1. 07 Jun, 2018 1 commit
  2. 31 May, 2018 3 commits
  3. 30 May, 2018 3 commits
  4. 29 May, 2018 2 commits
  5. 28 May, 2018 1 commit
  6. 25 May, 2018 1 commit
  7. 24 May, 2018 1 commit
  8. 09 May, 2018 1 commit
    • Oliver Smart's avatar
      Deal with "Method duplicity in test_process_components_cif_cli.py" · ee897993
      Oliver Smart authored
      For issue #42. This commit in trunk.
      
      Due to a type method test_subdir_in_files_created was defined twice.
      Have renamed the two occurrences to:
      * test_subdirs_in_files_are_created
      * test_subdirs_in_images_are_created
      
      Tests work in trunk branch:
              (test-rdkit_27) Olivers-MBP:ccd_utils osmart$ pytest -v -k test_subdirs_in pdbeccdutils/tests/test_process_components_cif_cli.py
              =========================================================================== test session starts ===========================================================================
              platform darwin -- Python 2.7.14, pytest-3.5.0, py-1.5.3, pluggy-0.6.0 -- /Users/osmart/anaconda3/envs/test-rdkit_27/bin/python
              cachedir: .pytest_cache
              rootdir: /Users/osmart/ccd_utils_py27/ccd_utils, inifile:
              collected 93 items / 81 deselected
      
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[mmcif] PASSED                                    [  8%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[sdf] PASSED                                      [ 16%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[sdf_nh] PASSED                                   [ 25%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[sdf_r] PASSED                                    [ 33%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[sdf_r_nh] PASSED                                 [ 41%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[pdb] PASSED                                      [ 50%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[pdb_r] PASSED                                    [ 58%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[cml] PASSED                                      [ 66%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[xyz] PASSED                                      [ 75%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_files_are_created[xyz_r] PASSED                                    [ 83%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_images_are_created[svg_with_atom_labels] PASSED                    [ 91%]
              pdbeccdutils/tests/test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdirs_in_images_are_created[svg_without_atom_labels] PASSED                 [100%]
      
              ================================================================ 12 passed, 81 deselected in 1.01 seconds =================================================================
      ee897993
  9. 08 May, 2018 2 commits
    • Oliver Smart's avatar
      b9e62472
    • Oliver Smart's avatar
      track down error to matplotlib. · 93edf4fa
      Oliver Smart authored
      For issue #46.
      
      Running
      
      	ccd_mogul_cli ccd_mmcif_test_files/GLC.cif GLC_ccd_mogul_cli.html --debug
      
      Produces output:
      
      	DEBUG: classification number=1 very-common
      	DEBUG: call to ring_histogram_svg
      	QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/5894', please create it with 0700 permissions.
      	Segmentation fault
      
      So crash occurs on line 551: 'fig = plt.figure()'
      
      	549     def ring_histogram_svg(self, strangeness):
      	550         logging.debug('call to ring_histogram_svg')
      	551         fig = plt.figure()
      	552         logging.debug('after plt.figure()')
      
      as never print the debug message 'after plt.figure()'.
      93edf4fa
  10. 30 Mar, 2018 6 commits
    • Oliver Smart's avatar
      rename cut down components cif file to cut_down_components.cif · c8a6423e
      Oliver Smart authored
      from components.cif.first_five_comps as this is clearer.
      
      work for issue #37 and #38
      c8a6423e
    • Oliver Smart's avatar
      separate utilities for tests from others to make refactoring · 78e3c02d
      Oliver Smart authored
      cleaner.
      
      work for issue #37 and #38
      78e3c02d
    • Oliver Smart's avatar
      separate utilities for tests from others to make refactoring · 56b47e37
      Oliver Smart authored
      cleaner.
      
      work for issue #37 and #38
      56b47e37
    • Oliver Smart's avatar
      move utilities.py to the tests subdirectory prior to seperating test · 165245eb
      Oliver Smart authored
      specific ones.
      
