Add-ons: Import-Export: Atomic Blender PDB/XYZ division error #105322

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Byeongyoon-Kim · 2024-05-09T14:32:36+02:00

Byeongyoon-Kim commented

2024-05-09 14:32:36 +02:00

System Information
Operating system: Windows-10-10.0.22631-SP0 64 Bits
Graphics card: NVIDIA GeForce RTX 4060/PCIe/SSE2 NVIDIA Corporation 4.6.0 NVIDIA 552.22

Blender Version
Broken: version: version: 4.0.2, branch: blender-v4.0-release, commit date: 2023-12-05 07:41, hash: 9be62e85b727
Worked: (newest version of Blender that worked as expected)

Addon Information
Name: Atomic Blender PDB/XYZ (1, 8, 1)
Author: Clemens Barth

Short description of error

Dear developer.
When I imported the attached file 'Cabon monooxide_v1.pdb with the addon, it showed error massage below.

Python: Traceback (most recent call last):
  File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_gui.py", line 203, in execute
    import_pdb(self.ball,
  File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 1542, in import_pdb
    sticks = draw_sticks_dupliverts(all_atoms,
  File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 863, in draw_sticks_dupliverts
    n_b   = b / b.length
ZeroDivisionError: Vector division: divide by zero error

Then, I found by chance that slight differenct coordinations with same structure works without error: the attached 'Carbon monooxide_v2.pdb' file. Whether I turn on the 'bonds' option or not.

In another case, the attached 'acetonitirile3_cd_ob.pdb' file only works without checking 'bonds' in import option (the option for double and triple bonds). with enabling the option, it resulting the following error:

Python: Traceback (most recent call last):
  File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_gui.py", line 203, in execute
    import_pdb(self.ball,
  File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 1423, in import_pdb
    all_sticks = read_pdb_file_sticks(filepath_pdb,
  File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 429, in read_pdb_file_sticks
    dist_n = dist_n / dist_n.length
ZeroDivisionError: Vector division: divide by zero error

I have failed to figure out the solution in my ability. Please check this issue.
Many thanks,

Sincerely yours,

Exact steps for others to reproduce the error
The error have been reproduced with newely installed blender 4.0 and 4.1 either. and distinct PCs. newely installed blender opened, check addon 'atomic blender PDB/XYZ' in preference, file-import-PDB, then import the attached file with default options.

**System Information** Operating system: Windows-10-10.0.22631-SP0 64 Bits Graphics card: NVIDIA GeForce RTX 4060/PCIe/SSE2 NVIDIA Corporation 4.6.0 NVIDIA 552.22 **Blender Version** Broken: version: version: 4.0.2, branch: blender-v4.0-release, commit date: 2023-12-05 07:41, hash: `9be62e85b727` Worked: (newest version of Blender that worked as expected) **Addon Information** Name: Atomic Blender PDB/XYZ (1, 8, 1) Author: Clemens Barth **Short description of error** Dear developer. When I imported the attached file 'Cabon monooxide_v1.pdb with the addon, it showed error massage below. ``` Python: Traceback (most recent call last): File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_gui.py", line 203, in execute import_pdb(self.ball, File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 1542, in import_pdb sticks = draw_sticks_dupliverts(all_atoms, File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 863, in draw_sticks_dupliverts n_b = b / b.length ZeroDivisionError: Vector division: divide by zero error ``` Then, I found by chance that slight differenct coordinations with same structure works without error: the attached 'Carbon monooxide_v2.pdb' file. Whether I turn on the 'bonds' option or not. In another case, the attached 'acetonitirile3_cd_ob.pdb' file only works without checking 'bonds' in import option (the option for double and triple bonds). with enabling the option, it resulting the following error: ``` Python: Traceback (most recent call last): File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_gui.py", line 203, in execute import_pdb(self.ball, File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 1423, in import_pdb all_sticks = read_pdb_file_sticks(filepath_pdb, File "C:\Program Files\Blender Foundation\Blender 4.0\4.0\scripts\addons\io_mesh_atomic\pdb_import.py", line 429, in read_pdb_file_sticks dist_n = dist_n / dist_n.length ZeroDivisionError: Vector division: divide by zero error ``` I have failed to figure out the solution in my ability. Please check this issue. Many thanks, Sincerely yours, **Exact steps for others to reproduce the error** The error have been reproduced with newely installed blender 4.0 and 4.1 either. and distinct PCs. newely installed blender opened, check addon 'atomic blender PDB/XYZ' in preference, file-import-PDB, then import the attached file with default options.

acetonitrile3_cd_ob.pdb

1.0 KiB

Carbon monooxide_v2.pdb

450 B

Carbon monooxide_v1.pdb

450 B

Byeongyoon-Kim added the