From 92b403b69c612f62f74489b18f85e33a1040738e Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Sun, 22 Jun 2025 22:30:40 -0300 Subject: [PATCH 1/9] Refactor scripts starting with "A" character --- aaindex.py => scripts/aaindex.py | 0 anglebetweenhelices.py => scripts/anglebetweenhelices.py | 0 annotate_v.py => scripts/annotate_v.py | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename aaindex.py => scripts/aaindex.py (100%) rename anglebetweenhelices.py => scripts/anglebetweenhelices.py (100%) rename annotate_v.py => scripts/annotate_v.py (100%) diff --git a/aaindex.py b/scripts/aaindex.py similarity index 100% rename from aaindex.py rename to scripts/aaindex.py diff --git a/anglebetweenhelices.py b/scripts/anglebetweenhelices.py similarity index 100% rename from anglebetweenhelices.py rename to scripts/anglebetweenhelices.py diff --git a/annotate_v.py b/scripts/annotate_v.py similarity index 100% rename from annotate_v.py rename to scripts/annotate_v.py From 060ac2646d458b4da1fe05ef2d414e523154da78 Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Sun, 22 Jun 2025 22:32:41 -0300 Subject: [PATCH 2/9] Refactor scripts starting with "B" character --- b2transparency.py => scripts/b2transparency.py | 0 bbPlane.py => scripts/bbPlane.py | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename b2transparency.py => scripts/b2transparency.py (100%) rename bbPlane.py => scripts/bbPlane.py (100%) diff --git a/b2transparency.py b/scripts/b2transparency.py similarity index 100% rename from b2transparency.py rename to scripts/b2transparency.py diff --git a/bbPlane.py b/scripts/bbPlane.py similarity index 100% rename from bbPlane.py rename to scripts/bbPlane.py From 59ca0794f166461f955b5d657d3c2aea45071e43 Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Sun, 22 Jun 2025 22:42:29 -0300 Subject: [PATCH 3/9] Refactor scripts starting with "C" character --- ccp4_contact.py => scripts/ccp4_contact.py | 0 ccp4_ncont.py => scripts/ccp4_ncont.py | 0 ccp4_pisa.py => scripts/ccp4_pisa.py | 0 center_of_mass.py => scripts/center_of_mass.py | 0 centroid.py => scripts/centroid.py | 0 cgo_arrow.py => scripts/cgo_arrow.py | 0 color_by_conservation.py => scripts/color_by_conservation.py | 0 colorblindfriendly.py => scripts/colorblindfriendly.py | 0 colorbydisplacement.py => scripts/colorbydisplacement.py | 0 colorbyrmsd.py => scripts/colorbyrmsd.py | 0 cubes.py => scripts/cubes.py | 0 cyspka.py => scripts/cyspka.py | 0 12 files changed, 0 insertions(+), 0 deletions(-) rename ccp4_contact.py => scripts/ccp4_contact.py (100%) rename ccp4_ncont.py => scripts/ccp4_ncont.py (100%) rename ccp4_pisa.py => scripts/ccp4_pisa.py (100%) rename center_of_mass.py => scripts/center_of_mass.py (100%) rename centroid.py => scripts/centroid.py (100%) rename cgo_arrow.py => scripts/cgo_arrow.py (100%) rename color_by_conservation.py => scripts/color_by_conservation.py (100%) rename colorblindfriendly.py => scripts/colorblindfriendly.py (100%) rename colorbydisplacement.py => scripts/colorbydisplacement.py (100%) rename colorbyrmsd.py => scripts/colorbyrmsd.py (100%) rename cubes.py => scripts/cubes.py (100%) rename cyspka.py => scripts/cyspka.py (100%) diff --git a/ccp4_contact.py b/scripts/ccp4_contact.py similarity index 100% rename from ccp4_contact.py rename to scripts/ccp4_contact.py diff --git a/ccp4_ncont.py b/scripts/ccp4_ncont.py similarity index 100% rename from ccp4_ncont.py rename to scripts/ccp4_ncont.py diff --git a/ccp4_pisa.py b/scripts/ccp4_pisa.py similarity index 100% rename from ccp4_pisa.py rename to scripts/ccp4_pisa.py diff --git a/center_of_mass.py b/scripts/center_of_mass.py similarity index 100% rename from center_of_mass.py