Python rdkit.Chem.MolToMolBlock() Examples

The following are 8 code examples of rdkit.Chem.MolToMolBlock(). 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 , or try the search function .
Example #1
Source File: plotter.py    From ARC with MIT License 5 votes vote down vote up 
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
Example #2
Source File: cli.py    From MolVS with MIT License 5 votes vote down vote up 
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')
Example #3
Source File: chemical.py    From thermo with MIT License 5 votes vote down vote up 
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.'
Example #4
Source File: chopRDKit03.py    From eMolFrag with GNU General Public License v3.0 5 votes vote down vote up 
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)
Example #5
Source File: newFrag02.py    From eMolFrag with GNU General Public License v3.0 5 votes vote down vote up 
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)
Example #6
Source File: chopRDKit03.py    From eMolFrag with GNU General Public License v3.0 5 votes vote down vote up 
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)
Example #7
Source File: newFrag02.py    From eMolFrag with GNU General Public License v3.0 5 votes vote down vote up 
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)
Example #8
Source File: chopRDKit03.py    From eMolFrag with GNU General Public License v3.0 5 votes vote down vote up 
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)