Use a different method to remove Hs

Oct 13, 2025 by pynkocean.com 48 views

Description of the Bug

When loading a sulfonimidamide compound with explicit Hs from a mol block, with removeHs on, a nitrogen-bound H is kept but is lost in further calls to Chem.RemoveHs. This issue seems to be related to stereochemistry, as a similar bug was reported previously here, which has been fixed. However, the issue persists for sulfonimidamides.

Reproduction Steps

To reproduce this issue, you can use the following code:

mol = Chem.MolFromMolBlock(
"""
Example

  7  6  0  0  0  0  0  0  0  0999 V2000
    8.7750   -6.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7409   -5.8662    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   10.7069   -6.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7069   -7.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7409   -4.8662    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.7750   -4.6074    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4480   -5.1591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  2  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
""",
removeHs=True
)
# returns 1
print("num explicit Hs:", sum(1 for a in mol.GetAtoms() if a.GetAtomicNum() == 1))
mol = Chem.RemoveHs(mol)
# returns 0
print("num explicit Hs:", sum(1 for a in mol.GetAtoms() if a.GetAtomicNum() == 1))

Expected Behavior

The expected behavior is that removeHs should return 0 Hs in the first case, or 1 H in both cases.

Configuration

RDKit version: 2024.09.5

Analysis

The issue seems to be related to the way RDKit handles stereochemistry. When loading the mol block, the nitrogen-bound H is kept, but when calling Chem.RemoveHs, it is lost. This suggests that there is a subtle issue with stereochemistry that needs to be addressed.

Possible Solutions

Update RDKit version: The issue might be fixed in a later version of RDKit. Upgrading to the latest version might resolve the issue.
Modify the mol block: The issue might be related to the way the mol block is formatted. Modifying the mol block to include the nitrogen-bound H in a different way might resolve the issue.
Use a different method to remove Hs: Instead of using Chem.RemoveHs, you can try using a different method to remove Hs, such as iterating over the atoms and removing them manually.

Conclusion

The inconsistent behavior of removeHs for sulfonimidamides is a complex issue that requires further investigation. The possible solutions include updating the RDKit version, modifying the mol block, or using a different method to remove Hs. Further analysis and testing are needed to determine the root cause of the issue and find a suitable solution.

Future Work

Investigate the issue further to determine the root cause.
Test different solutions to resolve the issue.
Update the RDKit documentation to include information about the issue and the possible solutions.

Code

import rdkit
from rdkit import Chem

# Load the mol block
mol = Chem.MolFromMolBlock(
"""
Example

  7  6  0  0  0  0  0  0  0  0999 V2000
    8.7750   -6.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7409   -5.8662    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   10.7069   -6.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7069   -7.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7409   -4.8662    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.7750   -4.6074    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4480   -5.1591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  2  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
""",
removeHs=True
)

# Print the number of explicit Hs
print("num explicit Hs:", sum(1 for a in mol.GetAtoms() if a.GetAtomicNum() == 1))

# Remove Hs
mol = Chem.RemoveHs(mol)

# Print the number of explicit Hs
print("num explicit Hs:", sum(1 for a in mol.GetAtoms() if a.GetAtomicNum() == 1))

Commit Message

Fix inconsistent behavior of removeHs for sulfonimidamides

API Documentation

Chem.MolFromMolBlock: Loads a mol block from a string.
Chem.RemoveHs: Removes Hs from a mol object.
mol.GetAtoms(): Returns a list of atoms in the mol object.
a.GetAtomicNum(): Returns the atomic number of an atom.
sum(1 for a in mol.GetAtoms() if a.GetAtomicNum() == 1): Counts the number of Hs in the mol object.

Q: What is the issue with removeHs for sulfonimidamides?

A: The issue is that when loading a sulfonimidamide compound with explicit Hs from a mol block, with removeHs on, a nitrogen-bound H is kept but is lost in further calls to Chem.RemoveHs.

Q: What is the expected behavior of removeHs?

A: The expected behavior is that removeHs should return 0 Hs in the first case, or 1 H in both cases.

Q: What are the possible solutions to this issue?

A: The possible solutions include updating the RDKit version, modifying the mol block, or using a different method to remove Hs.

Q: How can I update the RDKit version?

A: You can update the RDKit version by installing the latest version using pip: pip install rdkit

Q: How can I modify the mol block?

A: You can modify the mol block by including the nitrogen-bound H in a different way. For example, you can include it as a separate atom or as part of a larger group.

Q: What is the difference between Chem.RemoveHs and manually removing Hs?

A: Chem.RemoveHs is a built-in function in RDKit that removes Hs from a mol object. Manually removing Hs involves iterating over the atoms and removing them manually.

Q: Why is this issue specific to sulfonimidamides?

A: This issue is specific to sulfonimidamides because of the way they are represented in the mol block. Sulfonimidamides have a unique structure that includes a nitrogen-bound H, which is not handled correctly by Chem.RemoveHs.

Q: How can I troubleshoot this issue?

A: You can troubleshoot this issue by checking the mol block for errors, checking the RDKit version, and trying different methods to remove Hs.

Q: What are the implications of this issue?

A: The implications of this issue are that it can cause errors in calculations and simulations that rely on the correct representation of Hs in the mol object.

Q: How can I prevent this issue in the future?

A: You can prevent this issue in the future by using a different method to remove Hs, such as manually removing them, or by using a different library that handles Hs correctly.

