Python AllChem.Compute2DCoords方法代码示例

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def MolToQPixmap(mol, size=(300, 300), kekulize=True, wedgeBonds=True, fitImage=False, options=None,
                 **kwargs):
    """ Generates a drawing of a molecule on a Qt QPixmap
      """
    if not mol:
        raise ValueError('Null molecule provided')
    from rdkit.Chem.Draw.qtCanvas import Canvas
    canvas = Canvas(size)
    if options is None:
        options = DrawingOptions()
    options.bgColor = None
    if fitImage:
        options.dotsPerAngstrom = int(min(size) / 10)
    options.wedgeDashedBonds = wedgeBonds
    if kekulize:
        from rdkit import Chem
        mol = Chem.Mol(mol.ToBinary())
        Chem.Kekulize(mol)
    if not mol.GetNumConformers():
        from rdkit.Chem import AllChem
        AllChem.Compute2DCoords(mol)
    drawer = MolDrawing(canvas=canvas, drawingOptions=options)
    drawer.AddMol(mol, **kwargs)
    canvas.flush()
    return canvas.pixmap 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def MolToFile(mol, fileName, size=(300, 300), kekulize=True, wedgeBonds=True, imageType=None,
              fitImage=False, options=None, **kwargs):
    """ Generates a drawing of a molecule and writes it to a file
    """
    # original contribution from Uwe Hoffmann
    if not fileName:
        raise ValueError('no fileName provided')
    if not mol:
        raise ValueError('Null molecule provided')

    if imageType is None:
        imageType = os.path.splitext(fileName)[1][1:]

    if options is None:
        options = DrawingOptions()
    useAGG, useCairo, Canvas = _getCanvas()
    if fitImage:
        options.dotsPerAngstrom = int(min(size) / 10)
    options.wedgeDashedBonds = wedgeBonds
    if useCairo or useAGG:
        canvas = Canvas(size=size, imageType=imageType, fileName=fileName)
    else:
        options.radicalSymbol = '.'  # <- the sping canvas doesn't support unicode well
        canvas = Canvas(size=size, name=fileName, imageType=imageType)
    drawer = MolDrawing(canvas=canvas, drawingOptions=options)
    if kekulize:
        from rdkit import Chem
        mol = Chem.Mol(mol.ToBinary())
        Chem.Kekulize(mol)

    if not mol.GetNumConformers():
        from rdkit.Chem import AllChem
        AllChem.Compute2DCoords(mol)

    drawer.AddMol(mol, **kwargs)
    if useCairo or useAGG:
        canvas.flush()
    else:
        canvas.save() 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def MolToMPL(mol, size=(300, 300), kekulize=True, wedgeBonds=True, imageType=None, fitImage=False,
             options=None, **kwargs):
    """ Generates a drawing of a molecule on a matplotlib canvas
    """
    if not mol:
        raise ValueError('Null molecule provided')
    from experiment.figure.Draw.mplCanvas import Canvas
    canvas = Canvas(size)
    if options is None:
        options = DrawingOptions()
        options.bgColor = None
    if fitImage:
        options.dotsPerAngstrom = int(min(size) / 10)
    options.wedgeDashedBonds = wedgeBonds
    drawer = MolDrawing(canvas=canvas, drawingOptions=options)
    omol = mol
    if kekulize:
        from rdkit import Chem
        mol = Chem.Mol(mol.ToBinary())
        Chem.Kekulize(mol)

    if not mol.GetNumConformers():
        from rdkit.Chem import AllChem
        AllChem.Compute2DCoords(mol)

    drawer.AddMol(mol, **kwargs)
    omol._atomPs = drawer.atomPs[mol]
    for k, v in iteritems(omol._atomPs):
        omol._atomPs[k] = canvas.rescalePt(v)
    canvas._figure.set_size_inches(float(size[0]) / 100, float(size[1]) / 100)
    return canvas._figure 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def draw_structure(smiles_str, image_path, image_size=500):
  """
  Draw structure for the compound with the given SMILES string, in a PNG file
  with the given path.
  """
  mol = Chem.MolFromSmiles(smiles_str)
  if mol is None:
    print(("Unable to read original SMILES for %s" % cmpd_num))
  else:
    _discard = AllChem.Compute2DCoords(mol)
    Draw.MolToFile(mol, image_path, size=(image_size,image_size), fitImage=False) 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def visualize_mol(path, new_mol):
    AllChem.Compute2DCoords(new_mol)
    print(path)
    Draw.MolToFile(new_mol,path) 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def mols2grid_image(mols, molsPerRow):
    mols = [e if e is not None else Chem.RWMol() for e in mols]

    for mol in mols:
        AllChem.Compute2DCoords(mol)

    return Draw.MolsToGridImage(mols, molsPerRow=molsPerRow, subImgSize=(150, 150)) 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [as 别名]
def make2D(self):
        """Generate 2D coordinates for molecule"""
        AllChem.Compute2DCoords(self.Mol)
        self._clear_cache() 

# 需要导入模块: from rdkit.Chem import AllChem [as 别名]
# 或者: from rdkit.Chem.AllChem import Compute2DCoords [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