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Error when running "plot_LHOC.py"

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Error when running "plot_LHOC.py"
#1

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

Category: 
Post Situation: 
Sun, 2017-08-13 05:54
Sunyp_IM

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.

Sun, 2017-08-13 14:32
smlewis

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

 

Sun, 2017-08-13 18:05
Sunyp_IM

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'
 

Sun, 2017-08-13 19:16
smlewis

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 [u'arial'] not found. Falling back to DejaVu Sans
  (prop.get_family(), self.defaultFamily[fontext]))
 

Is there still something with it? 

Best regards.

Yeping

 

 

Tue, 2017-08-15 23:30
Sunyp_IM

Dunno, I'll send it along to the author.

Wed, 2017-08-16 08:30
smlewis