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- 0.7 -
diff --git a/docs/_modules/pyKVFinder/grid.html b/docs/_modules/pyKVFinder/grid.html index c295d8a2..312ed39e 100644 --- a/docs/_modules/pyKVFinder/grid.html +++ b/docs/_modules/pyKVFinder/grid.html @@ -1,3 +1,5 @@ + + @@ -5,19 +7,15 @@ pyKVFinder.grid — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -35,9 +33,6 @@ pyKVFinder -
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diff --git a/docs/_modules/pyKVFinder/main.html b/docs/_modules/pyKVFinder/main.html index a89a0000..18a10960 100644 --- a/docs/_modules/pyKVFinder/main.html +++ b/docs/_modules/pyKVFinder/main.html @@ -1,3 +1,5 @@ + + @@ -5,19 +7,15 @@ pyKVFinder.main — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -35,9 +33,6 @@ pyKVFinder -
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diff --git a/docs/_modules/pyKVFinder/utils.html b/docs/_modules/pyKVFinder/utils.html index 19ff50c3..7191df93 100644 --- a/docs/_modules/pyKVFinder/utils.html +++ b/docs/_modules/pyKVFinder/utils.html @@ -1,3 +1,5 @@ + + @@ -5,19 +7,15 @@ pyKVFinder.utils — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -35,9 +33,6 @@ pyKVFinder -
- 0.7 -
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- 0.7 -
diff --git a/docs/genindex.html b/docs/genindex.html index 3d94e16b..f4166a69 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -1,3 +1,5 @@ + + @@ -5,19 +7,15 @@ Index — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -35,9 +33,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/index.html b/docs/index.html index 2439394b..17000486 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Welcome to pyKVFinder’s documentation! — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -37,9 +35,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/Molecule.html b/docs/package/api_reference/Molecule.html index 43e9884f..fc810561 100644 --- a/docs/package/api_reference/Molecule.html +++ b/docs/package/api_reference/Molecule.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.Molecule — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
@@ -114,7 +109,7 @@

pyKVFinder.Molecule

-class pyKVFinder.Molecule(molecule: str | Path, radii: str | Path | Dict[str, Any] | None = None, model: int | None = None, nthreads: int | None = None, verbose: bool = False)[source]
+class pyKVFinder.Molecule(molecule: str | Path, radii: str | Path | Dict[str, Any] = None, model: int | None = None, nthreads: int | None = None, verbose: bool = False)[source]

A class for representing molecular structures.

Parameters:
diff --git a/docs/package/api_reference/box_file_template.html b/docs/package/api_reference/box_file_template.html index d901f4d5..d160c93a 100644 --- a/docs/package/api_reference/box_file_template.html +++ b/docs/package/api_reference/box_file_template.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Box configuration file template — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/calculate_frequencies.html b/docs/package/api_reference/calculate_frequencies.html index 91548ffa..ffffafed 100644 --- a/docs/package/api_reference/calculate_frequencies.html +++ b/docs/package/api_reference/calculate_frequencies.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.calculate_frequencies — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/constitutional.html b/docs/package/api_reference/constitutional.html index ad031215..f0da086b 100644 --- a/docs/package/api_reference/constitutional.html +++ b/docs/package/api_reference/constitutional.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.constitutional — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/depth.html b/docs/package/api_reference/depth.html index 6afef813..ab96671a 100644 --- a/docs/package/api_reference/depth.html +++ b/docs/package/api_reference/depth.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.depth — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/detect.html b/docs/package/api_reference/detect.html index 5c12dabe..3232bc7d 100644 --- a/docs/package/api_reference/detect.html +++ b/docs/package/api_reference/detect.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.detect — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/export.html b/docs/package/api_reference/export.html index 82f02268..3c3c06b3 100644 --- a/docs/package/api_reference/export.html +++ b/docs/package/api_reference/export.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.export — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/export_openings.html b/docs/package/api_reference/export_openings.html index 2dcd9a25..fd9b9573 100644 --- a/docs/package/api_reference/export_openings.html +++ b/docs/package/api_reference/export_openings.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.export_openings — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/get_vertices.html b/docs/package/api_reference/get_vertices.html index fc1180a1..a25ad254 100644 --- a/docs/package/api_reference/get_vertices.html +++ b/docs/package/api_reference/get_vertices.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.get_vertices — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/get_vertices_from_file.html b/docs/package/api_reference/get_vertices_from_file.html index 1bf1f059..29890f7c 100644 --- a/docs/package/api_reference/get_vertices_from_file.html +++ b/docs/package/api_reference/get_vertices_from_file.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.get_vertices_from_file — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/hydropathy.html b/docs/package/api_reference/hydropathy.html index 6e2f1465..626d5857 100644 --- a/docs/package/api_reference/hydropathy.html +++ b/docs/package/api_reference/hydropathy.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.hydropathy — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/hydrophobicity_scale_file_template.html b/docs/package/api_reference/hydrophobicity_scale_file_template.html index 40dcbc7e..4c4009f5 100644 --- a/docs/package/api_reference/hydrophobicity_scale_file_template.html +++ b/docs/package/api_reference/hydrophobicity_scale_file_template.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Hydrophobicity scale file template — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/index.html b/docs/package/api_reference/index.html index 892123fe..4c57a0f8 100644 --- a/docs/package/api_reference/index.html +++ b/docs/package/api_reference/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ API Reference — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/openings.html b/docs/package/api_reference/openings.html index 4d638489..22d2799b 100644 --- a/docs/package/api_reference/openings.html +++ b/docs/package/api_reference/openings.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.openings — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/plot_frequencies.html b/docs/package/api_reference/plot_frequencies.html index 4f1b9e25..b351d258 100644 --- a/docs/package/api_reference/plot_frequencies.html +++ b/docs/package/api_reference/plot_frequencies.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.plot_frequencies — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
@@ -176,7 +171,8 @@

