RosettaCommons / RosettaCommons/foundry

Custom ligand conformer issues

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bug
Dominant language
Python
Stars
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Forks
181
Avg merge
4d 4h
Merged PRs (30d)
2

Description

When a custom ligand is provided from PDB, it creates conformer generation issues.
Is there a way to provide conformers? Or the ligand can be provided in other formats (e.g., SMILE, SDF)?

15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.ml.transforms.rdkit_utils: Initial conformer generation based on distance geometry failed. Successful: 0. Falling back to generating a conformer starting from random coordinates.
15:39:09 WARNING atomworks.ml.transforms.rdkit_utils: Failed to generate 1 conformers for UNL. Falling back to zeros.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the custom-ligand case from PDB and inspect the warning paths named in atomworks.io.tools.rdkit and atomworks.ml.transforms.rdkit_utils. Determine whether the supported input should preserve supplied conformers or accept another ligand format; done means the custom ligand no longer falls back to failed or zero conformers.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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