本文整理匯總了Python中rdkit.Chem.AllChem.UFFOptimizeMolecule方法的典型用法代碼示例。如果您正苦於以下問題:Python AllChem.UFFOptimizeMolecule方法的具體用法?Python AllChem.UFFOptimizeMolecule怎麽用?Python AllChem.UFFOptimizeMolecule使用的例子?那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類rdkit.Chem.AllChem
的用法示例。
在下文中一共展示了AllChem.UFFOptimizeMolecule方法的6個代碼示例,這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚,您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: generate_structure_from_smiles
# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 別名]
def generate_structure_from_smiles(smiles):
# Generate a 3D structure from smiles
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
status = AllChem.EmbedMolecule(mol)
status = AllChem.UFFOptimizeMolecule(mol)
conformer = mol.GetConformer()
coordinates = conformer.GetPositions()
coordinates = np.array(coordinates)
atoms = get_atoms(mol)
return atoms, coordinates
示例2: _extra_docs
# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 別名]
def _extra_docs(self):
# method: to_smiles
self._to_smiles_core_names = ("rdkit.Chem.MolToSmarts",)
self._to_smiles_core_docs = ("http://rdkit.org/docs/source/rdkit.Chem.inchi.html?highlight=inchi#rdkit.Chem.inchi.MolToInchi",)
# method: to_smarts
self._to_smarts_core_names = ("rdkit.Chem.MolToSmarts",)
self._to_smarts_core_docs = ("http://rdkit.org/docs/source/rdkit.Chem.inchi.html?highlight=inchi#rdkit.Chem.inchi.MolToInchi",)
# method: to_inchi
self._to_inchi_core_names = ("rdkit.Chem.MolToInchi",)
self._to_inchi_core_docs = ("http://rdkit.org/docs/source/rdkit.Chem.inchi.html?highlight=inchi#rdkit.Chem.inchi.MolToInchi",)
# method: hydrogens
self._hydrogens_core_names = ("rdkit.Chem.AddHs","rdkit.Chem.RemoveHs")
self._hydrogens_core_docs = ("http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=addhs#rdkit.Chem.rdmolops.AddHs",
"http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=addhs#rdkit.Chem.rdmolops.RemoveHs")
#
self._to_xyz_core_names = ("rdkit.Chem.AllChem.MMFFOptimizeMolecule","rdkit.Chem.AllChem.UFFOptimizeMolecule")
self._to_xyz_core_docs =(
"http://rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=mmff#rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule",
"http://rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=mmff#rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule"
)
示例3: rdkit_optimize
# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 別名]
def rdkit_optimize(self, addHs=True):
if addHs:
self.mol = Chem.AddHs(self.mol)
AllChem.EmbedMolecule(self.mol, useExpTorsionAnglePrefs=True,useBasicKnowledge=True)
AllChem.UFFOptimizeMolecule(self.mol)
示例4: load_data_from_smiles
# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 別名]
def load_data_from_smiles(x_smiles, labels, add_dummy_node=True, one_hot_formal_charge=False):
"""Load and featurize data from lists of SMILES strings and labels.
Args:
x_smiles (list[str]): A list of SMILES strings.
labels (list[float]): A list of the corresponding labels.
add_dummy_node (bool): If True, a dummy node will be added to the molecular graph. Defaults to True.
one_hot_formal_charge (bool): If True, formal charges on atoms are one-hot encoded. Defaults to False.
Returns:
A tuple (X, y) in which X is a list of graph descriptors (node features, adjacency matrices, distance matrices),
and y is a list of the corresponding labels.
"""
x_all, y_all = [], []
for smiles, label in zip(x_smiles, labels):
try:
mol = MolFromSmiles(smiles)
try:
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol, maxAttempts=5000)
AllChem.UFFOptimizeMolecule(mol)
mol = Chem.RemoveHs(mol)
except:
AllChem.Compute2DCoords(mol)
afm, adj, dist = featurize_mol(mol, add_dummy_node, one_hot_formal_charge)
x_all.append([afm, adj, dist])
y_all.append([label])
except ValueError as e:
logging.warning('the SMILES ({}) can not be converted to a graph.\nREASON: {}'.format(smiles, e))
return x_all, y_all
示例5: to_xyz
# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 別名]
def to_xyz(self, optimizer=None, **kwargs):
"""
This function creates and stores the xyz coordinates for a pre-built molecule object.