pyKVFinder.plot_frequencies>>> plot_frequencies(frequencies, fn='barplots.pdf')

-../../_images/barplots.png +../../_images/barplots.png +
diff --git a/docs/package/api_reference/pyKVFinderResults.html b/docs/package/api_reference/pyKVFinderResults.html index d27f4b4d..7d0ecd6c 100644 --- a/docs/package/api_reference/pyKVFinderResults.html +++ b/docs/package/api_reference/pyKVFinderResults.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.pyKVFinderResults — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/read_cavity.html b/docs/package/api_reference/read_cavity.html index 6aec6554..bd6576f6 100644 --- a/docs/package/api_reference/read_cavity.html +++ b/docs/package/api_reference/read_cavity.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.read_cavity — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/read_pdb.html b/docs/package/api_reference/read_pdb.html index 04faa0c3..1b552554 100644 --- a/docs/package/api_reference/read_pdb.html +++ b/docs/package/api_reference/read_pdb.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.read_pdb — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/read_vdw.html b/docs/package/api_reference/read_vdw.html index 2eea1ea9..26dc625a 100644 --- a/docs/package/api_reference/read_vdw.html +++ b/docs/package/api_reference/read_vdw.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.read_vdw — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/read_xyz.html b/docs/package/api_reference/read_xyz.html index 5cb99509..5a04cecf 100644 --- a/docs/package/api_reference/read_xyz.html +++ b/docs/package/api_reference/read_xyz.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.read_xyz — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/run_workflow.html b/docs/package/api_reference/run_workflow.html index c3baab4d..feb33374 100644 --- a/docs/package/api_reference/run_workflow.html +++ b/docs/package/api_reference/run_workflow.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.run_workflow — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/spatial.html b/docs/package/api_reference/spatial.html index 124329d3..5b176524 100644 --- a/docs/package/api_reference/spatial.html +++ b/docs/package/api_reference/spatial.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.spatial — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/vdw_file_template.html b/docs/package/api_reference/vdw_file_template.html index cc86b889..2355b95c 100644 --- a/docs/package/api_reference/vdw_file_template.html +++ b/docs/package/api_reference/vdw_file_template.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Van der Waals radii file template — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/api_reference/write_results.html b/docs/package/api_reference/write_results.html index 3c7ccb0d..a52a3872 100644 --- a/docs/package/api_reference/write_results.html +++ b/docs/package/api_reference/write_results.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ pyKVFinder.write_results — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/examples/index.html b/docs/package/examples/index.html index 8d675d14..3ac06f44 100644 --- a/docs/package/examples/index.html +++ b/docs/package/examples/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Examples — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/installation/index.html b/docs/package/installation/index.html index e67a3826..96591e7e 100644 --- a/docs/package/installation/index.html +++ b/docs/package/installation/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Installation — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
diff --git a/docs/package/tutorial/index.html b/docs/package/tutorial/index.html index 772cb355..35558778 100644 --- a/docs/package/tutorial/index.html +++ b/docs/package/tutorial/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Tutorial — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
- 0.7 -
@@ -66,7 +61,7 @@
  • 1. Performing constitutional characterization
  • 6.1 Calculating and plotting frequencies
  • 7. Performing hydropathy characterization
  • -
  • 1. Performing depth characterization
  • +
  • 8. Performing depth characterization
  • 9. Exporting cavities
  • 10. Writing results
  • @@ -696,7 +691,8 @@