      work for issue #37 and #38
      165245eb
    • Oliver Smart's avatar
      refactoring unit test for process_components_cif_cli - split up main · 21050558
      Oliver Smart authored
      test running on cut down components cif by using pytest fixture and
      parametrize features.
      
      finished
      
      work for issue #37 and #38
      
      pytest output show tests work:
      
      (test-rdkit_27) Olivers-MacBook-Pro:tests osmart$ pytest -vv test_process_components_cif_cli.py
      ================================================================= test session starts ==================================================================
      platform darwin -- Python 2.7.14, pytest-3.5.0, py-1.5.3, pluggy-0.6.0 -- /Users/osmart/anaconda3/envs/test-rdkit_27/bin/python
      cachedir: ../../.pytest_cache
      rootdir: /Users/osmart/ccd_utils_py27/ccd_utils, inifile:
      collected 83 items
      
      test_process_components_cif_cli.py::TestCommandLineArgs::test_with_empty_args PASSED                                                             [  1%]
      test_process_components_cif_cli.py::TestCommandLineArgs::test_input_file_that_cannot_exist_raises_system_exit PASSED                             [  2%]
      test_process_components_cif_cli.py::TestRegressionTest::test_with_problematic_cif_7om PASSED                                                     [  3%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_output_dir_created PASSED                                                     [  4%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_files_created PASSED                                                   [  6%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-mmcif] PASSED                            [  7%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-sdf] PASSED                              [  8%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-sdf_nh] PASSED                           [  9%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-sdf_r] PASSED                            [ 10%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-sdf_r_nh] PASSED                         [ 12%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-pdb] PASSED                              [ 13%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-pdb_r] PASSED                            [ 14%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-cml] PASSED                              [ 15%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-xyz] PASSED                              [ 16%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[000-xyz_r] PASSED                            [ 18%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-mmcif] PASSED                            [ 19%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-sdf] PASSED                              [ 20%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-sdf_nh] PASSED                           [ 21%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-sdf_r] PASSED                            [ 22%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-sdf_r_nh] PASSED                         [ 24%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-pdb] PASSED                              [ 25%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-pdb_r] PASSED                            [ 26%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-cml] PASSED                              [ 27%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-xyz] PASSED                              [ 28%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[001-xyz_r] PASSED                            [ 30%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-mmcif] PASSED                            [ 31%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-sdf] PASSED                              [ 32%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-sdf_nh] PASSED                           [ 33%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-sdf_r] PASSED                            [ 34%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-sdf_r_nh] PASSED                         [ 36%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-pdb] PASSED                              [ 37%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-pdb_r] PASSED                            [ 38%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-cml] PASSED                              [ 39%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-xyz] PASSED                              [ 40%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[002-xyz_r] PASSED                            [ 42%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-mmcif] PASSED                            [ 43%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-sdf] PASSED                              [ 44%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-sdf_nh] PASSED                           [ 45%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-sdf_r] PASSED                            [ 46%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-sdf_r_nh] PASSED                         [ 48%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-pdb] PASSED                              [ 49%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-pdb_r] PASSED                            [ 50%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-cml] PASSED                              [ 51%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-xyz] PASSED                              [ 53%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[003-xyz_r] PASSED                            [ 54%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-mmcif] PASSED                            [ 55%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-sdf] PASSED                              [ 56%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-sdf_nh] PASSED                           [ 57%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-sdf_r] PASSED                            [ 59%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-sdf_r_nh] PASSED                         [ 60%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-pdb] PASSED                              [ 61%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-pdb_r] PASSED                            [ 62%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-cml] PASSED                              [ 63%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-xyz] PASSED                              [ 65%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_file_for_chem_comp_id[004-xyz_r] PASSED                            [ 66%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_images_created PASSED                                                  [ 67%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[svg_with_atom_labels] PASSED                          [ 68%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[svg_without_atom_labels] PASSED                       [ 69%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[000-svg_with_atom_labels] PASSED              [ 71%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[000-svg_without_atom_labels] PASSED           [ 72%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[001-svg_with_atom_labels] PASSED              [ 73%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[001-svg_without_atom_labels] PASSED           [ 74%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[002-svg_with_atom_labels] PASSED              [ 75%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[002-svg_without_atom_labels] PASSED           [ 77%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[003-svg_with_atom_labels] PASSED              [ 78%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[003-svg_without_atom_labels] PASSED           [ 79%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[004-svg_with_atom_labels] PASSED              [ 80%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_there_is_a_svg_for_chem_comp_id[004-svg_without_atom_labels] PASSED           [ 81%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_file_chem_comp_dot_list PASSED                                                [ 83%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_file_chem_dot_xml PASSED                                                      [ 84%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_file_readme_dot_html_file PASSED                                              [ 85%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[mmcif] PASSED                                                [ 86%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[sdf] PASSED                                                  [ 87%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[sdf_nh] PASSED                                               [ 89%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[sdf_r] PASSED                                                [ 90%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[sdf_r_nh] PASSED                                             [ 91%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[pdb] PASSED                                                  [ 92%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[pdb_r] PASSED                                                [ 93%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[cml] PASSED                                                  [ 95%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[xyz] PASSED                                                  [ 96%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_files[xyz_r] PASSED                                                [ 97%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_images[svg_with_atom_labels] PASSED                                [ 98%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_tarball_in_images[svg_without_atom_labels] PASSED                             [100%]
      
