Skip to content

sdf2mol: keep properties from file and add tests #173

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
JochenSiegWork merged 2 commits into from
May 8, 2025
Merged

sdf2mol: keep properties from file and add tests #173

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1887d7e
sdf2mol: keep properties from file and add tests
JochenSiegWork May 8, 2025
db2a372
fix missing raises in docstring
JochenSiegWork May 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 14 additions & 4 deletions molpipeline/any2mol/sdf2mol.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

from __future__ import annotations

from typing import Any
from typing import TYPE_CHECKING, Any

try:
from typing import Self # type: ignore[attr-defined]
Expand All @@ -17,7 +17,9 @@
StringToMolPipelineElement as _StringToMolPipelineElement,
)
from molpipeline.abstract_pipeline_elements.core import InvalidInstance
from molpipeline.utils.molpipeline_types import OptionalMol

if TYPE_CHECKING:
from molpipeline.utils.molpipeline_types import OptionalMol


class SDFToMol(_StringToMolPipelineElement):
Expand All @@ -38,13 +40,16 @@ def __init__(
Parameters
----------
identifier: str, default='enumerate'
Method of assigning identifiers to molecules. At the moment molecules are counted.
Method of assigning identifiers to molecules. Per default, an increasing
integer count is assigned to each molecule. If 'smiles' is chosen, the
identifier is the SMILES representation of the molecule.
name: str, default='SDF2Mol'
Name of PipelineElement
n_jobs: int, default=1
Number of cores used for processing.
uuid: str | None, optional
uuid of PipelineElement, by default None

"""
super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
self.identifier = identifier
Expand All @@ -62,6 +67,7 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
-------
dict[str, Any]
Dictionary containing all parameters defining the object.

"""
params = super().get_params(deep)
if deep:
Expand All @@ -82,6 +88,7 @@ def set_params(self, **parameters: Any) -> Self:
-------
Self
SDFToMol with updated parameters.

"""
super().set_params(**parameters)
if "identifier" in parameters:
Expand All @@ -104,14 +111,17 @@ def pretransform_single(self, value: str) -> OptionalMol:
-------
OptionalMol
Molecule if transformation was successful, else InvalidInstance.

"""
if not isinstance(value, (str, bytes)):
return InvalidInstance(
self.uuid,
"Invalid SDF string!",
self.name,
)
mol = Chem.MolFromMolBlock(value)
supplier = Chem.SDMolSupplier()
supplier.SetData(value)
mol = next(supplier, None)
if mol is None:
return InvalidInstance(
self.uuid,
Expand Down
237 changes: 237 additions & 0 deletions tests/test_elements/test_any2mol/test_sdf2mol.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,237 @@
"""Tests for SDF to mol."""

import unittest

from rdkit import Chem

from molpipeline.abstract_pipeline_elements.core import InvalidInstance
from molpipeline.any2mol.sdf2mol import SDFToMol


class TestSDFToMol(unittest.TestCase):
"""Test class for SDFToMol."""

def setUp(self) -> None:
"""Set up test fixtures."""
self.sdf_str_benzaldehyde = """240
-OEChem-05082503512D

14 14 0 0 0 0 0 0 0999 V2000
3.7321 1.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 0.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 -0.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -0.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 -1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 -1.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4631 0.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2690 0.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4631 -1.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2690 -1.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 -2.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3291 1.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 8 2 0 0 0 0
2 3 2 0 0 0 0
2 4 1 0 0 0 0
2 8 1 0 0 0 0
3 5 1 0 0 0 0
3 9 1 0 0 0 0
4 6 2 0 0 0 0
4 10 1 0 0 0 0
5 7 2 0 0 0 0
5 11 1 0 0 0 0
6 7 1 0 0 0 0
6 12 1 0 0 0 0
7 13 1 0 0 0 0
8 14 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
240

> <PUBCHEM_COMPOUND_CANONICALIZED>
1

> <PUBCHEM_CACTVS_COMPLEXITY>
72.5

$$$$
"""

self.sdf_str_aspirin = """2244
-OEChem-05082504263D

21 21 0 0 0 0 0 0 0999 V2000
1.2333 0.5540 0.7792 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6952 -2.7148 -0.7502 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7958 -2.1843 0.8685 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7813 0.8105 -1.4821 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0857 0.6088 0.4403 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7927 -0.5515 0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7288 1.8464 0.4133 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1426 -0.4741 -0.2184 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0787 1.9238 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7855 0.7636 -0.2453 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1409 -1.8536 0.1477 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1094 0.6715 -0.3113 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5305 0.5996 0.1635 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1851 2.7545 0.6593 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.7247 -1.3605 -0.4564 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5797 2.8872 0.0506 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8374 0.8238 -0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7290 1.4184 0.8593 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2045 0.6969 -0.6924 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7105 -0.3659 0.6426 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2555 -3.5916 -0.7337 H 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
1 12 1 0 0 0 0
2 11 1 0 0 0 0
2 21 1 0 0 0 0
3 11 2 0 0 0 0
4 12 2 0 0 0 0
5 6 1 0 0 0 0
5 7 2 0 0 0 0
6 8 2 0 0 0 0
6 11 1 0 0 0 0
7 9 1 0 0 0 0
7 14 1 0 0 0 0
8 10 1 0 0 0 0
8 15 1 0 0 0 0
9 10 2 0 0 0 0
9 16 1 0 0 0 0
10 17 1 0 0 0 0
12 13 1 0 0 0 0
13 18 1 0 0 0 0
13 19 1 0 0 0 0
13 20 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
2244

