Re: [Rdkit-discuss] High-quality matplotlib drawing?
That's an interesting question. I think there probably are some ways of
tweaking this and improving things, but I don't have a convenient way to
test. If you can share the python (+data) you used to construct that PDF I
will see if I can come up with a solution.
-greg
On Thu, Aug 8, 2019 at 2:23 AM Wout Bittremieux
wrote:
> Dear RDKit team,
>
> I'm trying to draw a molecule on a spectrum plot from Matplotlib using
> MolToImage. This is some abbreviated code:
>
> ```
> import matplotlib.pyplot as plt
> from rdkit import Chem
> from rdkit.Chem import Draw
>
> fig, ax = plt.subplots()
>
> ax.plot(...)
>
> im = Draw.MolToImage(Chem.MolFromSmiles(smiles))
> ax.imshow(im, aspect='auto', extent=(x, x+width, y, y + height))
>
> plt.savefig('fig.pdf')
> plt.close()
> ```
>
> Unfortunately the quality of the molecule drawing is rather poor (see
> attachment; nonsensical spectrum and molecule). This seems to be true
> for non-SVG drawing in general, and unfortunately it's not really
> possible to combine SVG output with Matplotlib functionality.
>
> Is there any way I can improve the quality of the MolToImage output?
> I've tried to change some of the DrawingOptions, but the result always
> remains very pixelated and low quality.
>
> Thank you,
> Wout
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[Rdkit-discuss] High-quality matplotlib drawing?
Dear RDKit team,
I'm trying to draw a molecule on a spectrum plot from Matplotlib using
MolToImage. This is some abbreviated code:
```
import matplotlib.pyplot as plt
from rdkit import Chem
from rdkit.Chem import Draw
fig, ax = plt.subplots()
ax.plot(...)
im = Draw.MolToImage(Chem.MolFromSmiles(smiles))
ax.imshow(im, aspect='auto', extent=(x, x+width, y, y + height))
plt.savefig('fig.pdf')
plt.close()
```
Unfortunately the quality of the molecule drawing is rather poor (see
attachment; nonsensical spectrum and molecule). This seems to be true
for non-SVG drawing in general, and unfortunately it's not really
possible to combine SVG output with Matplotlib functionality.
Is there any way I can improve the quality of the MolToImage output?
I've tried to change some of the DrawingOptions, but the result always
remains very pixelated and low quality.
Thank you,
Wout
fig.pdf
Description: Adobe PDF document
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Re: [Rdkit-discuss] GetSubstructMatches() as smiles
On Aug 7, 2019, at 13:08, Paolo Tosco wrote:
> You can use
>
> Chem.MolFragmentToSmiles(mol, match)
>
> where match is a tuple of atom indices returned by GetSubstructMatch().
Note however that if only the atom indices are given then
Chem.MolFragmentToSmiles() will include all bonds which connect those atoms,
even if the original SMARTS does not match those bonds. For example:
>>> from rdkit import Chem
>>> pat = Chem.MolFromSmarts("*~*~*~*") # match 4 linear atoms
>>> mol = Chem.MolFromSmiles("C1CCC1") # ring of size 4
>>> atom_indices = mol.GetSubstructMatch(pat)
>>> atom_indices
(0, 1, 2, 3)
>>> Chem.MolFragmentToSmiles(mol, atom_indices) # returns the ring
'C1CCC1'
If this is important, then you need to pass the correct bond indices to
MolFragmentToSmiles(). This can be done by using the bonds in the query graph
to get the bond indices in the molecule graph. I believe the following is
correct:
def get_match_bond_indices(query, mol, match_atom_indices):
bond_indices = []
for query_bond in query.GetBonds():
atom_index1 = match_atom_indices[query_bond.GetBeginAtomIdx()]
atom_index2 = match_atom_indices[query_bond.GetEndAtomIdx()]
bond_indices.append(mol.GetBondBetweenAtoms(
atom_index1, atom_index2).GetIdx())
return bond_indices
(Does a function like this already exist in RDKit?)
I'll use it to get the bond indices for the *~*~*~* match:
>>> bond_indices = get_match_bond_indices(pat, mol, atom_indices)
>>> bond_indices
[0, 1, 2]
Passing the atom and bond indices gives the expected match SMILES:
>>> Chem.MolFragmentToSmiles(mol, atom_indices, bond_indices)
''
Cheers,
Andrew
da...@dalkescientific.com
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Re: [Rdkit-discuss] GetSubstructMatches() as smiles
Hi Mel, You can use Chem.MolFragmentToSmiles(mol, match) where match is a tuple of atom indices returned by GetSubstructMatch(). Cheers, p. > On 7 Aug 2019, at 11:36, Melissa Adasme wrote: > > Dear rdkitters, > > I'm trying to find substructures (query molecules built from SMARTS) matching > my molecules (SMILES). I found the GetSubstructMatches() method which works > pretty well returning the indices of matching atoms in my molecule. > > I wonder if there is a way to directly obtain the SMILES of the found > substructures instead of the atom indexes or maybe a way to transform the > indexes to smiles? > > Many thanks in advance! > Mel > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] GetSubstructMatches() as smiles
Dear rdkitters, I'm trying to find substructures (query molecules built from SMARTS) matching my molecules (SMILES). I found the GetSubstructMatches() method which works pretty well returning the indices of matching atoms in my molecule. I wonder if there is a way to directly obtain the SMILES of the found substructures instead of the atom indexes or maybe a way to transform the indexes to smiles? Many thanks in advance! Mel ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