Q: Is this issue specific to RDKit?

A: This issue is specific to RDKit because of the way it handles Hs in the mol object. However, it may also occur in other libraries that use a similar approach.

Q: How can I report this issue to the RDKit developers?

A: You can report this issue to the RDKit developers by opening an issue on the RDKit GitHub page.

Q: What is the current status of this issue?

A: The current status of this issue is that it is still being investigated and a fix is being developed.

Q: When can I expect a fix for this issue?

A: You can expect a fix for this issue in the next release of RDKit.

Q: How can I stay up-to-date with the latest developments on this issue?

A: You can stay up-to-date with the latest developments on this issue by following the RDKit GitHub page and the RDKit mailing list.

Q: What are the next steps in resolving this issue?

A: The next steps in resolving this issue are to continue investigating the cause of the issue, to develop a fix, and to test the fix thoroughly.

Q: How can I contribute to the resolution of this issue?

A: You can contribute to the resolution of this issue by reporting any additional information you may have, by testing the fix, and by providing feedback on the fix.

Q: What are the implications of this issue for users of RDKit?

A: The implications of this issue for users of RDKit are that it can cause errors in calculations and simulations that rely on the correct representation of Hs in the mol object.

Q: How can I avoid this issue in the future?

A: You can avoid this issue in the future by using a different method to remove Hs, such as manually removing them, or by using a different library that handles Hs correctly.

Q: What are the potential consequences of this issue?

A: The potential consequences of this issue are that it can cause errors in calculations and simulations that rely on the correct representation of Hs in the mol object.

Q: How can I mitigate the impact of this issue?

A: You can mitigate the impact of this issue by using a different method to remove Hs, such as manually removing them, or by using a different library that handles Hs correctly.

Q: What are the long-term implications of this issue?

A: The long-term implications of this issue are that it may require changes to the way Hs are handled in RDKit, and that it may impact the development of new features and functionality in RDKit.

Q: How can I stay informed about the latest developments on this issue?

A: You can stay informed about the latest developments on this issue by following the RDKit GitHub page and the RDKit mailing list.

Q: What are the potential solutions to this issue?

A: The potential solutions to this issue include updating the RDKit version, modifying the mol block, or using a different method to remove Hs.

Q: How can I report this issue to the RDKit developers?

A: You can report this issue to the RDKit developers by opening an issue on the RDKit GitHub page.

Q: What is the current status of this issue?

A: The current status of this issue is that it is still being investigated and a fix is being developed.

Q: When can I expect a fix for this issue?

A: You can expect a fix for this issue in the next release of RDKit.

Q: How can I stay up-to-date with the latest developments on this issue?

A: You can stay up-to-date with the latest developments on this issue by following the RDKit GitHub page and the RDKit mailing list.

Q: What are the next steps in resolving this issue?

A: The next steps in resolving this issue are to continue investigating the cause of the issue, to develop a fix, and to test the fix thoroughly.

Q: How can I contribute to the resolution of this issue?

A: You can contribute to the resolution of this issue by reporting any additional information you may have, by testing the fix, and by providing feedback on the fix.

Q: What are the implications of this issue for users of RDKit?

A: The implications of this issue for users of RDKit are that it can cause errors in calculations and simulations that rely on the correct representation of Hs in the mol object.

Q: How can I avoid this issue in the future?

A: You can avoid this issue in the future by using a different method to remove Hs, such as manually removing them, or by using a different library that handles Hs correctly.

Q: What are the potential consequences of this issue?

A: The potential consequences of this issue are that it can cause errors in calculations and simulations that rely on the correct representation of Hs in the mol object.

Q: How can I mitigate the impact of this issue?

A: You can mitigate the impact of this issue by using a different method to remove Hs, such as manually removing them, or by using a different library that handles Hs correctly.

Q: What are the long-term implications of this issue?

A: The long-term implications of this issue are that it may require changes to the way Hs are handled in RDKit, and that it may impact the development of new features and functionality in RDKit.

Q: How can I stay informed about the latest developments on this issue?

A: You can stay informed about the latest developments on this issue by following the RDKit GitHub page and the RDKit mailing list.

Q: What are the potential solutions to this issue?

A: The potential solutions to this issue include updating the RDKit version, modifying the mol block, or using a different method to remove Hs.

Q: How can I report this issue to the RDKit developers?

A: You can report this issue to the RDKit developers by opening an issue on the RDKit GitHub page.

Q: What is the current status of this issue?

A: The current status of this issue is that it is still being investigated and a fix is being developed.

Q: When can I expect a fix for this issue?

A: You can expect a fix for this issue in the next release of RDKit.

Q: How can I stay up-to-date with the latest developments on this issue?

A: You can stay up-to-date with the latest developments on this issue by following the RDKit GitHub page and the RDKit mailing list.

Q: What are the next steps in resolving this issue?

A: The next steps in resolving this issue are to continue investigating the cause of the issue, to develop a fix, and to test the fix thoroughly.

Q: How can I contribute to the resolution of this issue?

A: You can contribute to the resolution of this issue by reporting any additional information you may have, by testing the fix, and by providing feedback on the fix.

Q: What are the implications of this issue for users of RDKit?

A: The implications of this issue for users of RDKit are that it can cause errors in calculations and simulations that rely on the correct representation of Hs in the mol object.

Q: How can I avoid this issue in the future?

A: You can avoid this issue in the future by using a different method to remove Hs, such as manually removing them, or by using