can not recognize rg_mcs

[MachineGUN001]

hi,

thanks for your great and interesting work.

that's a new thought for SAR analysis.

when I try to run finding_cores_from_whole_dataset.py script, the error occured ass below:

53 Unrepresented rgs
Traceback (most recent call last):
File "c:\Users\LSY.conda\envs\Resgen\lib\site-packages\pandas\core\indexes\base.py", line 3802, in get_loc
return self._engine.get_loc(casted_key)
File "pandas_libs\index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas_libs\index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc
File "pandas_libs\hashtable_class_helper.pxi", line 5745, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas_libs\hashtable_class_helper.pxi", line 5753, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: '[Li][Co][Ge][Na]=Na[Ge]Li([Ga])[Ga]'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "e:\Cheminfo_Workshop\14_SAR_Analysis\reduced_graph_visualisation-main\python\reduced_graph_core_extraction\finding_cores_from_whole_dataset.py", line 354, in
final_df = core_generator(merge_df)
File "e:\Cheminfo_Workshop\14_SAR_Analysis\reduced_graph_visualisation-main\python\reduced_graph_core_extraction\finding_cores_from_whole_dataset.py", line 344, in core_generator
core_df = core_cluster_generator(core_df,
File "e:\Cheminfo_Workshop\14_SAR_Analysis\reduced_graph_visualisation-main\python\reduced_graph_core_extraction\finding_cores_from_whole_dataset.py", line 303, in core_cluster_generator
centroid, mcs_smarts = finding_centroid(unrepresented_rgs,
File "e:\Cheminfo_Workshop\14_SAR_Analysis\reduced_graph_visualisation-main\python\reduced_graph_core_extraction\finding_cores_from_whole_dataset.py", line 110, in finding_centroid
rg_neighbours = similarity_matrix[rg].tolist()
File "c:\Users\LSY.conda\envs\Resgen\lib\site-packages\pandas\core\frame.py", line 3807, in getitem
indexer = self.columns.get_loc(key)
File "c:\Users\LSY.conda\envs\Resgen\lib\site-packages\pandas\core\indexes\base.py", line 3804, in get_loc
raise KeyError(key) from err
KeyError: '[Li][Co][Ge][Na]=Na[Ge]Li([Ga])[Ga]'

the step 1 and 2 folllowed by README instruction worked well, but it doest work in step 3 with finding_cores_from_whole_dataset.py.

how can I fix it up?

many thanks,

[MachineGUN001]

for another question,

as README instruction, the commandline,

Step 2: Run python/MCS/mcs_similarity_matrix.py
     Example code:
$ python mcs_similarity_matrix.py -i output_rg.txt -s output_rg.sdf -o rg_mcs.txt

but actually, I can see the function of this scripy with parameters below.

usage: mcs_similarity_matrix.py [-h] [-i INPUT] [-s OUTPUT_SMILES]
[-r OUTPUT_RG] [-p REPRESENTATIONTYPE]
[-t SEPARATOR] [-v]

Arguments for the Reduced Graph Code

options:
-h, --help show this help message and exit
-i INPUT Name of the input file
-s OUTPUT_SMILES Name of the output of the smiles mcs file
-r OUTPUT_RG Name of the output of the smiles rg file
-p REPRESENTATIONTYPE
The type of representation used to cluster: both
smiles rg
-t SEPARATOR File separator in the input file
-v Switches on verbose mode

could you please check the command line and how to input and output the right files? thanks