rename to scripts/center_of_mass.py diff --git a/centroid.py b/scripts/centroid.py similarity index 100% rename from centroid.py rename to scripts/centroid.py diff --git a/cgo_arrow.py b/scripts/cgo_arrow.py similarity index 100% rename from cgo_arrow.py rename to scripts/cgo_arrow.py diff --git a/color_by_conservation.py b/scripts/color_by_conservation.py similarity index 100% rename from color_by_conservation.py rename to scripts/color_by_conservation.py diff --git a/colorblindfriendly.py b/scripts/colorblindfriendly.py similarity index 100% rename from colorblindfriendly.py rename to scripts/colorblindfriendly.py diff --git a/colorbydisplacement.py b/scripts/colorbydisplacement.py similarity index 100% rename from colorbydisplacement.py rename to scripts/colorbydisplacement.py diff --git a/colorbyrmsd.py b/scripts/colorbyrmsd.py similarity index 100% rename from colorbyrmsd.py rename to scripts/colorbyrmsd.py diff --git a/cubes.py b/scripts/cubes.py similarity index 100% rename from cubes.py rename to scripts/cubes.py diff --git a/cyspka.py b/scripts/cyspka.py similarity index 100% rename from cyspka.py rename to scripts/cyspka.py From 07a6304ce9fb76e593ff1964aafe77de5164858d Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Sun, 22 Jun 2025 22:47:31 -0300 Subject: [PATCH 4/9] Refactor scripts starting with "D" character --- Draw_Protein_Dimensions.py => scripts/Draw_Protein_Dimensions.py | 0 displacementmap.py => scripts/displacementmap.py | 0 drawgridbox.py => scripts/drawgridbox.py | 0 dynamic_mesh.py => scripts/dynamic_mesh.py | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename Draw_Protein_Dimensions.py => scripts/Draw_Protein_Dimensions.py (100%) rename displacementmap.py => scripts/displacementmap.py (100%) rename drawgridbox.py => scripts/drawgridbox.py (100%) rename dynamic_mesh.py => scripts/dynamic_mesh.py (100%) diff --git a/Draw_Protein_Dimensions.py b/scripts/Draw_Protein_Dimensions.py similarity index 100% rename from Draw_Protein_Dimensions.py rename to scripts/Draw_Protein_Dimensions.py diff --git a/displacementmap.py b/scripts/displacementmap.py similarity index 100% rename from displacementmap.py rename to scripts/displacementmap.py diff --git a/drawgridbox.py b/scripts/drawgridbox.py similarity index 100% rename from drawgridbox.py rename to scripts/drawgridbox.py diff --git a/dynamic_mesh.py b/scripts/dynamic_mesh.py similarity index 100% rename from dynamic_mesh.py rename to scripts/dynamic_mesh.py From 0fd751aebeca2c13059d6d427ce917059bf457f4 Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Sun, 22 Jun 2025 23:43:36 -0300 Subject: [PATCH 5/9] Refactor scripts starting with E/F/G/H/I/L/P characters --- elbow_angle.py => scripts/elbow_angle.py | 0 ex.py => scripts/ex.py | 0 findseq.py => scripts/findseq.py | 0 .../forster_distance_calculator.py | 0 frame_slider.py => scripts/frame_slider.py | 0 get_raw_distances.py => scripts/get_raw_distances.py | 0 grepset.py => scripts/grepset.py | 0 hbplus.py => scripts/hbplus.py | 0 modevectors.py => scripts/modevectors.py | 0 nmr_cnstr.py => scripts/nmr_cnstr.py | 0 perp_maker.py => scripts/perp_maker.py | 0 plot_noe.py => scripts/plot_noe.py | 0 poseview.py => scripts/poseview.py | 0 propka.py => scripts/propka.py | 0 pymol2glmol.py => scripts/pymol2glmol.py | 0 15 files changed, 0 insertions(+), 0 deletions(-) rename elbow_angle.py => scripts/elbow_angle.py (100%) rename ex.py => scripts/ex.py (100%) rename findseq.py => scripts/findseq.py (100%) rename forster_distance_calculator.py => scripts/forster_distance_calculator.py (100%) rename frame_slider.py => scripts/frame_slider.py (100%) rename get_raw_distances.py => scripts/get_raw_distances.py (100%) rename grepset.py => scripts/grepset.py (100%) rename hbplus.py => scripts/hbplus.py (100%) rename modevectors.py => scripts/modevectors.py (100%) rename nmr_cnstr.py => scripts/nmr_cnstr.py (100%) rename perp_maker.py => scripts/perp_maker.py (100%) rename plot_noe.py => scripts/plot_noe.py (100%) rename poseview.py => scripts/poseview.py (100%) rename propka.py => scripts/propka.py (100%) rename pymol2glmol.py => scripts/pymol2glmol.py (100%) diff --git a/elbow_angle.py b/scripts/elbow_angle.py similarity index 100% rename from elbow_angle.py rename to scripts/elbow_angle.py diff --git a/ex.py b/scripts/ex.py similarity index 100% rename from ex.py rename to scripts/ex.py diff --git a/findseq.py b/scripts/findseq.py similarity index 100% rename from findseq.py rename to scripts/findseq.py diff --git a/forster_distance_calculator.py b/scripts/forster_distance_calculator.py similarity index 100% rename from forster_distance_calculator.py rename to scripts/forster_distance_calculator.py diff --git a/frame_slider.py b/scripts/frame_slider.py similarity index 100% rename from frame_slider.py rename to scripts/frame_slider.py diff --git a/get_raw_distances.py b/scripts/get_raw_distances.py similarity index 100% rename from get_raw_distances.py rename to scripts/get_raw_distances.py diff --git a/grepset.py b/scripts/grepset.py similarity index 100% rename from grepset.py rename to scripts/grepset.py diff --git a/hbplus.py b/scripts/hbplus.py similarity index 100% rename from hbplus.py rename to scripts/hbplus.py diff --git a/modevectors.py b/scripts/modevectors.py similarity index 100% rename from modevectors.py rename to scripts/modevectors.py diff --git a/nmr_cnstr.py b/scripts/nmr_cnstr.py similarity index 100% rename from nmr_cnstr.py rename to scripts/nmr_cnstr.py diff --git a/perp_maker.py b/scripts/perp_maker.py similarity index 100% rename from perp_maker.py rename to scripts/perp_maker.py diff --git a/plot_noe.py b/scripts/plot_noe.py similarity index 100% rename from plot_noe.py rename to scripts/plot_noe.py diff --git a/poseview.py b/scripts/poseview.py similarity index 100% rename from poseview.py rename to scripts/poseview.py diff --git a/propka.py b/scripts/propka.py similarity index 100% rename from propka.py rename to scripts/propka.py diff --git a/pymol2glmol.py b/scripts/pymol2glmol.py similarity index 100% rename from pymol2glmol.py rename to scripts/pymol2glmol.py From daf5fc47d18378421bd35b5e21a357fc85d775a4 Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Sun, 22 Jun 2025 23:57:24 -0300 Subject: [PATCH 6/9] Refactor scripts starting with "R" character --- draw_rotation_axis.py => scripts/draw_rotation_axis.py | 0 removealt.py => scripts/removealt.py | 0 renumber.py => scripts/renumber.py | 0 rotkit.py => scripts/rotkit.py | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename draw_rotation_axis.py => scripts/draw_rotation_axis.py (100%) rename removealt.py => scripts/removealt.py (100%) rename renumber.py => scripts/renumber.py (100%) rename rotkit.py => scripts/rotkit.py (100%) diff --git a/draw_rotation_axis.py b/scripts/draw_rotation_axis.py similarity index 100% rename from draw_rotation_axis.py rename to scripts/draw_rotation_axis.py diff --git a/removealt.py b/scripts/removealt.py similarity index 100% rename from removealt.py rename to scripts/removealt.py diff --git a/renumber.py b/scripts/renumber.py similarity index 100% rename from renumber.py rename to scripts/renumber.py diff --git a/rotkit.py b/scripts/rotkit.py similarity index 100% rename from rotkit.py rename to scripts/rotkit.py From 8cfb84b66c5fe3009441cc1e2ae86472e4ca3ce2 Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Mon, 