Pymol-Scripts · pslacerda · Jun 22, 2025 · Jun 22, 2025
diff --git a/pytest.ini b/pytest.ini
@@ -0,0 +1,5 @@
+[pytest]
+pythonpath = scripts
+python_files = scripts/*.py
+python_functions = test_*
+norecursedirs = examples files_for_examples modules plugins
diff --git a/Draw_Protein_Dimensions.py → scripts/Draw_Protein_Dimensions.py b/Draw_Protein_Dimensions.py → scripts/Draw_Protein_Dimensions.py
diff --git a/scripts/__init__.py b/scripts/__init__.py
diff --git a/aKMT_Lys_pred.py → scripts/aKMT_Lys_pred.py b/aKMT_Lys_pred.py → scripts/aKMT_Lys_pred.py
diff --git a/aaindex.py → scripts/aaindex.py b/aaindex.py → scripts/aaindex.py
diff --git a/anglebetweenhelices.py → scripts/anglebetweenhelices.py b/anglebetweenhelices.py → scripts/anglebetweenhelices.py
diff --git a/annotate_v.py → scripts/annotate_v.py b/annotate_v.py → scripts/annotate_v.py
diff --git a/b2transparency.py → scripts/b2transparency.py b/b2transparency.py → scripts/b2transparency.py
diff --git a/bbPlane.py → scripts/bbPlane.py b/bbPlane.py → scripts/bbPlane.py
diff --git a/cb_colors.py → scripts/cb_colors.py b/cb_colors.py → scripts/cb_colors.py
diff --git a/ccp4_contact.py → scripts/ccp4_contact.py b/ccp4_contact.py → scripts/ccp4_contact.py
diff --git a/ccp4_ncont.py → scripts/ccp4_ncont.py b/ccp4_ncont.py → scripts/ccp4_ncont.py
diff --git a/ccp4_pisa.py → scripts/ccp4_pisa.py b/ccp4_pisa.py → scripts/ccp4_pisa.py
diff --git a/center_of_mass.py → scripts/center_of_mass.py b/center_of_mass.py → scripts/center_of_mass.py
diff --git a/centroid.py → scripts/centroid.py b/centroid.py → scripts/centroid.py
diff --git a/cgoCircle.py → scripts/cgoCircle.py b/cgoCircle.py → scripts/cgoCircle.py
diff --git a/cgo_arrow.py → scripts/cgo_arrow.py b/cgo_arrow.py → scripts/cgo_arrow.py
diff --git a/cgo_grid.py → scripts/cgo_grid.py b/cgo_grid.py → scripts/cgo_grid.py
diff --git a/color_by_conservation.py → scripts/color_by_conservation.py b/color_by_conservation.py → scripts/color_by_conservation.py
diff --git a/colorblindfriendly.py → scripts/colorblindfriendly.py b/colorblindfriendly.py → scripts/colorblindfriendly.py
diff --git a/colorbydisplacement.py → scripts/colorbydisplacement.py b/colorbydisplacement.py → scripts/colorbydisplacement.py
diff --git a/colorbyrmsd.py → scripts/colorbyrmsd.py b/colorbyrmsd.py → scripts/colorbyrmsd.py
diff --git a/cubes.py → scripts/cubes.py b/cubes.py → scripts/cubes.py
diff --git a/cyspka.py → scripts/cyspka.py b/cyspka.py → scripts/cyspka.py
diff --git a/displacementmap.py → scripts/displacementmap.py b/displacementmap.py → scripts/displacementmap.py
diff --git a/distancetoatom.py → scripts/distancetoatom.py b/distancetoatom.py → scripts/distancetoatom.py
diff --git a/draw_rotation_axis.py → scripts/draw_rotation_axis.py b/draw_rotation_axis.py → scripts/draw_rotation_axis.py
diff --git a/drawgridbox.py → scripts/drawgridbox.py b/drawgridbox.py → scripts/drawgridbox.py
diff --git a/dssr_block.py → scripts/dssr_block.py b/dssr_block.py → scripts/dssr_block.py
diff --git a/dynamic_mesh.py → scripts/dynamic_mesh.py b/dynamic_mesh.py → scripts/dynamic_mesh.py
diff --git a/elbow_angle.py → scripts/elbow_angle.py b/elbow_angle.py → scripts/elbow_angle.py
diff --git a/ex.py → scripts/ex.py b/ex.py → scripts/ex.py
diff --git a/extra_fit.py → scripts/extra_fit.py b/extra_fit.py → scripts/extra_fit.py
diff --git a/findSurfaceCharge.py → scripts/findSurfaceCharge.py b/findSurfaceCharge.py → scripts/findSurfaceCharge.py
diff --git a/findSurfaceResidues.py → scripts/findSurfaceResidues.py b/findSurfaceResidues.py → scripts/findSurfaceResidues.py
diff --git a/findseq.py → scripts/findseq.py b/findseq.py → scripts/findseq.py
@@ -203,3 +203,11 @@ def checkParams(needle, haystack, selName, het, matchMode):
         print("Error: selName was not a string.")
