Reading local PDB file failed, got file from PDB database. No bug info printed and it stayed 0% instead of 100%.

[DUAN-GAO]

Describe the bug Reading local PDB file failed, got file from PDB database. No bug info printed and it stayed 0% instead of 100%. To Reproduce Output： Reading PDB file... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% -:--:--

That's all I got from running the below code：

file = "mmdb_8FYW.pdb"

from graphein.protein.config import ProteinGraphConfig
from graphein.protein.graphs import construct_graph

config = ProteinGraphConfig(

)
G = construct_graph(path=file, config=config)
print(G)

Expected behavior The reading finished and a graph printed. Screenshots

• OS: [Win 10]
• Python Version 3.9.21
• Graphein Version [1.7.7] & pip installed

Additional context Could u help, many thanks.

[a-r-j]

Hi @DUAN-GAO could you kindly share the PDB file so I can reproduce the error?

[DUAN-GAO]

Great thanks. https://drive.google.com/file/d/1pEQuboMqHsGnivvA0mu-vAkBplXm0Ck7/view?usp=drive_link

[prabhsuratsingh]

When i try to read a pdb file, i also get the same error Reading PDB file... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% -:--:--make: *** [Makefile:7: run] Error -1073740791

From what i found out this is Error code: STATUS_STACK_BUFFER_OVERRUN, i could be wrong. I verified the pdb file from BioPython's pdb parser, and it was valid. Even RCSB 3D viewer is rendering the protein. This wasnt happening a year ago when i last used graphein. Could this be happening because i re-installed C++ Build Tools?