mmpdb transform --min-constant-size N - AttributeError: 'Fragmentation' object has no attribute 'num_variable_heavies' #60

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opened 2025-10-14 17:04:20 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:04:20 -06:00

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Originally created by @Niaev on 11/27/2019

On Windows, the options --min-variable-size and --min-constant-size of transform command aren't working. It is saying that, in the line 909 in mmpdblib/analysis_algorithms.py, a Fragmentation object has no attribute 'num_variable_heavies'.

I'm on Windows 10 and using Anaconda Prompt, mmpdb works fine.

I tried the same command on Linux and it worked, but I think it's relevant to report the issue on Windows.

(base) C:\Users\me\Desktop\mmpdb-2.1>python mmpdb transform --smiles CC=CC=CC=O --min-variable-size 5 my_data.mmpdb
Traceback (most recent call last):
  File "mmpdb", line 10, in <module>
    commandline.main()
  File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\commandline.py", line 988, in main
    parsed_args.command(parsed_args.subparser, parsed_args)
  File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\commandline.py", line 678, in transform_command
    do_analysis.transform_command(parser, args)
  File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\do_analysis.py", line 116, in transform_command
    explain = explain,
  File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\analysis_algorithms.py", line 764, in transform
    cursor=cursor, explain=explain)
  File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\analysis_algorithms.py", line 909, in make_transform
    if min_variable_size and frag.num_variable_heavies < min_variable_size:
AttributeError: 'Fragmentation' object has no attribute 'num_variable_heavies'

*Originally created by @Niaev on 11/27/2019* On Windows, the options `--min-variable-size` and `--min-constant-size` of **transform** command aren't working. It is saying that, in the line 909 in `mmpdblib/analysis_algorithms.py`, a Fragmentation object has no attribute 'num_variable_heavies'. I'm on Windows 10 and using Anaconda Prompt, mmpdb works fine. I tried the same command on Linux and it worked, but I think it's relevant to report the issue on Windows. ``` (base) C:\Users\me\Desktop\mmpdb-2.1>python mmpdb transform --smiles CC=CC=CC=O --min-variable-size 5 my_data.mmpdb Traceback (most recent call last): File "mmpdb", line 10, in <module> commandline.main() File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\commandline.py", line 988, in main parsed_args.command(parsed_args.subparser, parsed_args) File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\commandline.py", line 678, in transform_command do_analysis.transform_command(parser, args) File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\do_analysis.py", line 116, in transform_command explain = explain, File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\analysis_algorithms.py", line 764, in transform cursor=cursor, explain=explain) File "C:\Users\me\Desktop\mmpdb-2.1\mmpdblib\analysis_algorithms.py", line 909, in make_transform if min_variable_size and frag.num_variable_heavies < min_variable_size: AttributeError: 'Fragmentation' object has no attribute 'num_variable_heavies' ```