Python Chem.MolToMolBlock方法代码示例

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import MolToMolBlock [as 别名]
def show_sticks(xyz=None, species=None, project_directory=None):
    """
    Draws the molecule in a "sticks" style according to the supplied xyz coordinates.
    Returns whether successful of not. If successful, saves the image using draw_3d.
    Either ``xyz`` or ``species`` must be specified.

    Args:
        xyz (str, dict, optional): The coordinates to display.
        species (ARCSpecies, optional): xyz coordinates will be taken from the species.
        project_directory (str): ARC's project directory to save a draw_3d image in.

    Returns:
        bool: Whether the show_sticks drawing was successful. ``True`` if it was.
    """
    xyz = check_xyz_species_for_drawing(xyz, species)
    if species is None:
        s_mol, b_mol = molecules_from_xyz(xyz)
        mol = b_mol if b_mol is not None else s_mol
    else:
        mol = species.mol.copy(deep=True)
    try:
        conf, rd_mol = rdkit_conf_from_mol(mol, xyz)
    except (ValueError, AttributeError):
        return False
    if conf is None:
        return False
    mb = Chem.MolToMolBlock(rd_mol)
    p = p3D.view(width=400, height=400)
    p.addModel(mb, 'sdf')
    p.setStyle({'stick': {}})
    # p.setBackgroundColor('0xeeeeee')
    p.zoomTo()
    p.show()
    if project_directory is not None:
        draw_3d(xyz=xyz, species=species, project_directory=project_directory, save_only=True)
    return True 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import MolToMolBlock [as 别名]
def _write_mol(mol, args):
    if args.outtype in {'smi', 'smiles'} or args.outfile.name.endswith('smi') or args.outfile.name.endswith('smiles'):
        args.outfile.write(Chem.MolToSmiles(mol))
        args.outfile.write('\n')
    elif args.outtype in {'mol', 'sdf'} or args.outfile.name.endswith('mol') or args.outfile.name.endswith('sdf'):
        args.outfile.write(Chem.MolToMolBlock(mol))
    else:
        args.outfile.write(Chem.MolToSmiles(mol))
        args.outfile.write('\n') 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import MolToMolBlock [as 别名]
def draw_3d(self, width=300, height=500, style='stick', Hs=True): # pragma: no cover
        r'''Interface for drawing an interactive 3D view of the molecule.
        Requires an HTML5 browser, and the libraries RDKit, pymol3D, and
        IPython. An exception is raised if all three of these libraries are
        not installed.

        Parameters
        ----------
        width : int
            Number of pixels wide for the view
        height : int
            Number of pixels tall for the view
        style : str
            One of 'stick', 'line', 'cross', or 'sphere'
        Hs : bool
            Whether or not to show hydrogen

        Examples
        --------
        >>> Chemical('cubane').draw_3d()
        <IPython.core.display.HTML object>
        '''
        try:
            import py3Dmol
            from IPython.display import display
            if Hs:
                mol = self.rdkitmol_Hs
            else:
                mol = self.rdkitmol
            AllChem.EmbedMultipleConfs(mol)
            mb = Chem.MolToMolBlock(mol)
            p = py3Dmol.view(width=width,height=height)
            p.addModel(mb,'sdf')
            p.setStyle({style:{}})
            p.zoomTo()
            display(p.show())
        except:
            return 'py3Dmol, RDKit, and IPython are required for this feature.' 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import MolToMolBlock [as 别名]
def ReconnectDoubleBond(parentMol, inputFrags):
    parentMolblock = Chem.MolToMolBlock(parentMol)
    fragmentMolblocks = []
    for i in range(len(inputFrags)):
        tempFragStr = Chem.MolToMolBlock(inputFrags[i])
        fragmentMolblocks.append(tempFragStr)

    newFragmentMolBlocks = []
    dbFragList = []
    for i in range(len(inputFrags)):
        tempValue = FindDoubleBonds(inputFrags[i])
        if tempValue >= 0:
            # Find C.2 = C.2 bond
            dbFragList.append(fragmentMolblocks[i])
        else:
            newFragmentMolBlocks.append(fragmentMolblocks[i])

    reconnectedDBFrags = ProcessDoubleBonds(parentMolblock, dbFragList)
    newFragmentMolBlocks = newFragmentMolBlocks + reconnectedDBFrags

    newFragmentMol = []
    for i in range(len(newFragmentMolBlocks)):
        tempFragMol = Chem.MolFromMolBlock(newFragmentMolBlocks[i])
        newFragmentMol.append(tempFragMol)

    # return tuple mol-objects
    return tuple(newFragmentMol) 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import MolToMolBlock [as 别名]
def ReconnectDoubleBond(parentMol, inputFrags):
    parentMolblock = Chem.MolToMolBlock(parentMol)
    fragmentMolblocks = []
    for i in range(len(inputFrags)):
        tempFragStr = Chem.MolToMolBlock(inputFrags[i])
        fragmentMolblocks.append(tempFragStr)

    newFragmentMolBlocks = []
    dbFragList = []
    for i in range(len(inputFrags)):
        tempValue = FindDoubleBonds(inputFrags[i])
        if tempValue >= 0:
            # Find C.2 = C.2 bond
            dbFragList.append(fragmentMolblocks[i])
        else:
            newFragmentMolBlocks.append(fragmentMolblocks[i])
    
    reconnectedDBFrags = ProcessDoubleBonds(parentMolblock, dbFragList)
    
    newFragmentMolBlocks = newFragmentMolBlocks + reconnectedDBFrags
    
    newFragmentMol = []
    for i in range(len(newFragmentMolBlocks)):
        tempFragMol = Chem.MolFromMolBlock(newFragmentMolBlocks[i],sanitize=False)
        newFragmentMol.append(tempFragMol)

    # return tuple mol-objects
    return tuple(newFragmentMol) 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import MolToMolBlock [as 别名]
def ReconnectDoubleBond(parentMol, inputFrags):
    parentMolblock = Chem.MolToMolBlock(parentMol,kekulize=False)
    fragmentMolblocks = []
    for i in range(len(inputFrags)):
        tempFragStr = Chem.MolToMolBlock(inputFrags[i],kekulize=False)
        fragmentMolblocks.append(tempFragStr)

    newFragmentMolBlocks = []
    dbFragList = []
    for i in range(len(inputFrags)):
        tempValue = FindDoubleBonds(inputFrags[i])
        if tempValue >= 0:
            # Find C.2 = C.2 bond
            dbFragList.append(fragmentMolblocks[i])
        else:
            newFragmentMolBlocks.append(fragmentMolblocks[i])

    reconnectedDBFrags = ProcessDoubleBonds(parentMolblock, dbFragList)
    newFragmentMolBlocks = newFragmentMolBlocks + reconnectedDBFrags

    newFragmentMol = []
    for i in range(len(newFragmentMolBlocks)):
        tempFragMol = Chem.MolFromMolBlock(newFragmentMolBlocks[i], sanitize=False)
        newFragmentMol.append(tempFragMol)
    #print('test')
    # return tuple mol-objects
    return tuple(newFragmentMol)