def visualize(self, show_ports=False, shader='lambert',
drawing_type='ball and stick', camera_type='perspective',
element_properties=None):
"""Visualize the Compound using imolecule. """
json_mol = self._to_json(show_ports)
imolecule.draw(json_mol, format='json', shader=shader,
drawing_type=drawing_type, camera_type=camera_type,
element_properties=element_properties)
def draw(self, method: str = 'imolecule', **kwargs: Any) -> None:
bond = self.bondmatrix(1.3)
if method == 'imolecule':
import imolecule # type: ignore
obj = {
'atoms': [{
'element': atom.specie,
'location': atom.coord.tolist()
} for atom in self],
'bonds': [{
'atoms': [i, j],
'order': 1
} for i in range(len(self)) for j in range(i) if bond[i, j]]
}
imolecule.draw(obj, 'json', **kwargs)
def visualize_Molecules(molecules, angstroms=False):
'''
Returns a 3D representation of a list of molecules
INPUTS:
molecules --> a list of Pyquante molecules
angstroms --> a True or False value indicating if it is in angstroms.
'''
renders = []
for mol in molecules:
mol = mol.copy()
# convert angstrom to bohr
if angstroms:
for atom in mol:
coords = [a / ang2bohr for a in atom.pos()]
atom.update_coords(coords)
# create as xyz string
xyz_str = mol.as_string()
renders.append(
imolecule.draw(xyz_str,
size=(200, 150),
format='xyz',
shader="phong",
display_html=False))
columns = ('<div class="col-xs-6 col-sm-3">{}</div>'.format(r)
for r in renders)
return display(HTML('<div class="row">{}</div>'.format("".join(columns))))
def visualize(self, show_ports=False):
"""Visualize the Compound using nglview. """
if run_from_ipython():
structure = self.to_trajectory(show_ports)
return nglview.show_mdtraj(structure)
else:
try:
"""Visualize the Compound using imolecule. """
import imolecule
json_mol = self._to_json(show_ports)
imolecule.draw(json_mol, format='json', shader='lambert',
drawing_type='ball and stick', camera_type='perspective',
element_properties=None)
except ImportError:
raise RuntimeError('Visualization is only supported in Jupyter '
'Notebooks.')
def renderPolymorphs(polymorphs, shader='basic'):
""" Displays geometries of all polymorphs in the current generation """
renders = (imolecule.draw(p.gzmat_string, format='gzmat', size=(200, 150),
shader=shader, display_html=False, resizeable=False) \
for p in polymorphs)
columns = ('<div class="col-xs-6 col-sm-3">{}</div>'.format(r)
for r in renders)
display(HTML('<div class="row">{}</div>'.format("".join(columns))))
def _repr_html_(self):
"""For IPython notebook, renders 3D pybel.Molecule webGL objects."""
# Returning None defers to _repr_svg_
if not ipython_3d:
return None
try:
import imolecule
except ImportError:
raise ImportError("Cannot import 3D rendering. Please install " "with `pip install imolecule`.")
return imolecule.draw(self.clone, format="pybel", display_html=False)
def visualize(self, show_ports=False):
"""Visualize the Compound using nglview. """
nglview = import_('nglview')
if run_from_ipython():
structure = self.to_trajectory(show_ports)
return nglview.show_mdtraj(structure)
else:
try:
"""Visualize the Compound using imolecule. """
import imolecule
json_mol = self._to_json(show_ports)
imolecule.draw(json_mol,
format='json',
shader='lambert',
drawing_type='ball and stick',
camera_type='perspective',
element_properties=None)
except ImportError:
raise RuntimeError(
'Visualization is only supported in Jupyter '
'Notebooks.')
def _repr_html_(self):
"""For IPython notebook, renders 3D pybel.Molecule webGL objects."""
# Returning None defers to _repr_svg_
if not ipython_3d:
return None
try:
import imolecule
except ImportError:
raise ImportError("Cannot import 3D rendering. Please install "
"with `pip install imolecule`.")
return imolecule.draw(self.clone, format="pybel", display_html=False)
def _toJSON(mol):
"""For IPython notebook, renders 3D webGL objects."""
if not ipython_3d or not mol.GetNumConformers():
return None
try:
import imolecule
except ImportError:
raise ImportError("Cannot import 3D rendering. Please install "
"with `pip install imolecule`.")
conf = mol.GetConformer()
if not conf.Is3D():
return None
mol = Chem.Mol(mol)
try:
Chem.Kekulize(mol)
except Exception:
mol = Chem.Mol(mol)
size = molSize_3d
# center the molecule:
atomps = numpy.array(
[list(conf.GetAtomPosition(x)) for x in range(mol.GetNumAtoms())])
avgP = numpy.average(atomps, 0)
atomps -= avgP
# Convert the relevant parts of the molecule into JSON for rendering
atoms = [{
"element": atom.GetSymbol(),
"location": list(atomps[atom.GetIdx()])
} for atom in mol.GetAtoms()]
bonds = [{
"atoms": [bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx()],
"order": int(bond.GetBondTypeAsDouble())
} for bond in mol.GetBonds()]
mol = {"atoms": atoms, "bonds": bonds}
return imolecule.draw({
"atoms": atoms,
"bonds": bonds
},
format="json",
size=molSize_3d,
drawing_type=drawing_type_3d,
camera_type=camera_type_3d,
shader=shader_3d,
display_html=False)
def visualize_Mol(molecule, angstroms=True):
'''
Returns a 3D representation of a molecule
INPUTS:
molecule --> a Pyquante molecule
angstroms --> a True or False value indicating if it is in angstroms.
