here:
# https://github.com/arose/nglview/issues/802#issuecomment-492501051
colorscheme = nglview.color._ColorScheme(
colorscheme,
label=f"colorscheme_{secrets.token_hex(10)}",
)
highlight_selection = ', '.join(highlight_selectionlist)
highlight_colorscheme = nglview.color._ColorScheme(
highlight_colorscheme,
label=f"colorscheme_{secrets.token_hex(10)}",
)
# color and style widget; set assembly to BU1 (biological unit 1) as here:
# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
w.clear_representations()
if isinstance(representation, str):
representation = [representation]
for r in representation:
w.add_representation(
r,
selection=selection,
color=colorscheme,
assembly='BU1',
)
if highlight_representation and highlight_selection:
w.add_representation(
highlight_representation,
selection=highlight_selection,
color=highlight_colorscheme,
assembly='BU1',
)
if orientation:
if len(orientation) != 16:
raise ValueError('`orientation` not list of 16 numbers')
w._set_camera_orientation(orientation)
return w
def view(self):
linker_path = self.export()
return nglview.show_structure_file(linker_path)
def show(*args,
camera='perspective',
move='auto',
div=5,
distance=(-10, -10),
axis=0,
caps=True,
save=None,
group=True,
rotate=None):
"""
Show given structure(s) using nglview
- save: file_path -> save pdb file to given path
- camera: 'perspective' / 'orthographic'
- move: 'auto' / 'single' / None -> separate multiple structures equally distant from each other
- distance: tuple (x, y) -> separation distance
- axis: 0 / 1 / 2 -> separation direction (0:x, 1:y, 2:z)
- caps: bool -> capitalize atom names so they show true colors in nglview+
- group: bool -> group molecules in pdb file (to show bonds properly in nglview)
- rotate: 0 / 1 / 2 -> rotate 90 degrees in (0:x, 1:y, 2:z) axis (view in xy plane)
"""
if move is 'auto':
translation_vectors = arrange_structure_positions(len(args),
div=div,
distance=distance)
elif move is 'single':
translation_vectors = axis_translation(len(args),
distance=distance[0],
axis=axis)
else:
translation_vectors = [[0, 0, 0]] * len(args)
atom_names = []
atom_coors = []
group_numbers = []
for mol_index, (molecule, vec) in enumerate(zip(args, translation_vectors),
start=1):
atom_names += molecule.atom_names
coordinates = molecule.atom_coors
if rotate is not None:
coordinates = rotate_90(coordinates, axis=rotate)
coordinates = translate(coordinates, vector=vec)
atom_coors += coordinates
group_numbers += [mol_index] * len(molecule.atom_names)
# nglview require atom names in all caps to color them properly
if caps:
atom_names = [name.upper() for name in atom_names]
# nglview requires molecules to be grouped separately to show proper bonding
if not group:
group_numbers = [1] * len(atom_names)
temp_pdb_file = tempfile.NamedTemporaryFile(mode='w+', suffix='.pdb')
write_pdb(temp_pdb_file, atom_names, atom_coors, group=group_numbers)
view = nglview.show_structure_file(temp_pdb_file.name)
view.camera = camera
temp_pdb_file.close()
if save is not None:
with open(save, 'w') as save_file:
write_pdb(save_file, atom_names, atom_coors, group=group_numbers)
return view
