Dear Rodrigo and Alexandre,

Thank you for providing a solution to convert the HADDOCK output into an mmcif file, this is really useful.
I am currently preparing for a PDB-Dev submission and would like to encode my HADDOCK output in an mmcif file.
Unfortunately, I am rather new to all of this and I am having troubles running the haddock2mmcif script.
The problem might be the installation of python and VSCode on my computer but I am not 100% sure.
The installation of haddock2mmcif seems to have worked properly but I can't seem to use the haddock2mmcif command directly in VSCode.

So when I run it with C:\Users\dschuster\Scripts\haddock2mmcif.exe --output example.cif E2A-HPR/
I get the following output:

2023-06-06 10:43:19,157 cli:140 INFO - Input run directory: E2A-HPR
2023-06-06 10:43:19,157 cli:145 INFO - Initializing System
2023-06-06 10:43:19,157 cli:153 INFO - Creating Asymetric Units
2023-06-06 10:43:19,158 cli:161 INFO - Reading E2A-HPR\begin\complex_1.pdb
2023-06-06 10:43:19,168 cli:168 INFO - Creating entity based on chain A
2023-06-06 10:43:19,168 cli:168 INFO - Creating entity based on chain B
2023-06-06 10:43:19,169 cli:180 INFO - Adding Asymetric Units to the System
2023-06-06 10:43:19,169 cli:186 INFO - Organizing Asymetric Units into Modeled Assembly
2023-06-06 10:43:19,169 cli:191 INFO - Defining the protocol
2023-06-06 10:43:19,169 cli:201 INFO - Ranking the clusters from E2A-HPR\structures\it1\water\analysis\cluster.out based on E2A-HPR\structures\it1\water\file.list
2023-06-06 10:43:19,180 cli:208 INFO - Getting the interface cutoff from E2A-HPR\run.cns
2023-06-06 10:43:19,194 cli:216 INFO - Processing cluster1_1.pdb
Traceback (most recent call last):
File "C:\Users\dschuster\Scripts\haddock2mmcif-script.py", line 33, in
sys.exit(load_entry_point('haddock2mmcif', 'console_scripts', 'haddock2mmcif')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "c:\users\dschuster\haddock2mmcif\src\haddock2mmcif\cli.py", line 225, in main
cluster_pdb.get_interface(cutoff=interface_cutoff)
File "c:\users\dschuster\haddock2mmcif\src\haddock2mmcif\modules\pdb.py", line 82, in get_interface
out = subprocess.check_output(shlex.split(cmd)) # nosec
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\dschuster\Lib\subprocess.py", line 466, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\dschuster\Lib\subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\dschuster\Lib\subprocess.py", line 1024, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Users\dschuster\Lib\subprocess.py", line 1509, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [WinError 2] The system cannot find the file specified

Do you maybe have any idea what could be wrong on my side? I would be thankful for any and all help and guidance. Really trying to get this mmcif file ready for our submission 😄

Thank you and all the best,
Dina

Describe the bug
Conversion pipeline stops after the seven highest ranked clusters, no output file is generated.
The bug can be reproduced by different people, as well as when using a different HADDOCK output folder for the conversion.

Last few lines before error:

2023-06-06 15:31:47,910 cli:216 INFO - Processing cluster3_1.pdb
2023-06-06 15:31:48,587 cli:216 INFO - Processing cluster3_2.pdb
2023-06-06 15:31:49,264 cli:216 INFO - Processing cluster3_3.pdb
2023-06-06 15:31:49,941 cli:216 INFO - Processing cluster3_4.pdb
2023-06-06 15:31:50,619 cli:256 INFO - Finalizing group cluster Rank: 7 Number:3

Error message:

Traceback (most recent call last):
File "/usr/local/bin/haddock2mmcif", line 33, in
sys.exit(load_entry_point('haddock2mmcif', 'console_scripts', 'haddock2mmcif')())
File "/mnt/c/Users/dschuster/haddock2mmcif/src/haddock2mmcif/cli.py", line 215, in main
for structure in clustered_structures[cluster_name]:
KeyError: 5

To Reproduce
https://wenmr.science.uu.nl/haddock2.4/run/6879610780/129967-AC8-Gbg_2
I am not sure if this run can still be found - I would otherwise also be happy to share the files in a different way

Expected behavior
Expected haddock2mmcif to convert HADDOCK output to mmcif file.

Additional context
My output has 10 clusters (cluster 1, 2, 3, 4, 6, 8, 9, 14, 15, 16)