def test_show_rdkit():
rdkit_mol = Chem.AddHs(Chem.MolFromSmiles('COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
AllChem.EmbedMultipleConfs(rdkit_mol, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
view = nv.show_rdkit(rdkit_mol, parmed=False)
assert not view._trajlist
view = nv.show_rdkit(rdkit_mol, parmed=True)
assert view._trajlist
view = nv.RdkitStructure(rdkit_mol)
def test_show_rdkit():
rdkit_mol = Chem.AddHs(
Chem.MolFromSmiles(
'COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
AllChem.EmbedMultipleConfs(
rdkit_mol, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
view = nv.show_rdkit(rdkit_mol, parmed=False)
assert not view._trajlist
view = nv.show_rdkit(rdkit_mol, parmed=True)
assert view._trajlist
view = nv.RdkitStructure(rdkit_mol)
def show_molecule_3D_structure(mol):
"""
Given an RDKit mol object, return an NGLView 3D viewer
"""
mol.RemoveAllConformers()
ids = AllChem.EmbedMultipleConfs(mol, numConfs=1)
return nv.show_rdkit(mol)
def test_show_rdkit():
import rdkit.Chem as Chem
rdkit_mol = Chem.AddHs(
Chem.MolFromSmiles(
'COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
AllChem.EmbedMultipleConfs(rdkit_mol,
useExpTorsionAnglePrefs=True,
useBasicKnowledge=True)
# FIXME: create test_adaptor.py?
# Test RdkitStructure
structure = nglview.RdkitStructure(rdkit_mol)
assert "HETATM" in structure.get_structure_string()
structure = nglview.RdkitStructure(rdkit_mol, ext="sdf")
assert "RDKit 3D" in structure.get_structure_string()
structure2 = nglview.RdkitStructure(rdkit_mol, ext="sdf", conf_id=0)
assert "RDKit 3D" in structure2.get_structure_string()
assert structure.get_structure_string() == structure2.get_structure_string(
)
structure3 = nglview.RdkitStructure(rdkit_mol, ext="sdf", conf_id=1)
assert "RDKit 3D" in structure3.get_structure_string()
assert structure.get_structure_string() != structure3.get_structure_string(
)
# Test show_rdkit
with patch.object(Chem, 'MolToPDBBlock') as mock_MolToPDBBlock,\
patch.object(Chem, 'MolToMolBlock') as mock_MolToMolBlock:
nglview.show_rdkit(rdkit_mol, fmt='sdf', conf_id=1)
assert mock_MolToMolBlock.called
assert not mock_MolToPDBBlock.called
assert mock_MolToMolBlock.call_args_list[-1][-1] == {'confId': 1}
with patch.object(Chem, 'MolToPDBBlock') as mock_MolToPDBBlock,\
patch.object(Chem, 'MolToMolBlock') as mock_MolToMolBlock:
nglview.show_rdkit(rdkit_mol)
assert not mock_MolToMolBlock.called
assert mock_MolToPDBBlock.called
assert mock_MolToPDBBlock.call_args_list[-1][-1] == {'confId': -1}
def conformers(
mol: Chem.rdchem.Mol,
conf_id: int = -1,
n_confs: Union[int, List[int]] = None,
align_conf: bool = True,
n_cols: int = 3,
sync_views: bool = True,
remove_hs: bool = True,
width: str = "auto",
):
"""Visualize the conformer(s) of a molecule.
Args:
mol: a molecule.
conf_id: The ID of the conformer to show. -1 shows
the first conformer. Only works if `n_confs` is None.
n_confs: Can be a number of conformers
to shows or a list of conformer indices. When None, only the first
conformer is displayed. When -1, show all conformers.
align_conf: Whether to align conformers together.
n_cols: Number of columns. Defaults to 3.
sync_views: Wether to sync the multiple views.
remove_hs: Wether to remove the hydrogens of the conformers.
width: The width of the returned view. Defaults to "auto".
"""
widgets = _get_ipywidgets()
nv = _get_nglview()
if mol.GetNumConformers() == 0:
raise ValueError(
"The molecule has 0 conformers. You can generate conformers with `dm.conformers.generate(mol)`."
)
# Clone the molecule
mol = copy.deepcopy(mol)
if remove_hs:
mol = Chem.RemoveHs(mol) # type: ignore
else:
mol = Chem.AddHs(mol) # type: ignore
if n_confs is None:
return nv.show_rdkit(mol, conf_id=conf_id)
# If n_confs is int, convert to list of conformer IDs
if n_confs == -1:
n_confs = [conf.GetId() for conf in mol.GetConformers()]
elif isinstance(n_confs, int):
if n_confs > mol.GetNumConformers():
n_confs = mol.GetNumConformers()
n_confs = list(range(n_confs)) # type: ignore
if align_conf:
rdMolAlign.AlignMolConformers(mol, confIds=n_confs)
# Get number of rows
n_rows = len(n_confs) // n_cols
n_rows += 1 if (len(n_confs) % n_cols) > 0 else 0
# Create a grid
grid = widgets.GridspecLayout(n_rows, n_cols) # type: ignore
# Create and add views to the grid.
widget_coords = itertools.product(range(n_rows), range(n_cols))
views = []
for i, (conf_id, (x, y)) in enumerate(zip(n_confs, widget_coords)):
view = nv.show_rdkit(mol, conf_id=conf_id)
view.layout.width = width
view.layout.align_self = "stretch"
grid[x, y] = view
views.append(view)
# Sync views
if sync_views:
for view in views:
view._set_sync_camera(views)
return grid
def view(self, **kwargs):
self.minimize()
view = nv.show_rdkit(self.rdmol, **kwargs)
return view
xs, vs, particle_distribution = simulation(net, g=g.heterograph)
# In[43]:
import nglview as nv
from rdkit.Geometry import Point3D
from rdkit import Chem
from rdkit.Chem import AllChem
conf_idx = 1
mol = g.mol.to_rdkit()
AllChem.EmbedMolecule(mol)
conf = mol.GetConformer()
xs, vs, particle_distribution = simulation(net, g=g.heterograph)
x = xs[-1]
for idx_atom in range(mol.GetNumAtoms()):
conf.SetAtomPosition(
idx_atom,
Point3D(
float(x[idx_atom, conf_idx, 0]),
float(x[idx_atom, conf_idx, 1]),
float(x[idx_atom, conf_idx, 2]),
))
nv.show_rdkit(mol)
# In[ ]: