From 7dfd75e4bc08bb1121e843f8e014021ccc3f1922 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Sat, 23 Sep 2023 12:38:18 -0300 Subject: [PATCH] Update pyKVFinderResults docstring and documentation --- docs/.buildinfo | 2 +- docs/.doctrees/_about/index.doctree | Bin 14052 -> 14036 bytes .../.doctrees/_api_reference/Molecule.doctree | Bin 132180 -> 131714 bytes .../calculate_frequencies.doctree | Bin 22317 -> 22283 bytes .../_api_reference/constitutional.doctree | Bin 74889 -> 74855 bytes docs/.doctrees/_api_reference/depth.doctree | Bin 39286 -> 39252 bytes docs/.doctrees/_api_reference/detect.doctree | Bin 88563 -> 88529 bytes docs/.doctrees/_api_reference/export.doctree | Bin 61831 -> 61797 bytes .../_api_reference/export_openings.doctree | Bin 44032 -> 43998 bytes .../_api_reference/get_vertices.doctree | Bin 27496 -> 27462 bytes .../get_vertices_from_file.doctree | Bin 47026 -> 46992 bytes .../_api_reference/hydropathy.doctree | Bin 77769 -> 77735 bytes docs/.doctrees/_api_reference/index.doctree | Bin 4264 -> 4248 bytes .../.doctrees/_api_reference/openings.doctree | Bin 50510 -> 50476 bytes .../_api_reference/plot_frequencies.doctree | Bin 21892 -> 21858 bytes .../_api_reference/pyKVFinderResults.doctree | Bin 148094 -> 147964 bytes .../_api_reference/read_cavity.doctree | Bin 54652 -> 54618 bytes .../.doctrees/_api_reference/read_pdb.doctree | Bin 25573 -> 25539 bytes .../.doctrees/_api_reference/read_vdw.doctree | Bin 44229 -> 44195 bytes .../.doctrees/_api_reference/read_xyz.doctree | Bin 23190 -> 23156 bytes .../_api_reference/run_workflow.doctree | Bin 122009 -> 121975 bytes docs/.doctrees/_api_reference/spatial.doctree | Bin 41175 -> 41141 bytes .../_api_reference/write_results.doctree | Bin 88975 -> 88941 bytes .../_cfg_files/box_file_template.doctree | Bin 6885 -> 6869 bytes ...hydrophobicity_scale_file_template.doctree | Bin 13734 -> 13718 bytes .../_cfg_files/vdw_file_template.doctree | Bin 4610 -> 4594 bytes docs/.doctrees/_cli/index.doctree | Bin 41229 -> 41213 bytes docs/.doctrees/_installation/index.doctree | Bin 7358 -> 7342 bytes docs/.doctrees/_tutorial/index.doctree | Bin 233615 -> 233599 bytes docs/.doctrees/environment.pickle | Bin 4351080 -> 4374783 bytes docs/.doctrees/index.doctree | Bin 8265 -> 8249 bytes docs/_about/index.html | 2 +- docs/_api_reference/Molecule.html | 2 +- .../_api_reference/calculate_frequencies.html | 2 +- docs/_api_reference/constitutional.html | 2 +- docs/_api_reference/depth.html | 2 +- docs/_api_reference/detect.html | 2 +- docs/_api_reference/export.html | 2 +- docs/_api_reference/export_openings.html | 2 +- docs/_api_reference/get_vertices.html | 2 +- .../get_vertices_from_file.html | 2 +- docs/_api_reference/hydropathy.html | 2 +- docs/_api_reference/index.html | 2 +- docs/_api_reference/openings.html | 2 +- docs/_api_reference/plot_frequencies.html | 2 +- docs/_api_reference/pyKVFinderResults.html | 26 ++--- docs/_api_reference/read_cavity.html | 2 +- docs/_api_reference/read_pdb.html | 2 +- docs/_api_reference/read_vdw.html | 2 +- docs/_api_reference/read_xyz.html | 2 +- docs/_api_reference/run_workflow.html | 2 +- docs/_api_reference/spatial.html | 2 +- docs/_api_reference/write_results.html | 2 +- docs/_cfg_files/box_file_template.html | 20 ++-- .../hydrophobicity_scale_file_template.html | 44 ++++---- docs/_cfg_files/vdw_file_template.html | 2 +- docs/_cli/index.html | 104 +++++++++--------- docs/_installation/index.html | 18 +-- docs/_modules/index.html | 2 +- docs/_modules/pyKVFinder/grid.html | 54 ++++----- docs/_modules/pyKVFinder/main.html | 94 ++++++++-------- docs/_modules/pyKVFinder/utils.html | 24 ++-- docs/_static/documentation_options.js | 2 +- docs/_tutorial/index.html | 2 +- docs/genindex.html | 2 +- docs/index.html | 2 +- docs/search.html | 2 +- docs/searchindex.js | 2 +- pyKVFinder/__init__.py | 2 +- pyKVFinder/main.py | 16 +-- 70 files changed, 231 insertions(+), 231 deletions(-) diff --git a/docs/.buildinfo b/docs/.buildinfo index aac7713b..9cc100fe 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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patch delta 40 wcmX@N{M=N1N2d^<&|v+n{KR~{^wQL#qD1|o)ZF}%RNbP~ Mg8a=h85hU_04Nz02LJ#7 diff --git a/docs/_about/index.html b/docs/_about/index.html index 90dcfa57..2ad7be8d 100644 --- a/docs/_about/index.html +++ b/docs/_about/index.html @@ -4,7 +4,7 @@ - Issues — pyKVFinder 0.6.0 documentation + Issues — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/Molecule.html b/docs/_api_reference/Molecule.html index 36dea563..8738ab75 100644 --- a/docs/_api_reference/Molecule.html +++ b/docs/_api_reference/Molecule.html @@ -4,7 +4,7 @@ - pyKVFinder.Molecule — pyKVFinder 0.6.0 documentation + pyKVFinder.Molecule — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/calculate_frequencies.html b/docs/_api_reference/calculate_frequencies.html index b367a632..093038ae 100644 --- a/docs/_api_reference/calculate_frequencies.html +++ b/docs/_api_reference/calculate_frequencies.html @@ -4,7 +4,7 @@ - pyKVFinder.calculate_frequencies — pyKVFinder 0.6.0 documentation + pyKVFinder.calculate_frequencies — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/constitutional.html b/docs/_api_reference/constitutional.html index 7ff6647c..08f9b0e5 100644 --- a/docs/_api_reference/constitutional.html +++ b/docs/_api_reference/constitutional.html @@ -4,7 +4,7 @@ - pyKVFinder.constitutional — pyKVFinder 0.6.0 documentation + pyKVFinder.constitutional — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/depth.html b/docs/_api_reference/depth.html index 33f1dc77..b549e0b2 100644 --- a/docs/_api_reference/depth.html +++ b/docs/_api_reference/depth.html @@ -4,7 +4,7 @@ - pyKVFinder.depth — pyKVFinder 0.6.0 documentation + pyKVFinder.depth — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/detect.html b/docs/_api_reference/detect.html index e6d260aa..8988e5c2 100644 --- a/docs/_api_reference/detect.html +++ b/docs/_api_reference/detect.html @@ -4,7 +4,7 @@ - pyKVFinder.detect — pyKVFinder 0.6.0 documentation + pyKVFinder.detect — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/export.html b/docs/_api_reference/export.html index eae84abf..82a1cfb1 100644 --- a/docs/_api_reference/export.html +++ b/docs/_api_reference/export.html @@ -4,7 +4,7 @@ - pyKVFinder.export — pyKVFinder 0.6.0 documentation + pyKVFinder.export — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/export_openings.html b/docs/_api_reference/export_openings.html index 2d91b17c..ea19fa75 100644 --- a/docs/_api_reference/export_openings.html +++ b/docs/_api_reference/export_openings.html @@ -4,7 +4,7 @@ - pyKVFinder.export_openings — pyKVFinder 0.6.0 documentation + pyKVFinder.export_openings — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/get_vertices.html b/docs/_api_reference/get_vertices.html index 30194bd9..e370a54f 100644 --- a/docs/_api_reference/get_vertices.html +++ b/docs/_api_reference/get_vertices.html @@ -4,7 +4,7 @@ - pyKVFinder.get_vertices — pyKVFinder 0.6.0 documentation + pyKVFinder.get_vertices — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/get_vertices_from_file.html b/docs/_api_reference/get_vertices_from_file.html index ec419ddd..801fe4ee 100644 --- a/docs/_api_reference/get_vertices_from_file.html +++ b/docs/_api_reference/get_vertices_from_file.html @@ -4,7 +4,7 @@ - pyKVFinder.get_vertices_from_file — pyKVFinder 0.6.0 documentation + pyKVFinder.get_vertices_from_file — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/hydropathy.html b/docs/_api_reference/hydropathy.html index a152b028..f34e8ef6 100644 --- a/docs/_api_reference/hydropathy.html +++ b/docs/_api_reference/hydropathy.html @@ -4,7 +4,7 @@ - pyKVFinder.hydropathy — pyKVFinder 0.6.0 documentation + pyKVFinder.hydropathy — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/index.html b/docs/_api_reference/index.html index 9e24533e..7cd6cfa4 100644 --- a/docs/_api_reference/index.html +++ b/docs/_api_reference/index.html @@ -4,7 +4,7 @@ - Functions — pyKVFinder 0.6.0 documentation + Functions — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/openings.html b/docs/_api_reference/openings.html index 02a23bb5..295cdf25 100644 --- a/docs/_api_reference/openings.html +++ b/docs/_api_reference/openings.html @@ -4,7 +4,7 @@ - pyKVFinder.openings — pyKVFinder 0.6.0 documentation + pyKVFinder.openings — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/plot_frequencies.html b/docs/_api_reference/plot_frequencies.html index c2688de6..2ac80593 100644 --- a/docs/_api_reference/plot_frequencies.html +++ b/docs/_api_reference/plot_frequencies.html @@ -4,7 +4,7 @@ - pyKVFinder.plot_frequencies — pyKVFinder 0.6.0 documentation + pyKVFinder.plot_frequencies — pyKVFinder 0.6.7 documentation diff --git a/docs/_api_reference/pyKVFinderResults.html b/docs/_api_reference/pyKVFinderResults.html index 396db1f7..205feffa 100644 --- a/docs/_api_reference/pyKVFinderResults.html +++ b/docs/_api_reference/pyKVFinderResults.html @@ -4,7 +4,7 @@ - pyKVFinder.pyKVFinderResults — pyKVFinder 0.6.0 documentation + pyKVFinder.pyKVFinderResults — pyKVFinder 0.6.7 documentation @@ -416,10 +416,10 @@

pyKVFinder.pyKVFinderResultsExample

-
>>> from pyKVFinder import pyKVFinder
->>> import os
+
>>> import os
+>>> import pyKVFinder
 >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
+>>> results = pyKVFinder.run_workflow(pdb)
 >>> results.export()
 

 

@@ -467,10 +467,10 @@ 
pyKVFinder.pyKVFinderResultsExample

-
>>> from pyKVFinder import pyKVFinder
->>> import os
+
>>> import os
+>>> import pyKVFinder
 >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
+>>> results = pyKVFinder.run_workflow(pdb)
 >>> results.export_all()
 

 

@@ -510,10 +510,10 @@ 
pyKVFinder.pyKVFinderResultsExample

-
>>> from pyKVFinder import pyKVFinder
->>> import os
+
>>> import os
+>>> import pyKVFinder
 >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
+>>> results = pyKVFinder.run_workflow(pdb)
 >>> results.plot_frequencies()
 

 

@@ -541,10 +541,10 @@ 
pyKVFinder.pyKVFinderResultsExample

-
>>> from pyKVFinder import pyKVFinder
->>> import os
+
>>> import os
+>>> import pyKVFinder
 >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
+>>> results = pyKVFinder.run_workflow(pdb)
 >>> results.write()
 

 

diff --git a/docs/_api_reference/read_cavity.html b/docs/_api_reference/read_cavity.html
index 12a21bb2..81740413 100644
--- a/docs/_api_reference/read_cavity.html
+++ b/docs/_api_reference/read_cavity.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.read_cavity — pyKVFinder 0.6.0 documentation
+  pyKVFinder.read_cavity — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_api_reference/read_pdb.html b/docs/_api_reference/read_pdb.html
index a5286f64..7dcbe755 100644
--- a/docs/_api_reference/read_pdb.html
+++ b/docs/_api_reference/read_pdb.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.read_pdb — pyKVFinder 0.6.0 documentation
+  pyKVFinder.read_pdb — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_api_reference/read_vdw.html b/docs/_api_reference/read_vdw.html
index 145d1f31..8e505da7 100644
--- a/docs/_api_reference/read_vdw.html
+++ b/docs/_api_reference/read_vdw.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.read_vdw — pyKVFinder 0.6.0 documentation
+  pyKVFinder.read_vdw — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_api_reference/read_xyz.html b/docs/_api_reference/read_xyz.html
index beb54e23..cd7b5397 100644
--- a/docs/_api_reference/read_xyz.html
+++ b/docs/_api_reference/read_xyz.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.read_xyz — pyKVFinder 0.6.0 documentation
+  pyKVFinder.read_xyz — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_api_reference/run_workflow.html b/docs/_api_reference/run_workflow.html
index 0dea49ed..de5b8ed3 100644
--- a/docs/_api_reference/run_workflow.html
+++ b/docs/_api_reference/run_workflow.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.run_workflow — pyKVFinder 0.6.0 documentation
+  pyKVFinder.run_workflow — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_api_reference/spatial.html b/docs/_api_reference/spatial.html
index 01723637..89c7f904 100644
--- a/docs/_api_reference/spatial.html
+++ b/docs/_api_reference/spatial.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.spatial — pyKVFinder 0.6.0 documentation
+  pyKVFinder.spatial — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_api_reference/write_results.html b/docs/_api_reference/write_results.html
index 5f53d36a..4b6e9e81 100644
--- a/docs/_api_reference/write_results.html
+++ b/docs/_api_reference/write_results.html
@@ -4,7 +4,7 @@
   
 
   
-  pyKVFinder.write_results — pyKVFinder 0.6.0 documentation
+  pyKVFinder.write_results — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_cfg_files/box_file_template.html b/docs/_cfg_files/box_file_template.html
index 28bd3acb..6a2f5338 100644
--- a/docs/_cfg_files/box_file_template.html
+++ b/docs/_cfg_files/box_file_template.html
@@ -4,7 +4,7 @@
   
 
   
-  Box configuration file template — pyKVFinder 0.6.0 documentation
+  Box configuration file template — pyKVFinder 0.6.7 documentation
       
       
     
@@ -110,19 +110,19 @@
 
Box configuration file template

 
There are three methods for defining a custom 3D grid in pyKVFinder.

 
The first directly defines four vertices of the 3D grid (origin, X-axis, Y-axis and Z-axis), an example is shown below:

-
[box]
-# px = [x, y, z]
-p1 = [0.0, 0.0, 0.0]
-p2 = [1.0, 0.0, 0.0]
-p3 = [0.0, 1.0, 0.0]
-p4 = [0.0, 0.0, 1.0]
+
[box]
+# px = [x, y, z]
+p1 = [0.0, 0.0, 0.0]
+p2 = [1.0, 0.0, 0.0]
+p3 = [0.0, 1.0, 0.0]
+p4 = [0.0, 0.0, 1.0]
 

 

 
Example: custom-box.toml.

 
The second defines a list of residues and a padding, the template is shown below:

-
[box]
-residues = [ ["resnum", "chain", "resname",], ["resnum", "chain", "resname",], ]
-padding =  3.5
+
[box]
+residues = [ ["resnum", "chain", "resname",], ["resnum", "chain", "resname",], ]
+padding =  3.5
 

 

 
Example: residues-box.toml.

diff --git a/docs/_cfg_files/hydrophobicity_scale_file_template.html b/docs/_cfg_files/hydrophobicity_scale_file_template.html
index 608334d0..b5739c01 100644
--- a/docs/_cfg_files/hydrophobicity_scale_file_template.html
+++ b/docs/_cfg_files/hydrophobicity_scale_file_template.html
@@ -4,7 +4,7 @@
   
 
   
-  Hydrophobicity scale file template — pyKVFinder 0.6.0 documentation
+  Hydrophobicity scale file template — pyKVFinder 0.6.7 documentation
       
       
     
@@ -109,27 +109,27 @@
   

 
Hydrophobicity scale file template

 
The hydrophobicity scale file defines the name of the scale and the hydrophobicity value for each residue and when not defined, it assigns zero to the missing residues. The package contains six built-in hydrophobicity scales: Eisenberg & Weiss [1], Hessa & Heijne [2], Kyte & Doolittle [3], Moon & Fleming [4], Radzicka & Wolfenden [5], Wimley & White [6] and Zhao & London [7]. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:

