Comments (1)
Hi @AJVelezRueda,
Thank you for reporting this error.
We are working on a solution.
The problem seems to be with the order in which we perform the characterization. It seems that if we run constitutional characterization after depth characterization, a memory issue appears, generating the "Segmentation fault" message.
Until we fix it completely, here is a workaround to perform the analysis you shared with us:
import pyKVFinder
# PARAMETERS
path = "1H6J_B.pdb"
probe_out = 4.0
hydrophobicity_scale='EisenbergWeiss'
# Run 100 times pyKVFinder for 1H6J_B
for i in range(100):
# Atomic information
atomic = pyKVFinder.read_pdb("1H6J_B.pdb")
# Grid
vertices = pyKVFinder.get_vertices(atomic, probe_out=probe_out)
# Cavity detection
ncav, cavities = pyKVFinder.detect(atomic, vertices, probe_out=probe_out)
# Constitutional
residues = pyKVFinder.constitutional(cavities, atomic, vertices)
# Depth characterization
depth, avg_depth, max_depth = pyKVFinder.depth(cavities)
# Hydropathy characterization
surface, volume, area = pyKVFinder.spatial(cavities)
hydropathy, avg_hydropathy = pyKVFinder.hydropathy(surface, atomic, vertices, hydrophobicity_scale=hydrophobicity_scale)
# Export cavities
# NOTE: Uncomment to export cavities to PDB file
# pyKVFinder.export(f"cavity_{i:02d}.pdb", cavities, surface, vertices, B=depth, output_hydropathy=f"hydropathy_{i:02d}.pdb", scales=hydropathy)
Please let me know if this workaround solved your problem.
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