本文整理汇总了Python中rdkit.Chem.AllChem.UFFOptimizeMolecule方法的典型用法代码示例。如果您正苦于以下问题:Python AllChem.UFFOptimizeMolecule方法的具体用法?Python AllChem.UFFOptimizeMolecule怎么用?Python AllChem.UFFOptimizeMolecule使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类rdkit.Chem.AllChem
的用法示例。
在下文中一共展示了AllChem.UFFOptimizeMolecule方法的6个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: generate_structure_from_smiles
# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 别名]
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
# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 别名]
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
# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 别名]
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
# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 别名]
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
# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 别名]
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
# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import UFFOptimizeMolecule [as 别名]
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])