-
[EisenbergWeiss]
-ALA = -0.64
-ARG = 2.6
-ASN = 0.8
-ASP = 0.92
-CYS = -0.3
-GLN = 0.87
-GLU = 0.76
-GLY = -0.49
-HIS = 0.41
-ILE = -1.42
-LEU = -1.09
-LYS = 1.54
-MET = -0.66
-PHE = -1.22
-PRO = -0.12
-SER = 0.18
-THR = 0.05
-TRP = -0.83
-TYR = -0.27
-VAL = -1.11
+
[EisenbergWeiss]
+ALA = -0.64
+ARG = 2.6
+ASN = 0.8
+ASP = 0.92
+CYS = -0.3
+GLN = 0.87
+GLU = 0.76
+GLY = -0.49
+HIS = 0.41
+ILE = -1.42
+LEU = -1.09
+LYS = 1.54
+MET = -0.66
+PHE = -1.22
+PRO = -0.12
+SER = 0.18
+THR = 0.05
+TRP = -0.83
+TYR = -0.27
+VAL = -1.11
 

 

 
References
    
diff --git a/docs/_cfg_files/vdw_file_template.html b/docs/_cfg_files/vdw_file_template.html
index 3be188d0..88003394 100644
--- a/docs/_cfg_files/vdw_file_template.html
+++ b/docs/_cfg_files/vdw_file_template.html
@@ -4,7 +4,7 @@
   
 
   
-  Van der Waals radii file template — pyKVFinder 0.6.0 documentation
+  Van der Waals radii file template — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_cli/index.html b/docs/_cli/index.html
index 288d0a97..944eb588 100644
--- a/docs/_cli/index.html
+++ b/docs/_cli/index.html
@@ -4,7 +4,7 @@
   
 
   
-  Positional arguments — pyKVFinder 0.6.0 documentation
+  Positional arguments — pyKVFinder 0.6.7 documentation
       
       
     
@@ -113,15 +113,15 @@
            
    
              
   
    Command-line interface
    In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.
    
-
    $ pyKVFinder
-Usage: pyKVFinder [-h] [-v] [--version] [-b <str>] [-O <str>]
-                  [--nthreads <int>] [-d <str>] [-s <float>] [-i <float>]
-                  [-o <float>] [-V <float>] [-R <float>] [-S <str>]
-                  [--ignore_backbone] [-D] [--plot_frequencies]
-                  [--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle,
-                  MoonFleming, RadzickaWolfenden, WimleyWhite, ZhaoLondon, <.toml>}]]
-                  [-B <.toml>] [-L (<.pdb> | <.xyz>)] [--ligand_cutoff <float>]
-                  (<.pdb> | <.xyz>)
+
    $ pyKVFinder
+Usage: pyKVFinder [-h] [-v] [--version] [-b <str>] [-O <str>]
+                  [--nthreads <int>] [-d <str>] [-s <float>] [-i <float>]
+                  [-o <float>] [-V <float>] [-R <float>] [-S <str>]
+                  [--ignore_backbone] [-D] [--plot_frequencies]
+                  [--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle,
+                  MoonFleming, RadzickaWolfenden, WimleyWhite, ZhaoLondon, <.toml>}]]
+                  [-B <.toml>] [-L (<.pdb> | <.xyz>)] [--ligand_cutoff <float>]
+                  (<.pdb> | <.xyz>)
 
    
 
    
 
    
@@ -129,7 +129,7 @@ 
    Positional argumentsThe positional arguments are:
    
 
    
@@ -146,12 +146,12 @@ 
    Installationsection.
    
 
    To install the latest release on PyPI,
 run:
    
-
    pip install pyKVFinder
+
    pip install pyKVFinder
 
    
 
    
 
    Or to install the latest developmental version, run:
    
-
    git clone https://github.com/LBC-LNBio/pyKVFinder.git
-pip install pyKVFinder
+
    git clone https://github.com/LBC-LNBio/pyKVFinder.git
+pip install pyKVFinder
 
    
 
    
 

diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 81a9b8c9..7cd3a90d 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 
   
   
-  Overview: module code — pyKVFinder 0.6.0 documentation
+  Overview: module code — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/_modules/pyKVFinder/grid.html b/docs/_modules/pyKVFinder/grid.html
index 18aa772a..b6c73ab3 100644
--- a/docs/_modules/pyKVFinder/grid.html
+++ b/docs/_modules/pyKVFinder/grid.html
@@ -3,7 +3,7 @@
 
   
   
-  pyKVFinder.grid — pyKVFinder 0.6.0 documentation
+  pyKVFinder.grid — pyKVFinder 0.6.7 documentation
       
       
     
@@ -129,7 +129,7 @@ 
Source code for pyKVFinder.grid
     probe_out: Union[float, int] = 4.0,
     step: Union[float, int] = 0.6,
 ) -> numpy.ndarray:
-    """Gets 3D grid vertices.
+    """Gets 3D grid vertices.
 