    6.1 Calculating and plotting frequenciespyKVFinder.plot_frequencies is shown below.

    -
    ../../_images/plot-frequencies.png +../../_images/plot-frequencies.png +

    @@ -761,7 +757,7 @@

    7. Performing hydropathy characterization -

    1. Performing depth characterization

    +

    8. Performing depth characterization

    A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.

    pyKVFinder.depth takes the detected cavities and the grid spacing (step) and returns a tuple with a NumPy array with the depth of the cavity points in the 3D grid, a dictionary with the maximum depth of the detected cavities and a dictionary with the average depth of the detected cavities.

    >>> depths, max_depth, avg_depth = pyKVFinder.depth(cavities, step=step)
    @@ -1101,7 +1097,8 @@ 

    1. vdW volume
    >>> molecule.export("vdw-model.pdb")
     

    -../../_images/vdw-grid.png +../../_images/vdw-grid.png +

    @@ -1153,7 +1150,8 @@

    2. SES volume
    >>> molecule.preview()
     

    -../../_images/ses-grid.png +../../_images/ses-grid.png +

    @@ -1201,7 +1199,8 @@

    3. SAS volume
    >>> molecule.preview()
     

    -../../_images/sas-grid.png +../../_images/sas-grid.png +

    diff --git a/docs/plugins/chimerax/index.html b/docs/plugins/chimerax/index.html index c565067e..d10999df 100644 --- a/docs/plugins/chimerax/index.html +++ b/docs/plugins/chimerax/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Find Cavities — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
    - 0.7 -
    diff --git a/docs/plugins/cli/index.html b/docs/plugins/cli/index.html index 37f414a6..8b1cf194 100644 --- a/docs/plugins/cli/index.html +++ b/docs/plugins/cli/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Command-line interface — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
    - 0.7 -
    diff --git a/docs/plugins/pymol/index.html b/docs/plugins/pymol/index.html index 9590dac2..81aa56ae 100644 --- a/docs/plugins/pymol/index.html +++ b/docs/plugins/pymol/index.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ PyMOL pyKVFinder Tools — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
    - 0.7 -
    diff --git a/docs/plugins/pymol/tutorial/biomolecular-cavity-detection.html b/docs/plugins/pymol/tutorial/biomolecular-cavity-detection.html index 4eea67d8..fddf752b 100644 --- a/docs/plugins/pymol/tutorial/biomolecular-cavity-detection.html +++ b/docs/plugins/pymol/tutorial/biomolecular-cavity-detection.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Biomolecular cavity detection — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
    - 0.7 -
    @@ -118,7 +113,8 @@

    Biomolecular cavity detectionADN.pdb

    First, load the 1FMO.pdb and ADN.pdb file into PyMOL:

    -../../../_images/pymol_viewer_1.png +../../../_images/pymol_viewer_1.png +

    @@ -127,22 +123,26 @@

    Whole biomolecule detection../../../_images/main_tab_1.png +../../../_images/main_tab_1.png +

    To run pyKVFinder with the default parameters, just click Run pyKVFinder button.

    -../../../_images/main_tab_2.png +../../../_images/main_tab_2.png +

    After execution is complete, cavities PDB is loaded into PyMOL viewer as <Output Base Name>.KVFinder.output object and the results file is loaded on the Results tab. In addition, the focus automatically shifts to Results tab.

    -../../../_images/results_tab_1.png +../../../_images/results_tab_1.png +

    We can select cavities in the Volume or Surface Area lists to highlight them on a new object called cavities, identifying each cavity. Additionally, we can select cavity tags in the Interface Residues list to highlight residues around the cavities on a new object named residues.

    -../../../_images/results_tab_2.png +../../../_images/results_tab_2.png +

    @@ -151,7 +151,8 @@

    Whole biomolecule detection../../../_images/results_tab_3.png +../../../_images/results_tab_3.png +

    @@ -160,7 +161,8 @@

    Whole biomolecule detection../../../_images/results_tab_4.png +../../../_images/results_tab_4.png +

    @@ -185,7 +187,8 @@

    Changing cavity boundary

    Adjusting Probe Out

    As mentioned above, adjusting the Probe Out size changes the level of the cavity boundary. So let’s go back on the Main tab and change the Probe Out size to 8.0 Å. Run pyKVFinder again.

    -../../../_images/pymol_viewer_2.png +../../../_images/pymol_viewer_2.png +

    @@ -196,7 +199,8 @@

    Adjusting Probe Out sele

    -../../../_images/pymol_viewer_3.png +../../../_images/pymol_viewer_3.png +

    @@ -205,7 +209,8 @@

    Adjusting Probe Out

    Adjusting Removal Distance

    Besides adjusting the Probe Out size, we can also adjust the Removal Distance to change the cavity boundary. So let’s go back to the Main tab and change the Removal Distance to 1.2 Å and the size of Probe Out back to 4.0 Å. Run pyKVFinder again.

    -../../../_images/pymol_viewer_4.png +../../../_images/pymol_viewer_4.png +

    @@ -216,7 +221,8 @@

    Adjusting Removal Distance sele

    -../../../_images/pymol_viewer_5.png +../../../_images/pymol_viewer_5.png +

    @@ -236,25 +242,29 @@

    Steered detection

    Box adjustment mode explores closed regions with a custom box, which can be drawn via the GUI.

    On the Search Space tab, select Box Adjustment check box. This will enable a Box Adjustment frame, which handles the custom box in PyMOL viewer

    -../../../_images/search_space_tab_1.png +../../../_images/search_space_tab_1.png +

    Then, select the adenosine ligand on ADN object. This can be made on the PyMOL viewer by clicking on the ligand structure or using select resn ADN PyMOL command.

    Click on Draw Box Button. This will create a custom box that limits the search space. It is fully customizable, but we will not change it for now.

    -../../../_images/pymol_viewer_6.png +../../../_images/pymol_viewer_6.png +

    On the Main tab, change Removal Distance back to 2.4 Å. Run pyKVFinder again.

    -../../../_images/pymol_viewer_7.png +../../../_images/pymol_viewer_7.png +

    Now, let’s customize the box parameters to segment the binding site of our target protein.

    Each axis is associated with one color (red with X, green with Y and blue with Z). The adjustment is made by the arrows or directly setting the value in the entry on the Search Space tab in the Box Adjustment group. We can also adjust the box angles by the same procedure. After altering the values, just click on Redraw button to redraw the box object using the new values.

    Then, on the Search Space tab, reduce Maximum X to 1.0 Å and click Redraw Box. Run pyKVFinder again.

    -../../../_images/pymol_viewer_8.png +../../../_images/pymol_viewer_8.png +

    @@ -265,17 +275,20 @@

    Ligand adjustment modeA last feature is to limit the search around a structure. In this last example, let’s do a whole protein prospection again, but limiting the search space around ligands.

    First, on the Search Space tab, deselect Box Adjustment check box, which will disable the previous enabled Box Adjustment frame.

    Still on the Search Space tab, click on the check button Ligand Adjustment, which will enable the Refresh button, the Ligand PDB combo box and the Ligand Cutoff entry.

    -
    ../../../_images/search_space_tab_2.png +../../../_images/search_space_tab_2.png +

    Click the Refresh button to display all objects in the scene in the Ligand PDB combo box. Select the ADN on the combo box and reduce Ligand Cutoff to 3.0 Å. Run pyKVFinder again.

    -../../../_images/pymol_viewer_9.png +../../../_images/pymol_viewer_9.png +

    On the Search Space tab, increase Ligand Cutoff back to 5.0 Å. Back on the Main tab, increase Probe Out to 10.0 Å and reduce Removal Distance to 0.0 Å. Run pyKVFinder again.

