Autodesk / Autodesk/molecular-design-toolkit
Wrong bonding between residues surrounding missing ones
- Dominant language
- Python
- Stars
- 174
- Forks
- 37
- PR merge metrics
- No merged PRs in 30d
Description
This is a residue that appears right before several missing residues:
```python
mol = mdt.from_pdb('3p3k')
res = mol.residues[46]
```
MDT currently shows a bond between this and the next available residue, which is clearly wrong:
```python
>>> res.bonded_residues
[,
]
>>> res.distance(res.next_residue)
3.88332344777 ang
```
Also `res.next_residue` returns `''`, but should raise something along the lines of `StopIteration`, or maybe `MissingResidue` or maybe `PrematureTerminus`
I suppose it could also just return a `MissingResidue` object or something
Contributor guide
Research direction
Reproduce the case with mdt.from_pdb('3p3k') and residue 46, then trace how bonded_residues and next_residue handle gaps in the residue sequence. Confirm the intended missing-residue boundary behavior before changing it; done means no bond spans the missing residues and next_residue reports that boundary consistently.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100