     Parameters
     ----------
@@ -227,7 +227,7 @@ 
Source code for pyKVFinder.grid
     probe_out: Union[float, int] = 4.0,
     nthreads: Optional[int] = None,
 ) -> Tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]:
-    """Gets 3D grid vertices from box configuration file or parKVFinder
+    """Gets 3D grid vertices from box configuration file or parKVFinder
     parameters file, selects atoms inside custom 3D grid, define sine
     and cosine of 3D grid angles and define xyz grid units.
 
@@ -416,7 +416,7 @@ 
Source code for pyKVFinder.grid
 def _get_vertices_from_box(
     box: Dict[str, List[float]], probe_out: float = 4.0
 ) -> numpy.ndarray:
-    """Gets 3D grid vertices from box coordinates.
+    """Gets 3D grid vertices from box coordinates.
 
     Parameters
     ----------
@@ -514,7 +514,7 @@ 
Source code for pyKVFinder.grid
     xyzr: numpy.ndarray,
     probe_out: float = 4.0,
 ) -> numpy.ndarray:
-    """Gets 3D grid vertices based on a list of residues (name and chain)
+    """Gets 3D grid vertices based on a list of residues (name and chain)
     and a padding value.
 
     Parameters
@@ -564,7 +564,7 @@ 
Source code for pyKVFinder.grid
 def _get_dimensions(
     vertices: Union[numpy.ndarray, List[List[float]]], step: Union[float, int] = 0.6
 ) -> Tuple[int, int, int]:
-    """Gets dimensions of 3D grid from vertices.
+    """Gets dimensions of 3D grid from vertices.
 
     Parameters
     ----------
@@ -627,7 +627,7 @@ 
Source code for pyKVFinder.grid
 
 
 def _get_sincos(vertices: Union[numpy.ndarray, List[List[float]]]) -> numpy.ndarray:
-    """Gets sine and cossine of the grid rotation angles from a list of vertices
+    """Gets sine and cossine of the grid rotation angles from a list of vertices
     coordinates.
 
     Parameters
@@ -695,7 +695,7 @@ 
Source code for pyKVFinder.grid
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> Tuple[int, numpy.ndarray]:
-    """Detects biomolecular cavities.
+    """Detects biomolecular cavities.
 
     Cavity points that belongs to the same cavity are assigned with an integer
     in the grid.
@@ -1087,7 +1087,7 @@ 
Source code for pyKVFinder.grid
 
 
 def _select_cavities(cavities: numpy.ndarray, selection: List[int]) -> numpy.ndarray:
-    """Select cavities in the 3D grid by cavity labels.
+    """Select cavities in the 3D grid by cavity labels.
 
     Parameters
     ----------
@@ -1131,7 +1131,7 @@ 
Source code for pyKVFinder.grid
 
 
 def _get_cavity_name(index: int) -> str:
-    """Get cavity name, eg KAA, KAB, and so on, based on the index.
+    """Get cavity name, eg KAA, KAB, and so on, based on the index.
 
     Parameters
     ----------
@@ -1143,12 +1143,12 @@ 
Source code for pyKVFinder.grid
     cavity_name : str
         Cavity name
     """
-    cavity_name = f"K{chr(65 + int(index / 26) % 26)}{chr(65 + (index % 26))}"
+    cavity_name = f"K{chr(65 + int(index / 26) % 26)}{chr(65 + (index % 26))}"
     return cavity_name
 
 
 def _get_cavity_label(cavity_name: str) -> int:
-    """Get cavity label, eg 2, 3, and so on, based on the cavity name.
+    """Get cavity label, eg 2, 3, and so on, based on the cavity name.
 
     Parameters
     ----------
@@ -1181,7 +1181,7 @@ 
Source code for pyKVFinder.grid
     ncav: int,
     selection: Optional[List[int]] = None,
 ) -> Tuple[Dict[str, float], Dict[str, float]]:
-    """Processes arrays of volumes and areas.
+    """Processes arrays of volumes and areas.
 
