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.
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 ๐