Hi All,
I ran into repeated segmentation fault error when I tried to utilize the InterfaceAnalyzerMover to calcualte interaction energy between the two protein chains.
Here is my script:
import pyrosetta
from pyrosetta.rosetta.core.import_pose import pose_from_file
from pyrosetta.rosetta.protocols.analysis import InterfaceAnalyzerMover
import sys
def calculate_interface_energy(pdb_file, chain_target, chain_partners):
"""
Calculates the interaction energy between one chain and a complex formed by other chains in a protein structure.
Args:
pdb_file (str): Path to the PDB file.
chain_target (str): Identifier for the target chain.
chain_partners (str): Identifiers for the partner chains concatenated.
Returns:
float: The interaction energy between the target chain and the partner chains.
"""
# Load the PDB file into a Pose object
pose = pose_from_file(pdb_file)
# Define the complex as a combination of the target chain and partner chains
complex_identifier = chain_target + "_" + chain_partners
# Setup the InterfaceAnalyzerMover for the defined complex
interface_analyzer = InterfaceAnalyzerMover()
interface_analyzer.set_interface(complex_identifier)
interface_analyzer.test_move(pose) # Test the move to ensure the interface is correctly defined
interface_analyzer.apply(pose) # Apply the mover to the pose
# Retrieve the computed interface energy
interface_energy = interface_analyzer.get_interface_dG()
return interface_energy
def main():
# Specify your parameters
pdb_file = sys.argv[1]
chain_target = "A" # The single chain you are focusing on
chain_partners = "B" # The other chains, treated as a combined entity
# Initialize PyRosetta
pyrosetta.init(extra_options="-mute all -load_PDB_components false -extra_res_fa GDP.params")
# Calculate and print the interface energy
interface_energy = calculate_interface_energy(pdb_file, chain_target, chain_partners)
print(f"Interface energy between chain {chain_target} and chains {chain_partners}: {interface_energy} REU")
if __name__=="__main__":
main()
The seg-fault error happens with either test_move, or apply (when I comment out test_move)
I can't figure out the problem because it seems to me that the error stems from the underlying C++ script.
Any suggestion is appreciated.
P.S. I cannot attach the test input I used because it is too big and this forum doesn't take the zipped version. If the error cannot be replicated with a different input, I will try to paste the PDB content as plain text in replies.
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