     Parameters
     ----------
@@ -1228,7 +1228,7 @@ 
Source code for pyKVFinder.grid
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> Tuple[numpy.ndarray, Dict[str, float], Dict[str, float]]:
-    """Spatial characterization (volume and area) of the detected cavities.
+    """Spatial characterization (volume and area) of the detected cavities.
 
     Parameters
     ----------
@@ -1401,7 +1401,7 @@ 
Source code for pyKVFinder.grid
     ncav: int,
     selection: Optional[List[int]] = None,
 ) -> Tuple[Dict[str, float], Dict[str, float]]:
-    """Processes arrays of maximum and average depths.
+    """Processes arrays of maximum and average depths.
 
     Parameters
     ----------
@@ -1448,7 +1448,7 @@ 
Source code for pyKVFinder.grid
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> Tuple[numpy.ndarray, Dict[str, float], Dict[str, float]]:
-    """Characterization of the depth of the detected cavities, including depth
+    """Characterization of the depth of the detected cavities, including depth
     per cavity point and maximum and average depths of detected cavities.
 
     Parameters
@@ -1609,7 +1609,7 @@ 
Source code for pyKVFinder.grid
 def _process_residues(
     raw: List[str], ncav: int, selection: Optional[List[int]] = None
 ) -> Dict[str, List[List[str]]]:
-    """Processes raw list of residues from _constitutional to a list of
+    """Processes raw list of residues from _constitutional to a list of
     residue information per cavity name.
 
     Parameters
@@ -1659,7 +1659,7 @@ 
Source code for pyKVFinder.grid
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> Dict[str, List[List[str]]]:
-    """Constitutional characterization (interface residues) of the detected
+    """Constitutional characterization (interface residues) of the detected
     cavities.
 
     Parameters
@@ -1897,7 +1897,7 @@ 
Source code for pyKVFinder.grid
 def _process_hydropathy(
     raw_avg_hydropathy: numpy.ndarray, ncav: int, selection: Optional[List[int]] = None
 ) -> Dict[str, float]:
-    """Processes array of average hydropathy.
+    """Processes array of average hydropathy.
 
     Parameters
     ----------
@@ -1942,7 +1942,7 @@ 
Source code for pyKVFinder.grid
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> Tuple[numpy.ndarray, Dict[str, float]]:
-    """Hydropathy characterization of the detected cavities.
+    """Hydropathy characterization of the detected cavities.
 
     Map a target hydrophobicity scale per surface point and calculate average hydropathy of detected cavities.
 
@@ -2283,7 +2283,7 @@ 
Source code for pyKVFinder.grid
 
 
 def _get_opening_name(index: int) -> str:
-    """Get opening name, eg OAA, OAB, and so on, based on the index.
+    """Get opening name, eg OAA, OAB, and so on, based on the index.
 
     Parameters
     ----------
@@ -2295,12 +2295,12 @@ 
Source code for pyKVFinder.grid
     opening_name : str
         Opening name
     """
-    opening_name = f"O{chr(65 + int(index / 26) % 26)}{chr(65 + (index % 26))}"
+    opening_name = f"O{chr(65 + int(index / 26) % 26)}{chr(65 + (index % 26))}"
     return opening_name
 
 
 def _get_opening_label(opening_name: str) -> int:
-    """Get opening label, eg 2, 3, and so on, based on the opening name.
+    """Get opening label, eg 2, 3, and so on, based on the opening name.
 
     Parameters
     ----------
@@ -2331,7 +2331,7 @@ 
Source code for pyKVFinder.grid
     raw_openings: numpy.ndarray,
     opening2cavity: numpy.ndarray,
 ) -> Dict[str, Dict[str, float]]:
-    """Processes arrays of openings' areas.
+    """Processes arrays of openings' areas.
 
     Parameters
     ----------
@@ -2377,7 +2377,7 @@ 
Source code for pyKVFinder.grid
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> Tuple[int, numpy.ndarray, Dict[str, Dict[str, float]]]:
-    """[WIP] Identify openings of the detected cavities and calculate their areas.
+    """[WIP] Identify openings of the detected cavities and calculate their areas.
 
