When I run the following command:
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
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
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?
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.
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?
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.
42: rosetta_LHOC = rosetta_path + '/main/source/bin/packing_angle.macosclangrelease'
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
Is there still something with it?
Dunno, I'll send it along to the author.