      ============================================================== 83 passed in 1.49 seconds ===============================================================
      21050558
    • Oliver Smart's avatar
      refactoring unit test for process_components_cif_cli - split up main · 25dc14d9
      Oliver Smart authored
      test running on cut down components cif by using pytest fixture and
      parametrize features.
      
      partly done.
      
      work for issue #37 and #38
      
      pytest output show tests work:
      
      (test-rdkit_27) Olivers-MacBook-Pro:tests osmart$ pytest -vv test_process_components_cif_cli.py
      =================================== test session starts ====================================
      platform darwin -- Python 2.7.14, pytest-3.5.0, py-1.5.3, pluggy-0.6.0 -- /Users/osmart/anaconda3/envs/test-rdkit_27/bin/python
      cachedir: ../../.pytest_cache
      rootdir: /Users/osmart/ccd_utils_py27/ccd_utils, inifile:
      collected 15 items
      
      test_process_components_cif_cli.py::TestCommandLineArgs::test_with_empty_args PASSED [  6%]
      test_process_components_cif_cli.py::TestCommandLineArgs::test_input_file_that_cannot_exist_raises_system_exit PASSED [ 13%]
      test_process_components_cif_cli.py::TestRegressionTest::test_with_problematic_cif_7om PASSED [ 20%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_output_dir_created PASSED [ 26%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_files_subdir_created PASSED [ 33%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[mmcif] PASSED [ 40%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[sdf] PASSED [ 46%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[sdf_nh] PASSED [ 53%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[sdf_r] PASSED [ 60%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[sdf_r_nh] PASSED [ 66%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[pdb] PASSED [ 73%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[pdb_r] PASSED [ 80%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[cml] PASSED [ 86%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[xyz] PASSED [ 93%]
      test_process_components_cif_cli.py::TestCutDownComponentsCif::test_subdir_in_files_created[xyz_r] PASSED [100%]
      
      ================================ 15 passed in 1.18 seconds =================================
      25dc14d9
  11. 29 Mar, 2018 2 commits
    • Oliver Smart's avatar
      Get rid of --debug output as this appears in pytest output · 1f8ef2bb
      Oliver Smart authored
      Altering unit test for process_components_cif_cli get
      
      work for issue #37 and #38
      
      * to use pytest rather than nose, partly done
      * taking out yield tests - this needs to
      * to be clearer with use of classes to separate out different
        test types.
      
