Error when running “plot_LHOC.py”

This topic has 5 replies, 2 voices, and was last updated 7 years, 2 months ago by Anonymous.

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- August 13, 2017 at 12:54 pm #2713
  Anonymous
  Dear all,
  
  When I run the following command:
  
  $ROSETTA/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/plot_LHOC.py
  
  It gives the following error:
  
  /bin/sh: /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.macosclangrelease: No such file or directory
  
  Executing /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.macosclangrelease -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -s model-0.relaxed.pdb -pack_missing_sidechains false -out:file:score_only model-0.relaxe_LHOCs.score…
  
  Traceback (most recent call last):
  
  File “/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/plot_LHOC.py”, line 120, in <module>
  
  score_file = ScoreFile(i, infiles, outpath, names).plot_for_all_coordinates(tempfiles, angles_file)
  
  File “/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/ScoreFile.py”, line 64, in plot_for_all_coordinates
  
  self.load_template_data(tempfiles)
  
  File “/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/ScoreFile.py”, line 73, in load_template_data
  
  templates.calculate_angles()
  
  File “/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/TemplateScoreFiles.py”, line 38, in calculate_angles
  
  assert rc == 0, “Command %s failed!” %(LHOC_cmd)
  
  AssertionError: Command /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.macosclangrelease -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -s model-0.relaxed.pdb -pack_missing_sidechains false -out:file:score_only model-0.relaxe_LHOCs.score failed!
  
  It is strange that why the script calls the command “packing_angle.macosclangrelease” since my system is linux Centos. Is the a bug of plot_LHOC.py?
  
  Best regards.
  
  Yeping Sun
- August 13, 2017 at 9:32 pm #13653
  Anonymous
  I would say it’s closer to an “unimplemented feature” than a bug – it definitely hardcodes a mac path. I encourage you to just open the script up in a text editor and fix it yourself. You can even get away with `sed -i ‘s/macosclang/linuxgcc/’ plot_LHOC.py`. (I am assuming you are using gcc, correct less for clang.)
  
  The README in that directory does imply the hardcoding of the macos release. I’ve filed a bug for you, but it’s proably pretty low priority.
- August 14, 2017 at 1:05 am #13654
  Anonymous
  Hello, smlewis,
  
  Thank for the replay and for filing the bug.
  
  However, I have opened the plot_LHOC.py script with the text editor but cannot find where to fix, and there is no “macosclangrelease” tag at all. And `sed -i ‘s/macosclang/linuxgcc/’ plot_LHOC.py` changes nothing. The same error comes out after the “sed” substitution.
  
  Maybe the “macosclangrelease” tag is in some other script called by the plot_LHOC.py script? By what is it?
  
  Best regards,
  
  Yeping
  - August 14, 2017 at 2:16 am #13655
    Anonymous
    Yeah, you’re right, it’s line 42 in constants.py in the same directory. When I searched for the string I did the whole directory, instead of just the file, and didn’t notice which file it was in.
    
    constants.py
    
    42: rosetta_LHOC = rosetta_path + ‘/main/source/bin/packing_angle.macosclangrelease’
- August 16, 2017 at 6:30 am #13670
  Anonymous
  Hello smlewis,
  
  I have replaced the “macosclangrelease” with “linuxgccrelease” in Line 42 in the constants.py. However, when I ran the plot_LHOC.py script again, the expected plot wasn’t produced and the output log information ended with the following lines:
  
  Executing /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.linuxgccrelease -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -s model-9.relaxed.pdb -pack_missing_sidechains false -out:file:score_only model-9.relaxe_LHOCs.score… …done!
  
  /app/anaconda2/lib/python2.7/site-packages/matplotlib/font_manager.py:1297: UserWarning: findfont: Font family not found. Falling back to DejaVu Sans
  
  (prop.get_family(), self.defaultFamily[fontext]))
  
  Is there still something with it?
  
  Best regards.
  
  Yeping
  - August 16, 2017 at 3:30 pm #13673
    Anonymous
    Dunno, I’ll send it along to the author.
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