> <PUBCHEM_CONFORMER_RMSD>
0.6

$$$$
"""
self.sdf_str_benzaldehyde_aspirin = (
self.sdf_str_benzaldehyde + self.sdf_str_aspirin
)
self.invalid_sdf = "Not an SDF string"

def test_initialization(self) -> None:
"""Test initialization of SDFToMol."""
sdf2mol = SDFToMol(identifier="smiles", name="CustomName", n_jobs=2)
self.assertEqual(sdf2mol.identifier, "smiles")
self.assertEqual(sdf2mol.name, "CustomName")
self.assertEqual(sdf2mol.n_jobs, 2)
self.assertEqual(sdf2mol.mol_counter, 0)

def test_pretransform_valid_sdf(self) -> None:
"""Test transformation of valid SDF string.

Raises
------
AssertionError
If the transformation does not return a valid molecule.

"""
sdf2mol = SDFToMol()
# test sdf string with single molecule: benzaldehyde
mol = sdf2mol.pretransform_single(self.sdf_str_benzaldehyde)
self.assertIsInstance(mol, Chem.Mol)
if not isinstance(mol, Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mol.GetNumAtoms(), 8)

# test sdf string with single molecule: aspirin
mol = sdf2mol.pretransform_single(self.sdf_str_aspirin)
self.assertIsInstance(mol, Chem.Mol)
if not isinstance(mol, Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mol.GetNumAtoms(), 13)

# test sdf string with multiple molecules: benzaldehyde and aspirin
# the current behavior is to return the first molecule only
mol = sdf2mol.pretransform_single(self.sdf_str_benzaldehyde_aspirin)
self.assertIsInstance(mol, Chem.Mol)
if not isinstance(mol, Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mol.GetNumAtoms(), 8)

def test_pretransform_invalid_sdf(self) -> None:
"""Test handling of invalid SDF input."""
result = SDFToMol().pretransform_single(self.invalid_sdf)
self.assertIsInstance(result, InvalidInstance)

def test_transform(self) -> None:
"""Test transform function.

Raises
------
AssertionError
If the transformation does not return a valid molecule.

"""
# test list of sdf strings
mols = SDFToMol().transform([self.sdf_str_benzaldehyde, self.sdf_str_aspirin])
self.assertEqual(len(mols), 2)
self.assertIsInstance(mols[0], Chem.Mol)
self.assertIsInstance(mols[1], Chem.Mol)
if not isinstance(mols[0], Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mols[0].GetNumAtoms(), 8)
if not isinstance(mols[1], Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mols[1].GetNumAtoms(), 13)

# test single sdf string with multiple molecules
# only the first molecule in the SDF string will be read
mols = SDFToMol().transform([self.sdf_str_benzaldehyde_aspirin])
self.assertEqual(len(mols), 1)
self.assertIsInstance(mols[0], Chem.Mol)
if not isinstance(mols[0], Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mols[0].GetNumAtoms(), 8)

# test multiple sdf strings with multiple molecules
# the current behavior is to return the first molecule only
mols = SDFToMol().transform(
[self.sdf_str_benzaldehyde_aspirin, self.sdf_str_benzaldehyde],
)
self.assertEqual(len(mols), 2)
self.assertIsInstance(mols[0], Chem.Mol)
self.assertIsInstance(mols[1], Chem.Mol)
if not isinstance(mols[0], Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mols[0].GetNumAtoms(), 8)
if not isinstance(mols[1], Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertEqual(mols[1].GetNumAtoms(), 8)

def test_sdf_properties_transfer(self) -> None:
"""Test that properties from SDF are transferred to molecule.

Raises
------
AssertionError
If the transformation does not return a valid molecule.

"""
mol = SDFToMol().pretransform_single(self.sdf_str_benzaldehyde)
if not isinstance(mol, Chem.Mol):
# necessary for mypy
raise AssertionError("Expected a Chem.Mol object")
self.assertTrue(mol.HasProp("PUBCHEM_COMPOUND_CID"))
self.assertEqual(mol.GetProp("PUBCHEM_COMPOUND_CID"), "240")
self.assertTrue(mol.HasProp("PUBCHEM_COMPOUND_CANONICALIZED"))
self.assertEqual(mol.GetProp("PUBCHEM_COMPOUND_CANONICALIZED"), "1")
self.assertTrue(mol.HasProp("PUBCHEM_CACTVS_COMPLEXITY"))
self.assertEqual(mol.GetProp("PUBCHEM_CACTVS_COMPLEXITY"), "72.5")
Loading