Allow disabling 3D descriptors while enabling 2D descriptors #62
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### Summary
This PR adds support for disabling the calculation of 3D descriptors independently in the `from_smiles` function, while preserving backward compatibility.
### Problem
Currently, the `from_smiles` function uses a single `descriptors` flag to control both 2D and 3D descriptor calculation. However, some SMILES strings (e.g., "C") cause `RuntimeError` when 3D descriptors are enabled, even though they work fine with only 2D descriptors.
For example:
```python
from padelpy import from_smiles
# This raises RuntimeError
from_smiles("C", descriptors=True)
# This works fine
padeldescriptor(mol_dir="input.smi", d_file="output.csv", d_2d=True, d_3d=False)
### Solution
If `descriptors_3d` is not provided, it defaults to the value of descriptors (preserving current behavior).
If `descriptors_3d=False`, 3D descriptor calculation is skipped even when descriptors=True.
forgot to add the new flag for `from_mdl`
add usages of the new flag `descriptors_3d` for "from_mdl", "from_smiles", and "from_sdf" functions
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Summary
This PR adds support for disabling the calculation of 3D descriptors independently in the
from_smilesfunction, while preserving backward compatibility.Problem
Currently, the
from_smilesfunction uses a singledescriptorsflag to control both 2D and 3D descriptor calculation. However, some SMILES strings (e.g., "C") causeRuntimeErrorwhen 3D descriptors are enabled, even though they work fine with only 2D descriptors.For example:
Usage behavior
If
descriptors_3dis not provided, it defaults to the value of descriptors (preserving current behavior).If
descriptors_3d=False, 3D descriptor calculation is skipped even when descriptors=True.Usage example:
Potential fix for
This change may also help fix related issues such as #51 or #9 and #11.