Thanks Rocco! I just used AllChem.GenerateDepictionMatching2DStructure() with
a custom SMILES string as the template depiction for each resonance
structure. Due to the alternating double bonds switching places between the
two resonance structures, FindMCS did not seem to provide a SMARTS string
as a template depiction that worked for both resonance structures, so I
wrote SMILES strings as template depictions for each resonance structure
and confirmed that each substructure template has the same orientation.
Here is the working script:
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
import matplotlib.pyplot as plt
def draw_structure(mol_smiles_string, template_smiles_string, ax=None):
if not ax:
f, ax = plt.subplots()
m = Chem.MolFromSmiles(mol_smiles_string, sanitize=False)
m.UpdatePropertyCache()
Chem.SetHybridization(m)
t = Chem.MolFromSmiles(template_smiles_string, sanitize=False)
t.UpdatePropertyCache()
Chem.SetHybridization(t)
AllChem.Compute2DCoords(t)
AllChem.GenerateDepictionMatching2DStructure(m, t)
img = Draw.MolToImage(m)
return ax.imshow(img, interpolation='bessel')
fig = plt.figure(figsize=(10,5))
ax1 = plt.subplot2grid((1, 2), (0, 0))
ax2 = plt.subplot2grid((1, 2), (0, 1))
draw_structure(mol_smiles_string="CN(C2=O)C(C)=N\C2=C/C1=CC(F)=C([o-])C(F)=C1",
template_smiles_string="C=C/C1=CC(F)=C([o-])C(F)=C1", ax=ax1)
draw_structure(mol_smiles_string="CN(C=2[o-])C(C)=N\C2C=C1/C=C(F)C(=O)C(F)=C1",
template_smiles_string="CC=C1/C=C(F)C(=O)C(F)=C1", ax=ax2)
plt.tight_layout()
plt.show()
Output:
[image: image.png]
Best,
Jason
On Thu, Sep 20, 2018 at 3:09 PM Rocco Moretti <[email protected]> wrote:
> Instead of arbitrarily generating 2D coordinates (which can have any
> orientation), you probably want to use
> GenerateDepictionMatching2DStructure() to generate coordinates which match
> a common orientation for a substructure.
>
> See
> http://www.rdkit.org/docs/GettingStartedInPython.html#drawing-molecules
> for an example of how to use it.
>
> Note that this does require you to have a common core with which to align
> the depictions, but some of that can be automated with FindMCS (see
> http://www.rdkit.org/docs/GettingStartedInPython.html#maximum-common-substructure
> ).
>
> On Thu, Sep 20, 2018 at 4:54 PM, Jason Klima <[email protected]>
> wrote:
>
>> Hi,
>> I would like to visualize the following resonance structures in the same
>> orientation (i.e. the same atomic coordinates), however, the image on the
>> right appears to be drawn upside down compared to the image on the left,
>> while the element names (e.g. N, O, and F) in both images are right side
>> up. Mirroring the image on the right about a horizontal axis can be
>> accomplished with ax.set_ylim([0,300]) however the element names are
>> then upside down. How can I mirror the drawing on the right about a
>> horizontal axis without mirroring element names?
>>
>> from rdkit import Chem
>> from rdkit.Chem import Draw
>> import matplotlib.pyplot as plt
>> def draw_structure(smiles_string, ax=None):
>> m = Chem.MolFromSmiles(smiles_string, sanitize=False)
>> m.UpdatePropertyCache()
>> Chem.SetHybridization(m)
>> # ax.set_ylim([0,300]) # Flips image but element names also flip
>> return ax.imshow(Draw.MolToImage(m), interpolation='bessel')
>> fig = plt.figure(figsize=(10,5))
>> ax1 = plt.subplot2grid((1, 2), (0, 0))
>> ax2 = plt.subplot2grid((1, 2), (0, 1))
>> draw_structure('CN(C2=O)C(C)=N\C2=C/C1=CC(F)=C([o-])C(F)=C1', ax=ax1)
>> draw_structure('CN(C=2[o-])C(C)=N\C2C=C1/C=C(F)C(=O)C(F)=C1', ax=ax2)
>> plt.tight_layout()
>> plt.show()
>>
>> Output:
>> [image: image.png]
>>
>> Thanks,
>> Jason
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
--
Jason Klima
Graduate Research Assistant
Department of Biochemistry
University of Washington, Seattle
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