RosettaCommons / RosettaCommons/PyRosetta.notebooks
class RNA_DeNovoProtocolMover.de_novo_setup_from_command_line() or apply() can't run normally
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 709
- Forks
- 173
- Avg merge
- 5m
- Merged PRs (30d)
- 2
Description
When I create an RNA_DeNovoProtocolMover() using a Python script, it stops running and throws an error with code ‘139 (interrupted by signal 11:SIGSEGV)’ either during initialization or when applying it.
This is my code:
from pyrosetta import init
init()
from pyrosetta import pose_from_pdb
from pyrosetta import rosetta
pose = pose_from_pdb('./example/7lyg.pdb') # 7lyg is an RNA
from pyrosetta.rosetta.protocols.rna.denovo.movers import RNA_DeNovoProtocolMover
rna_denovo_mover = RNA_DeNovoProtocolMover()
fasta_files = rosetta.utility.vector1_std_string()
fasta_files.append('./example/7lyg.fasta')
rna_denovo_mover.set_fasta_files(fasta_files)
rna_denovo_mover.set_minimize_rna(True)
rna_denovo_mover.de_novo_setup_from_command_line()
rna_denovo_mover.apply(pose)
My English is not good. If there is anything offensive, please forgive me. Thanks !
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the reproducer in the issue: initialize PyRosetta, load example/7lyg.pdb, provide example/7lyg.fasta, and call RNA_DeNovoProtocolMover.de_novo_setup_from_command_line() or apply(pose). Compare both entry points while isolating the SIGSEGV; done means the RNA mover runs without error for this example.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100