23 Jun 2025 00:12:59 -0300 Subject: [PATCH 7/9] Refactor scripts starting with "S" character --- save_pdb_with_anisou.py => scripts/save_pdb_with_anisou.py | 0 save_settings.py => scripts/save_settings.py | 0 select_sites.py => scripts/select_sites.py | 0 show_bumps.py => scripts/show_bumps.py | 0 spectrum_states.py => scripts/spectrum_states.py | 0 spectrumany.py => scripts/spectrumany.py | 0 stereo_ray.py => scripts/stereo_ray.py | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename save_pdb_with_anisou.py => scripts/save_pdb_with_anisou.py (100%) rename save_settings.py => scripts/save_settings.py (100%) rename select_sites.py => scripts/select_sites.py (100%) rename show_bumps.py => scripts/show_bumps.py (100%) rename spectrum_states.py => scripts/spectrum_states.py (100%) rename spectrumany.py => scripts/spectrumany.py (100%) rename stereo_ray.py => scripts/stereo_ray.py (100%) diff --git a/save_pdb_with_anisou.py b/scripts/save_pdb_with_anisou.py similarity index 100% rename from save_pdb_with_anisou.py rename to scripts/save_pdb_with_anisou.py diff --git a/save_settings.py b/scripts/save_settings.py similarity index 100% rename from save_settings.py rename to scripts/save_settings.py diff --git a/select_sites.py b/scripts/select_sites.py similarity index 100% rename from select_sites.py rename to scripts/select_sites.py diff --git a/show_bumps.py b/scripts/show_bumps.py similarity index 100% rename from show_bumps.py rename to scripts/show_bumps.py diff --git a/spectrum_states.py b/scripts/spectrum_states.py similarity index 100% rename from spectrum_states.py rename to scripts/spectrum_states.py diff --git a/spectrumany.py b/scripts/spectrumany.py similarity index 100% rename from spectrumany.py rename to scripts/spectrumany.py diff --git a/stereo_ray.py b/scripts/stereo_ray.py similarity index 100% rename from stereo_ray.py rename to scripts/stereo_ray.py From b870a26ad3d6f7a1984b2ba0243a9a962dcc0d9d Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Mon, 23 Jun 2025 00:17:40 -0300 Subject: [PATCH 8/9] Refactor scripts starting with T/U/V/W characters --- tmalign.py => scripts/tmalign.py | 0 transformations.py => scripts/transformations.py | 0 uniprot_features.py => scripts/uniprot_features.py | 0 wfmesh.py => scripts/wfmesh.py | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename tmalign.py => scripts/tmalign.py (100%) rename transformations.py => scripts/transformations.py (100%) rename uniprot_features.py => scripts/uniprot_features.py (100%) rename wfmesh.py => scripts/wfmesh.py (100%) diff --git a/tmalign.py b/scripts/tmalign.py similarity index 100% rename from tmalign.py rename to scripts/tmalign.py diff --git a/transformations.py b/scripts/transformations.py similarity index 100% rename from transformations.py rename to scripts/transformations.py diff --git a/uniprot_features.py b/scripts/uniprot_features.py similarity index 100% rename from uniprot_features.py rename to scripts/uniprot_features.py diff --git a/wfmesh.py b/scripts/wfmesh.py similarity index 100% rename from wfmesh.py rename to scripts/wfmesh.py From eec6e695aed8409acd6370fda4f2d7238a52749a Mon Sep 17 00:00:00 2001 From: Pedro Lacerda Date: Mon, 23 Jun 2025 00:22:29 -0300 Subject: [PATCH 9/9] Fix test running --- pytest.ini | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pytest.ini b/pytest.ini index 70951953..ce8fcda1 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,9 +1,8 @@ [pytest] addopts = - --ignore-glob=_* --ignore-glob=gendocs.py --import-mode=importlib -pythonpath = . +pythonpath = scripts python_files = *.py python_functions = test_* norecursedirs = examples files_for_examples modules plugins