diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle index c590065..546c6fb 100644 Binary files a/docs/.doctrees/environment.pickle and b/docs/.doctrees/environment.pickle differ diff --git a/docs/.doctrees/package/tutorial/index.doctree b/docs/.doctrees/package/tutorial/index.doctree index a4ffb65..058c09c 100644 Binary files a/docs/.doctrees/package/tutorial/index.doctree and b/docs/.doctrees/package/tutorial/index.doctree differ diff --git a/docs/_sources/package/tutorial/index.rst.txt b/docs/_sources/package/tutorial/index.rst.txt index 6982dbe..dcf54ae 100644 --- a/docs/_sources/package/tutorial/index.rst.txt +++ b/docs/_sources/package/tutorial/index.rst.txt @@ -489,7 +489,7 @@ A spatial characterization, that includes volume, area and defining surface poin * `pyKVFinder.spatial <../api_reference/spatial.html>`_ -1. Performing constitutional characterization +6. Performing constitutional characterization ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ A constitutional characterization, that identifies the interface residues, is performed on the detected cavities. diff --git a/docs/package/tutorial/index.html b/docs/package/tutorial/index.html index 3555877..99f5a27 100644 --- a/docs/package/tutorial/index.html +++ b/docs/package/tutorial/index.html @@ -58,7 +58,7 @@
A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.
pyKVFinder.constitutional
takes the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) and a collection of detection parameters (step
, probe_in
, ignore_backbone
), and returns a dictionary with interface residues of each cavity.
>>> # Default ignore backbone contacts flag (ignore_backbone): False
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 435491e..c3fbd5a 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
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Detecting biomolecular cavities": [[28, "detecting-biomolecular-cavities"]], "4.1 Detecting biomolecular cavities with ligand adjustment": [[28, "detecting-biomolecular-cavities-with-ligand-adjustment"]], "5. Performing spatial characterization": [[28, "performing-spatial-characterization"]], "6. Performing constitutional characterization": [[28, "performing-constitutional-characterization"]], "6.1 Calculating and plotting frequencies": [[28, "calculating-and-plotting-frequencies"]], "7. Performing hydropathy characterization": [[28, "performing-hydropathy-characterization"]], "8. Performing depth characterization": [[28, "performing-depth-characterization"]], "9. 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"zn": [20, 28], "zr": [20, 28], "\u00e0": 0, "\u00e5": [32, 33]}, "titles": ["KVFinder suite", "Welcome to pyKVFinder\u2019s documentation!", "pyKVFinder.Molecule", "Box configuration file template", "pyKVFinder.calculate_frequencies", "pyKVFinder.constitutional", "pyKVFinder.depth", "pyKVFinder.detect", "pyKVFinder.export", "pyKVFinder.export_openings", "pyKVFinder.get_vertices", "pyKVFinder.get_vertices_from_file", "pyKVFinder.hydropathy", "Hydrophobicity scale file template", "API Reference", "pyKVFinder.openings", "pyKVFinder.plot_frequencies", "pyKVFinder.pyKVFinderResults", "pyKVFinder.read_cavity", "pyKVFinder.read_pdb", "pyKVFinder.read_vdw", "pyKVFinder.read_xyz", "pyKVFinder.run_workflow", "pyKVFinder.spatial", "Van der Waals radii file template", "pyKVFinder.write_results", "Examples", "Installation", "Tutorial", "Find Cavities", "Command-line interface", "PyMOL pyKVFinder Tools", "Biomolecular cavity detection", "Supramolecular cage cavity detection"], "titleterms": {"": 1, 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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 6982dbe..dcf54ae 100644
--- a/docs/source/package/tutorial/index.rst
+++ b/docs/source/package/tutorial/index.rst
@@ -489,7 +489,7 @@ A spatial characterization, that includes volume, area and defining surface poin
* `pyKVFinder.spatial <../api_reference/spatial.html>`_
-1. Performing constitutional characterization
+6. Performing constitutional characterization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.