Hi Valerio,
I should preface things by saying that this script would be considerably easier to write in ChimeraX, because in ChimeraX the "runCommand" equivalent actually returns results from the command instead of nothing.  So in ChimeraX you can directly determine if the clash-finding command actually found any clashes.
So clearly the body of your 'if' statement never executed since it includes illegal statements that would have produced errors if the body of the 'if' statement had been executed, whereas you got no output.  So the first thing is put "print file_names" right after the line that sets files_names and see if any of the file names contain your search string ("xxx").  If none of them do, then you need to figure out why: is folder_path wrong?; is search_string wrong?; do the files not end in .pdb?; etc. 
In addition, I can see some problems even if the 'if' statement body had executed.  You don't close the models at the end, so they will build up and "findclash" will find more and more clashes.  Your actual findclash command needs to be "findclash #0 test self".  There is no "chimera.clashClashList".  Probably the simplest way to determine if clashes were found is checking if the clashes pseudobond group has any pseudobonds in it.  You can do that with:

for m in chimera.openModels.list(hidden=True):
if getattr(m, 'category', None) == "contacts":
clashes_found = len(m.pseudoBonds) > 0
break

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Feb 12, 2025, at 2:23 AM, valerio chiarini via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Responsible,

I am working on a script that should iterate through several structures, check the structures for clashes among all atoms, and eliminate the pdb in any clashes are found.

Here is what I have worked out so far:

# -*- coding: utf-8 -*-

import os
from chimera import runCommand as rc
from chimera import replyobj
import chimera

# Specify folder
folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/"

# String to be found
search_string = "xxx"

# List of files in the folder
file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")]

print("File trovati nella cartella:" + str(file_names))

# Loop on every file containing 'search_string' in the name
for pdb_file in file_names:
    if search_string in pdb_file:
        pdb_path = os.path.join(folder_path, pdb_file)

        # Open the PDB
        rc("open {}".format(pdb_path))

        # Calculates clashes
        rc("findclash")
        rc("wait")

        # Verify if any clashes are found
        clashes = chimera.clashClashList()

        if clashes:
            # If clashes are found eliminates the file
            os.remove(pdb_path)
            print("Clash trovati, il file {} è stato eliminato.".format(pdb_file))
        else:
            # If no clash, exit normally
            print("Nessun clash trovato per {}.".format(pdb_file))


But no analisys is done at all. I have been searching through the script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in order to found some clue on this function but so far I have found none.

Could you help me on this issue?

Thank you in advance

Valerio Chiarini
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