'''
mol = molecule.copy()
# convert angstrom to bohr
if angstroms:
for atom in mol:
coords = [a / ang2bohr for a in atom.pos()]
atom.update_coords(coords)
# create as xyz string
xyz_str = mol.as_string()
return imolecule.draw(xyz_str, format='xyz', shader="phong")
def renderGeneration(self, generation_number=-1, shader='lambert'):
""" Displays geometries of all polymorphs in the current generation """
if generation_number > self.current_generation_number:
raise ValueError(
f"Generation {generation_number} does not exist (yet)")
if generation_number == -1:
generation = self.current_generation
else:
generation = self.population_timeline[generation_number]
renders = (imolecule.draw(p.gzmat_string, format='gzmat', size=(200, 150),
shader=shader, display_html=False, resizeable=False) \
for p in generation.values())
columns = ('<div class="col-xs-6 col-sm-3">{}</div>'.format(r)
for r in renders)
display(HTML('<div class="row">{}</div>'.format("".join(columns))))
def _toJSON(mol):
"""For IPython notebook, renders 3D webGL objects."""
if not ipython_3d or not mol.GetNumConformers():
return None
try:
import imolecule
except ImportError:
raise ImportError("Cannot import 3D rendering. Please install "
"with `pip install imolecule`.")
conf = mol.GetConformer()
if not conf.Is3D():
return None
mol = Chem.Mol(mol)
try:
Chem.Kekulize(mol)
except:
mol = Chem.Mol(mol)
size = molSize_3d
# center the molecule:
atomps = numpy.array([list(conf.GetAtomPosition(x))
for x in range(mol.GetNumAtoms())])
avgP = numpy.average(atomps, 0)
atomps -= avgP
# Convert the relevant parts of the molecule into JSON for rendering
atoms = [{"element": atom.GetSymbol(),
"location": list(atomps[atom.GetIdx()])}
for atom in mol.GetAtoms()]
bonds = [{"atoms": [bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx()],
"order": int(bond.GetBondTypeAsDouble())}
for bond in mol.GetBonds()]
mol = {"atoms": atoms, "bonds": bonds}
return imolecule.draw({"atoms": atoms, "bonds": bonds}, format="json",
size=molSize_3d, drawing_type=drawing_type_3d,
camera_type=camera_type_3d, shader=shader_3d,
display_html=False)
def viewms(objs, molSize=(160, 160), nmr=6):
if not isinstance(objs, (tuple, list)):
objs = [objs]
# convert to a file format recognizable by imolecule, i.e., sdf
ms = []
for obj in objs:
typ = type(obj)
if typ is Chem.rdchem.Mol:
ms.append(Chem.MolToMolBlock(obj))
elif typ is str: #oechem.OEGraphMol:
if os.path.exists(obj):
assert obj[-3:] in ['sdf', 'mol'
], '#ERROR: file format not supported'
ms.append(''.join(open(obj).readlines()))
else:
print(' ** assume smiles string ')
ms.append(Chem.MolToMolBlock(Chem.MolFromSmiles(obj)))
if len(ms) == 1:
return [imol.draw(ms[0], 'sdf', size=molSize)]
else:
return draw_imol.html(ms, 'sdf', size=molSize, nmr=nmr)
def draw(self, method='imolecule', **kwargs):
if method == 'imolecule':
import imolecule
imolecule.draw(self.to_json(), 'json', **kwargs)
def html(ms, fmt, size=(240, 240), nmr=6):
renders = (imol.draw(m, fmt, size=size, display_html=False)
for m in ms)
columns = ('<div class="col-xs-8 col-sm-4">{}</div>'.format(r)
for r in renders)
return HTML('<div class="row">{}</div>'.format("".join(columns)))
import imolecule
from IPython.display import display, HTML
carbons = ("c1{}c1".format("c" * i) for i in range(3, 5))
renderer = imolecule.draw(next(carbons), size=(200, 150), shader='lambert', display_html=False)
def visualize(smiles):
imolecule.draw(smiles)
def draw(self, method='imolecule', **kwargs):
if method == 'imolecule':
import imolecule
imolecule.draw(self.to_json(), 'json', **kwargs)
def fig_Structure(execution):
pdbFile = execution.read("PDBview", raw=True)
return imolecule.draw(pdbFile[7:])