Rdkit reb #177

rebadam · 2024-11-22T12:03:39Z

I added three things:

to_rdmol often fails, especially for the iffy compounds made with reactions discovery. I added an optional argument (presanitize) that iteratively sanitizes and update the bonds and atomic charges, untill sanitization succeeds.
I added a to_image function that makes a 2D image of a molecule. This uses the presanitize by default. It creates an image (svg (default), png, eps, pdf, jpeg), and optionally prints it to file. It works with our RDKit version, and when using a newer version, it uses newer features. I also works from jupyter notebooks.
I added a to_reaction_image function that tries to make a nice looking 2D reaction image.
I added some example molecules and a test script here.
Example.tar.gz

…ons + improved stability to_rdmol - to_rdmol now has an argument presanitize, which iteratively sanitized - improved bonding/atomic charges, until sanitization succeeds. - There are the functions to_image and get_reaction_image.

…n_image. - to_image now works with svg in JupyterLab

dormrod · 2024-11-25T15:50:32Z

Looks like a great feature!

Just a couple of overall comments:

I tidied up a few little things I spotted as I reviewed this (type-hints, unit-test etc.)
It might also be good to add a notebook example to https://github.com/SCM-NV/PLAMS/tree/trunk/examples, or modify one of the existing ones, to show how to use this new functionality?
We have a new changelog which we will use at the end of the year to produce the "what's new" functionality - please could you also add a line in there? https://github.com/SCM-NV/PLAMS/blob/trunk/CHANGELOG.md

dormrod · 2024-11-25T10:19:17Z

interfaces/molecule/rdkit.py

+    sanitize: bool = True,
+    properties: bool = True,
+    assignChirality: bool = False,
+    presanitize: bool = False,


Add presanitize to doc-string with description - might be worth also mentioning that sanitize must also be True for this to apply

dormrod · 2024-11-25T11:02:23Z

interfaces/molecule/rdkit.py

@@ -213,10 +219,11 @@ def plams_to_rd_bonds(bo):

    if sanitize:
        try:
-            Chem.SanitizeMol(rdmol)
+            if presanitize:
+                rdmol = _presanitize(plams_mol, rdmol)


It would be nice to have add unit-test cases which use this method in unit_tests/test_molecule_interfaces.TestRDKit (see e.g. test_to_rdmol_from_rdmol_roundtrip).

These could take some input molecules that have issues, and check the output is santised as expected.

Do you have some examples for which this santization is useful?

dormrod · 2024-11-25T11:07:37Z

interfaces/molecule/rdkit.py

@@ -1290,3 +1297,602 @@ def canonicalize_mol(mol, inplace=False, **kwargs):
        ret = mol.copy()
        ret.atoms = [at for _, at in sorted(zip(idx_rank, ret.atoms), reverse=True)]
        return ret
+
+
+@requires_optional_package("rdkit")


Updated as also requires optional package pillow, as users may not be using amspython.

I have also just sorted out the optional dependencies for PLAMS to make them easier to install, so also added the pillow dependency here: https://github.com/SCM-NV/PLAMS/blob/trunk/pyproject.toml#L59

dormrod · 2024-11-25T11:10:14Z

interfaces/molecule/rdkit.py

+
+
+@requires_optional_package("rdkit")
+def to_image(mol, remove_hydrogens=True, filename=None, format="svg", as_string=True):


(Added type hints)

dormrod · 2024-11-25T11:14:24Z

interfaces/molecule/rdkit.py

+    * ``mol`` -- PLAMS Molecule object
+    * ``remove_hydrogens`` -- Wether or not to remove the H-atoms from the image
+    * ``filename`` -- Optional: Name of image file to be created.
+    * ``format`` -- One of "svg", "png", "eps", "pdf", "jpeg"


(renamed to fmt to avoid clash with python keyword)

dormrod · 2024-11-25T11:17:17Z

interfaces/molecule/rdkit.py

+    # Draw the image
+    if classes[format.lower()] is None:
+        # With AMS version of RDKit MolsToGridImage fails for eps (because of paste)
+        img = Draw.MolToImage(rdmol, size=(200, 100))


Might be nice to have the size as an option to the function?

dormrod · 2024-11-25T14:45:47Z

interfaces/molecule/rdkit.py

+    return img_text
+
+
+def get_reaction_image_pil(reactants, products, format, width=200, height=100, as_string=True):


Make these "private" (_get_reaction_image_pil) or add to __init__?

dormrod · 2024-11-25T15:38:39Z

unit_tests/test_molecule_interfaces.py

@@ -230,6 +238,38 @@ def test_to_smiles_and_from_smiles_requires_rdkit_package(self, plams_mols, smil
            with pytest.raises(MissingOptionalPackageError):
                from_smiles(smiles[0])

+    def test_to_image_and_get_reaction_image_can_generate_img_files(self, xyz_folder):


I have converted the attached example to a unit test.

It's not too fancy, just makes sure the image files can be generated, but then they can be visually inspected too.

rebadam and others added 6 commits November 21, 2024 17:12

Merge branch 'trunk' into rdkitREB

77fa6bc

Rosa Bulo (REB) SCMSUITE-- SO102: Cleaned up to_image and get_reactio…

2d8a295

…n_image. - to_image now works with svg in JupyterLab

Rosa Bulo (REB) SCMSUITE-- SO102: Cleaned up formatting some more

df2653d

Rosa Bulo (REB) SCMSUITE-- SO102: Cleaned file for mypy

438c6dd

Minor changes and add unit test SO102

1b9c2f8

dormrod force-pushed the rdkitREB branch from 081921b to 1b9c2f8 Compare November 25, 2024 15:47

dormrod reviewed Nov 25, 2024

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Rdkit reb #177

Rdkit reb #177

rebadam commented Nov 22, 2024

dormrod commented Nov 25, 2024 •

edited

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		@requires_optional_package("rdkit")
		def to_image(mol, remove_hydrogens=True, filename=None, format="svg", as_string=True):

		return img_text


		def get_reaction_image_pil(reactants, products, format, width=200, height=100, as_string=True):

Rdkit reb #177

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Rdkit reb #177

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rebadam commented Nov 22, 2024

dormrod commented Nov 25, 2024 • edited Loading

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dormrod commented Nov 25, 2024 •

edited

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