      Refactor in master branch with existing process_components_cif - unit
      test now produces managable output:
      
      $ pytest test_process_components_cif_cli.py
      ============================================= test session starts ==============================================
      platform darwin -- Python 2.7.14, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
      rootdir: /Users/osmart/ccd_utils_py27/ccd_utils, inifile:
      collected 97 items
      
      test_process_components_cif_cli.py ..................................................................... [ 71%]
      ............................                                                                             [100%]
      
      =============================================== warnings summary ===============================================
      pdbeccdutils/tests/test_process_components_cif_cli.py::TestFileCreation::()::test_with_components_cif_first_file_comps
        yield tests are deprecated, and scheduled to be removed in pytest 4.0
      
      -- Docs: http://doc.pytest.org/en/latest/warnings.html
      ==================================== 97 passed, 1 warnings in 1.29 seconds =====================================
      1f8ef2bb
    • Oliver Smart's avatar
      Start refactoring unit test for process_components_cif_cli · 704079d4
      Oliver Smart authored
      work for issue #37 and #38
      
      * to use pytest rather than nose, partly done
      * taking out yield tests - this needs to
      * to be clearer with use of classes to separate out different
        test types.
      
      Refactor in master branch with existing process_components_cif - unit test works:
      
          $ pytest test_process_components_cif_cli.py
          .... loads of decbug output
          ===================================================================== warnings summary ======================================================================
          pdbeccdutils/tests/test_process_components_cif_cli.py::TestFileCreation::()::test_with_components_cif_first_file_comps
            yield tests are deprecated, and scheduled to be removed in pytest 4.0
      
          -- Docs: http://doc.pytest.org/en/latest/warnings.html
          =========================================================== 97 passed, 1 warnings in 1.30 seconds ===========================================================
      704079d4
  12. 22 Mar, 2018 1 commit
  13. 21 Mar, 2018 2 commits
  14. 20 Mar, 2018 2 commits
  15. 19 Mar, 2018 1 commit
  16. 08 Jan, 2018 2 commits
  17. 07 Jan, 2018 1 commit
  18. 04 Jan, 2018 1 commit
  19. 22 Nov, 2017 3 commits
  20. 21 Nov, 2017 4 commits
    • Oliver Smart's avatar
      Scoring Mogul rings - general code cleanup. · 7b4157c4
      Oliver Smart authored
      for issue #36 Mogul rings
      7b4157c4
    • Oliver Smart's avatar
      Scoring Mogul rings - find the query ring torsions using rdkit method. · eb89845f
      Oliver Smart authored
      See issue page for debug output.
      
      for issue #36 Mogul rings
      eb89845f
    • Oliver Smart's avatar
      Calculating torsion angle in rdkit passes (revised) unit test for GOL. · 14e207f7
      Oliver Smart authored
      for issue #36 Mogul rings
      14e207f7
    • Oliver Smart's avatar
      Start on calculating torsion angle in rdkit unit test for GOL. Torsion angle measured in coot. · 59f1b324
      Oliver Smart authored
      Initially fails with
      
      (new-rdkit-env3) [osmart@ebi-cli-003 pdbeccdutils]$ nosetests tests/test_pdb_ccd_rdkit_loading.py
      ...........[08:46:10] Explicit valence for atom # 2 Be, 4, is greater than permitted
      
      ERROR: Failure: AttributeError ('PdbChemicalComponentsRDKit' object has no attribute 'calculate_torsion')
      ----------------------------------------------------------------------
      Traceback (most recent call last):
        File "/ebi/msd/work2/osmart/conda/envs/new-rdkit-env3/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
          raise self.exc_val.with_traceback(self.tb)
        File "/ebi/msd/work2/osmart/conda/envs/new-rdkit-env3/lib/python3.5/site-packages/nose/loader.py", line 252, in generate
          for test in g():
        File "/nfs/msd/work2/osmart/ccd_utils/pdbeccdutils/tests/test_pdb_ccd_rdkit_loading.py", line 65, in test_torsion_calculation
          yield assert_almost_equals, 65.0067, gol.calculate_torsion( atom_indices=(0, 1, 2, 3), ideal=True), \
      AttributeError: 'PdbChemicalComponentsRDKit' object has no attribute 'calculate_torsion'
      
      ----------------------------------------------------------------------
      Ran 49 tests in 0.481s
      
      FAILED (errors=1)
      
      for issue #36 Mogul rings
      59f1b324