         return False
     return True
+
+
+def test_findseq():
+    cmd.fab('ACDEFG', 'm1')
+    cmd.fab('HIKLMN', 'm2')
+    cmd.do('findseq DEF, *, foundSeq')
+    assert cmd.count_atoms("foundSeq and m1") == 47
+    assert cmd.count_atoms("foundSeq and m2") == 0
diff --git a/flatten_obj.py → scripts/flatten_obj.py b/flatten_obj.py → scripts/flatten_obj.py
diff --git a/focal_blur.py → scripts/focal_blur.py b/focal_blur.py → scripts/focal_blur.py
diff --git a/format_bonds.py → scripts/format_bonds.py b/format_bonds.py → scripts/format_bonds.py
diff --git a/forster_distance_calculator.py → scripts/forster_distance_calculator.py b/forster_distance_calculator.py → scripts/forster_distance_calculator.py
diff --git a/frame_slider.py → scripts/frame_slider.py b/frame_slider.py → scripts/frame_slider.py
diff --git a/get_colors.py → scripts/get_colors.py b/get_colors.py → scripts/get_colors.py
diff --git a/get_raw_distances.py → scripts/get_raw_distances.py b/get_raw_distances.py → scripts/get_raw_distances.py
diff --git a/grepset.py → scripts/grepset.py b/grepset.py → scripts/grepset.py
diff --git a/gridbox.py → scripts/gridbox.py b/gridbox.py → scripts/gridbox.py
diff --git a/hbplus.py → scripts/hbplus.py b/hbplus.py → scripts/hbplus.py
diff --git a/inertia_tensor.py → scripts/inertia_tensor.py b/inertia_tensor.py → scripts/inertia_tensor.py
diff --git a/isoslider.py → scripts/isoslider.py b/isoslider.py → scripts/isoslider.py
diff --git a/load_img_stack.py → scripts/load_img_stack.py b/load_img_stack.py → scripts/load_img_stack.py
diff --git a/load_nrrd.py → scripts/load_nrrd.py b/load_nrrd.py → scripts/load_nrrd.py
diff --git a/modevectors.py → scripts/modevectors.py b/modevectors.py → scripts/modevectors.py
diff --git a/movie_color_fade.py → scripts/movie_color_fade.py b/movie_color_fade.py → scripts/movie_color_fade.py
diff --git a/movie_fade.py → scripts/movie_fade.py b/movie_fade.py → scripts/movie_fade.py
diff --git a/nmr_cnstr.py → scripts/nmr_cnstr.py b/nmr_cnstr.py → scripts/nmr_cnstr.py
diff --git a/perp_maker.py → scripts/perp_maker.py b/perp_maker.py → scripts/perp_maker.py
diff --git a/plane.py → scripts/plane.py b/plane.py → scripts/plane.py
diff --git a/plot_noe.py → scripts/plot_noe.py b/plot_noe.py → scripts/plot_noe.py
diff --git a/poseview.py → scripts/poseview.py b/poseview.py → scripts/poseview.py
diff --git a/propka.py → scripts/propka.py b/propka.py → scripts/propka.py
diff --git a/pymol2glmol.py → scripts/pymol2glmol.py b/pymol2glmol.py → scripts/pymol2glmol.py
diff --git a/pymolscriptrepo.py → scripts/pymolscriptrepo.py b/pymolscriptrepo.py → scripts/pymolscriptrepo.py
diff --git a/quickdisplays.py → scripts/quickdisplays.py b/quickdisplays.py → scripts/quickdisplays.py
diff --git a/removealt.py → scripts/removealt.py b/removealt.py → scripts/removealt.py
diff --git a/renumber.py → scripts/renumber.py b/renumber.py → scripts/renumber.py
diff --git a/rotkit.py → scripts/rotkit.py b/rotkit.py → scripts/rotkit.py
diff --git a/save_mopac.py → scripts/save_mopac.py b/save_mopac.py → scripts/save_mopac.py
diff --git a/save_pdb_with_anisou.py → scripts/save_pdb_with_anisou.py b/save_pdb_with_anisou.py → scripts/save_pdb_with_anisou.py
diff --git a/save_settings.py → scripts/save_settings.py b/save_settings.py → scripts/save_settings.py
diff --git a/select_sites.py → scripts/select_sites.py b/select_sites.py → scripts/select_sites.py
diff --git a/show_bumps.py → scripts/show_bumps.py b/show_bumps.py → scripts/show_bumps.py
diff --git a/show_ligand_interactions.py → scripts/show_ligand_interactions.py b/show_ligand_interactions.py → scripts/show_ligand_interactions.py
diff --git a/spectrum_states.py → scripts/spectrum_states.py b/spectrum_states.py → scripts/spectrum_states.py
diff --git a/spectrumany.py → scripts/spectrumany.py b/spectrumany.py → scripts/spectrumany.py
diff --git a/spectrumbar.py → scripts/spectrumbar.py b/spectrumbar.py → scripts/spectrumbar.py
diff --git a/stereo_ray.py → scripts/stereo_ray.py b/stereo_ray.py → scripts/stereo_ray.py
diff --git a/tmalign.py → scripts/tmalign.py b/tmalign.py → scripts/tmalign.py
diff --git a/togroup.py → scripts/togroup.py b/togroup.py → scripts/togroup.py
diff --git a/transformations.py → scripts/transformations.py b/transformations.py → scripts/transformations.py
diff --git a/uniprot_features.py → scripts/uniprot_features.py b/uniprot_features.py → scripts/uniprot_features.py
diff --git a/viol_noes.py → scripts/viol_noes.py b/viol_noes.py → scripts/viol_noes.py
diff --git a/wfmesh.py → scripts/wfmesh.py b/wfmesh.py → scripts/wfmesh.py