def test_load_rdkit_mol(self):
from rdkit import Chem
m1 = Chem.MolFromSmiles('C1=CC=CN=C1')
parm = pmd.load_rdkit(m1)
self.assertEqual([atom.name for atom in parm.atoms],
['C1', 'C2', 'C3', 'C4', 'N1', 'C5'])
self.assertEqual(parm.residues[0].name, 'UNL')
def test_load_rdkit_mol(self):
from rdkit import Chem
m1 = Chem.MolFromSmiles('C1=CC=CN=C1')
parm = pmd.load_rdkit(m1)
self.assertEqual([atom.name for atom in parm.atoms],
['C1', 'C2', 'C3', 'C4', 'N1', 'C5'])
self.assertEqual(parm.residues[0].name, 'UNL')
def show_rdkit(rdkit_mol, **kwargs):
'''Show rdkit's Mol.
Parameters
----------
rdkit_mol : rdkit.Chem.rdchem.Mol
kwargs : additional keyword argument
Examples
--------
>>> import nglview as nv
>>> from rdkit import Chem # doctest: +SKIP
... from rdkit.Chem import AllChem
... m = Chem.AddHs(Chem.MolFromSmiles('COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
... _ = AllChem.EmbedMultipleConfs(m, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
... view = nv.show_rdkit(m)
... view # doctest: +SKIP
>>> # add component m2
>>> # create file-like object
>>> from nglview.show import StringIO
>>> m2 = Chem.AddHs(Chem.MolFromSmiles('N[C@H](C)C(=O)O')) # doctest: +SKIP
... fh = StringIO(Chem.MolToPDBBlock(m2))
... view.add_component(fh, ext='pdb')
>>> # load as trajectory, need to have ParmEd
>>> view = nv.show_rdkit(m, parmed=True) # doctest: +SKIP
'''
from rdkit import Chem
fh = StringIO(Chem.MolToPDBBlock(rdkit_mol))
try:
use_parmed = kwargs.pop("parmed")
except KeyError:
use_parmed = False
if not use_parmed:
view = NGLWidget()
view.add_component(fh, ext='pdb', **kwargs)
return view
else:
import parmed as pmd
parm = pmd.load_rdkit(rdkit_mol)
parm_nv = ParmEdTrajectory(parm)
# set option for ParmEd
parm_nv.only_save_1st_model = False
# set option for NGL
# wait for: https://github.com/arose/ngl/issues/126
# to be fixed in NGLView
# parm_nv.params = dict(firstModelOnly=True)
return NGLWidget(parm_nv, **kwargs)
def show_rdkit(rdkit_mol, **kwargs):
'''Show rdkit's Mol.
Parameters
----------
rdkit_mol : rdkit.Chem.rdchem.Mol
kwargs : additional keyword argument
Examples
--------
>>> import nglview as nv
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> m = Chem.AddHs(Chem.MolFromSmiles('COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
>>> AllChem.EmbedMultipleConfs(m, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
>>> view = nv.show_rdkit(m)
>>> view
>>> # add component m2
>>> # create file-like object
>>> fh = StringIO(Chem.MolToPDBBlock(m2))
>>> view.add_component(fh, ext='pdb')
>>> # load as trajectory, need to have ParmEd
>>> view = nv.show_rdkit(m, parmed=True)
'''
from rdkit import Chem
fh = StringIO(Chem.MolToPDBBlock(rdkit_mol))
try:
use_parmed = kwargs.pop("parmed")
except KeyError:
use_parmed = False
if not use_parmed:
view = NGLWidget()
view.add_component(fh, ext='pdb', **kwargs)
return view
else:
import parmed as pmd
parm = pmd.load_rdkit(rdkit_mol)
parm_nv = ParmEdTrajectory(parm)
# set option for ParmEd
parm_nv.only_save_1st_model = False
# set option for NGL
# wait for: https://github.com/arose/ngl/issues/126
# to be fixed in NGLView
# parm_nv.params = dict(firstModelOnly=True)
return NGLWidget(parm_nv, **kwargs)