    -../../../_images/pymol_viewer_10.png +../../../_images/pymol_viewer_10.png +

    diff --git a/docs/plugins/pymol/tutorial/cage-cavity-detection.html b/docs/plugins/pymol/tutorial/cage-cavity-detection.html index 2ae70127..524bfc8e 100644 --- a/docs/plugins/pymol/tutorial/cage-cavity-detection.html +++ b/docs/plugins/pymol/tutorial/cage-cavity-detection.html @@ -1,3 +1,5 @@ + + @@ -6,19 +8,15 @@ Supramolecular cage cavity detection — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
    - 0.7 -
    @@ -117,7 +112,8 @@

    Supramolecular cage cavity detection../../../_images/pymol_viewer_11.png +../../../_images/pymol_viewer_11.png +

    @@ -127,13 +123,15 @@

    Supramolecular cage cavity detection../../../_images/main_tab_3.png +../../../_images/main_tab_3.png +

    3. Select the object C1 to be analyzed with pyKVFinder

    From the Input PDB drop-down menu, select the object C1. If it does not appear, press the Refresh button.

    -../../../_images/main_tab_4.png +../../../_images/main_tab_4.png +

    @@ -153,20 +151,23 @@

    Supramolecular cage cavity detection../../../_images/main_tab_5.png +../../../_images/main_tab_5.png +

    5. Define the Output Directory

    The output directory is where the results will be saved. Set the output directory where results will be saved by clicking Browse….

    -../../../_images/main_tab_6.png +../../../_images/main_tab_6.png +

    The cavity file will be saved as <Output Base Name>.KVFinder.output.pdb (PDB format) and the results file as <Output Base Name>.KVFinder.results.toml (TOML format).

    6. Run pyKVFinder

    In PyMOL pyKVFinder Tools, click on the Run pyKVFinder button to start the cavity detection process.

    -../../../_images/main_tab_7.png +../../../_images/main_tab_7.png +

    @@ -175,14 +176,16 @@

    Supramolecular cage cavity detection../../../_images/results_tab_5.png +../../../_images/results_tab_5.png +

    7. Visual analysis of the detected cavities

    The calculated cavity characterizations can be found in the Results tab.

    We can select cavities in the Volume or Surface Area lists to highlight them on a new object called cavities, identifying each cavity.

    -../../../_images/results_tab_6.png +../../../_images/results_tab_6.png +

    @@ -191,7 +194,8 @@

    Supramolecular cage cavity detection../../../_images/results_tab_7.png +../../../_images/results_tab_7.png +

    @@ -203,7 +207,7 @@

    Supramolecular cage cavity detection

    Video tutorial

    A video tutorial is available to guide you step-by-step through the process of using pyKVFinder software to characterize cavities in supramolecular cages.

    -
    +

    diff --git a/docs/search.html b/docs/search.html index 23a6f043..5c277272 100644 --- a/docs/search.html +++ b/docs/search.html @@ -1,3 +1,5 @@ + + @@ -5,20 +7,16 @@ Search — pyKVFinder 0.7.2 documentation - + - - - - - - - + + + + + @@ -38,9 +36,6 @@ pyKVFinder -
    - 0.7 -
    diff --git a/docs/searchindex.js b/docs/searchindex.js index 424754a8..435491e3 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Loading van der Waals radii dictionary": [[28, "loading-van-der-waals-radii-dictionary"]], "1. Performing constitutional characterization": [[28, "performing-constitutional-characterization"]], "1. Performing depth characterization": [[28, "performing-depth-characterization"]], "1. vdW volume": [[28, "vdw-volume"]], "10. 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"write_result": 25}}) \ No newline at end of file diff --git a/docs/source/package/tutorial/index.rst b/docs/source/package/tutorial/index.rst index 46228c93..6982dbec 100644 --- a/docs/source/package/tutorial/index.rst +++ b/docs/source/package/tutorial/index.rst @@ -630,7 +630,7 @@ A hydropathy characterization, that maps a target hydrophobicity scale on surfac * `pyKVFinder.hydropathy <../api_reference/hydropathy.html>`_ -1. Performing depth characterization +8. Performing depth characterization ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.