RosettaCommons / RosettaCommons/PyRosetta.notebooks

class RNA_DeNovoProtocolMover.de_novo_setup_from_command_line() or apply() can't run normally

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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 !

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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

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