Python rdkit.Chem.AllChem.Compute2DCoords() Examples

The following are 8 code examples of rdkit.Chem.AllChem.Compute2DCoords(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module rdkit.Chem.AllChem , or try the search function .
Example #1
Source File: __init__.py    From 3DGCN with MIT License 6 votes vote down vote up 
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
Example #2
Source File: __init__.py    From 3DGCN with MIT License 5 votes vote down vote up 
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()
Example #3
Source File: __init__.py    From 3DGCN with MIT License 5 votes vote down vote up 
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
Example #4
Source File: struct_utils.py    From AMPL with MIT License 5 votes vote down vote up 
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)
Example #5
Source File: utils.py    From constrained-graph-variational-autoencoder with MIT License 5 votes vote down vote up 
def visualize_mol(path, new_mol):
    AllChem.Compute2DCoords(new_mol)
    print(path)
    Draw.MolToFile(new_mol,path)
Example #6
Source File: utils.py    From MolGAN with MIT License 5 votes vote down vote up 
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))
Example #7
Source File: rdk.py    From oddt with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up 
def make2D(self):
        """Generate 2D coordinates for molecule"""
        AllChem.Compute2DCoords(self.Mol)
        self._clear_cache()
Example #8
Source File: data_utils.py    From MAT with MIT License 5 votes vote down vote up 
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