Error when running “plot_LHOC.py”

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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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