Parameters
----------
optimizer: None or str, optional (default: None)
If None, the geometries will be extracted from the available source of 3D structure (if any).
Otherwise, any of the 'UFF' or 'MMFF' force fileds should be passed to embed and optimize geometries using 'rdkit.Chem.AllChem.UFFOptimizeMolecule' or
'rdkit.Chem.AllChem.MMFFOptimizeMolecule' methods, respectively.
kwargs:
The arguments that can be passed to the corresponding forcefileds.
The documentation is available at:
- UFFOptimizeMolecule: http://rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=mmff#rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule
- MMFFOptimizeMolecule: http://rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=mmff#rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule
Notes
-----
- The geometry will be stored in the `xyz` attribute.
- The molecule object must be created in advance.
- The hydrogens won't be added to the molecule automatically. You should add it manually using `hydrogens` method.
- If the molecule object has been built using 2D representations (e.g., SMILES or InChi), the conformer
doesn't exist and you nedd to set the optimizer parameter to any of the force fields.
- If the 3D info exist but you still need to run optimization, the 3D structure will be embedded from scratch (i.e., the current atom coordinates will be removed.)
"""
# rdkit molecule must exist
engine = self._check_original_molecule()
# any futher process depends on the state of the optimizer and available 3D info
if self.xyz and optimizer is None:
return True # the required info is available
elif self.pybel_molecule:
if optimizer is None :
self._to_xyz_pybel() # pybel molecule always contains the 3D info
else:
# build the rdkit molecule from 2D info
smiles = self.pybel_molecule.write('smi').strip().split('\t')[0]
self._load_rdkit(smiles, 'smiles', from_load=False)
self.creator = ('SMILES', smiles)
self.hydrogens('add')
self._to_xyz_rdkit(optimizer, **kwargs)
elif engine == 'rdkit':
self._to_xyz_rdkit(optimizer, **kwargs)
示例6: _to_xyz_rdkit
# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 別名]
def _to_xyz_rdkit(self, optimizer, **kwargs):
"""
The internal function creates and stores the xyz coordinates for a pre-built molecule object.
"""
# add hydrogens >> commented out and left for the users to take care of it using hydrogens method.
# self.hydrogens('add')
# embeding and optimization
if optimizer:
AllChem.EmbedMolecule(self.rdkit_molecule)
if optimizer == 'MMFF':
if AllChem.MMFFHasAllMoleculeParams(self.rdkit_molecule):
AllChem.MMFFOptimizeMolecule(self.rdkit_molecule, **kwargs)
else:
msg = "The MMFF parameters are not available for all of the molecule's atoms."
raise ValueError(msg)
elif optimizer == 'UFF':
if AllChem.UFFHasAllMoleculeParams(self.rdkit_molecule):
AllChem.UFFOptimizeMolecule(self.rdkit_molecule, **kwargs)
else:
msg = "The UFF parameters are not available for all of the molecule's atoms."
raise ValueError(msg)
else:
msg = "The '%s' is not a legit value for the optimizer parameter."%str(optimizer)
raise ValueError(msg)
# get conformer
try:
conf = self.rdkit_molecule.GetConformer()
except ValueError:
msg = "The conformation has not been built yet (maybe due to the 2D representation of the creator).\n" \
"You should set the optimizer value if you wish to embed and optimize the 3D geometry."
raise ValueError(msg)
geometry = conf.GetPositions()
atoms_list = self.rdkit_molecule.GetAtoms()
atomic_nums = np.array([i.GetAtomicNum() for i in atoms_list])
atomic_symbols = np.array([i.GetSymbol() for i in atoms_list])
self._xyz = XYZ(geometry, atomic_nums.reshape(-1,1), atomic_symbols.reshape(-1,1))
if optimizer=='UFF':
self._UFF_args = update_default_kwargs(self._default_UFF_args, kwargs,
self._to_xyz_core_names[1], self._to_xyz_core_docs[1])
elif optimizer=='MMFF':
self._MMFF_args = update_default_kwargs(self._default_MMFF_args, kwargs,
self._to_xyz_core_names[0], self._to_xyz_core_docs[0])