     Parameters
     ----------
@@ -2595,7 +2595,7 @@ 
Source code for pyKVFinder.grid
     append: bool = False,
     model: int = 0,
 ) -> None:
-    """Export cavitiy (H) and surface (HA) points to PDB-formatted file with
+    """Export cavitiy (H) and surface (HA) points to PDB-formatted file with
     a variable (B; optional) in B-factor column, and hydropathy to
     PDB-formatted file in B-factor column at surface points (HA).
 
@@ -2851,7 +2851,7 @@ 
Source code for pyKVFinder.grid
     append: bool = False,
     model: int = 0,
 ) -> None:
-    """Export opening points (H) to a PDB-formatted file.
+    """Export opening points (H) to a PDB-formatted file.
 
     Parameters
     ----------
diff --git a/docs/_modules/pyKVFinder/main.html b/docs/_modules/pyKVFinder/main.html
index 2132b460..fa354470 100644
--- a/docs/_modules/pyKVFinder/main.html
+++ b/docs/_modules/pyKVFinder/main.html
@@ -3,7 +3,7 @@
 
   
   
-  pyKVFinder.main — pyKVFinder 0.6.0 documentation
+  pyKVFinder.main — pyKVFinder 0.6.7 documentation
       
       
     
@@ -142,7 +142,7 @@ 
Source code for pyKVFinder.main
 
 
 def cli() -> None:
-    """pyKVFinder Command Line Interface (CLI).
+    """pyKVFinder Command Line Interface (CLI).
 
     Parameters
     ----------
@@ -184,7 +184,7 @@ 
Source code for pyKVFinder.main
 
     # Start logging
     logging.basicConfig(
-        filename=f"{os.path.join(args.output_directory, 'KVFinder.log')}",
+        filename=f"{os.path.join(args.output_directory, 'KVFinder.log')}",
         level=logging.INFO,
         format="%(message)s",
     )
@@ -257,7 +257,7 @@ 
Source code for pyKVFinder.main
     logging.info(f"> Step: {args.step} \u00c5")
     logging.info(f"> Probe In: {args.probe_in} \u00c5")
     logging.info(f"> Probe Out: {args.probe_out} \u00c5")
-    logging.info(f"> Voxel volume: {args.step * args.step * args.step} \u00c5\u00b3")
+    logging.info(f"> Voxel volume: {args.step * args.step * args.step} \u00c5\u00b3")
     logging.info(f"> p1: {args.vertices[0]}")
     logging.info(f"> p2: {args.vertices[1]}")
     logging.info(f"> p3: {args.vertices[2]}")
@@ -386,7 +386,7 @@ 
Source code for pyKVFinder.main
 
 
 
[docs]class pyKVFinderResults(object):
-    """A class containing pyKVFinder detection and characterization results.
+    """A class containing pyKVFinder detection and characterization results.
 
     Parameters
     ----------
@@ -554,7 +554,7 @@ 
Source code for pyKVFinder.main
         output: Union[str, pathlib.Path] = "cavity.pdb",
         nthreads: Optional[int] = None,
     ) -> None:
-        """Exports cavitiy (H) and surface (HA) points to PDB-formatted file
+        """Exports cavitiy (H) and surface (HA) points to PDB-formatted file
         with a variable (B; optional) in B-factor column, and hydropathy to
         PDB-formatted file in B-factor column at surface points (HA).
 
@@ -575,10 +575,10 @@ 
Source code for pyKVFinder.main
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.export()
         """
         export(
@@ -598,7 +598,7 @@ 
Source code for pyKVFinder.main
         fn: Union[str, pathlib.Path] = "results.toml",
         output: Optional[Union[str, pathlib.Path]] = None
     ) -> None:
-        """
+        """
         Writes file paths and cavity characterization to TOML-formatted file
 
         Parameters
@@ -619,10 +619,10 @@ 
Source code for pyKVFinder.main
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.write()
         """
         write_results(
@@ -641,7 +641,7 @@ 
Source code for pyKVFinder.main
         )

 
 
[docs]    def plot_frequencies(self, pdf: Union[str, pathlib.Path] = "barplots.pdf"):
-        """Plot bar charts of frequencies (residues and classes of residues) in
+        """Plot bar charts of frequencies (residues and classes of residues) in
         a PDF file.
 
         Parameters
@@ -674,10 +674,10 @@ 
Source code for pyKVFinder.main
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.plot_frequencies()
         """
         plot_frequencies(self.frequencies, pdf)

@@ -690,7 +690,7 @@ 
Source code for pyKVFinder.main
         pdf: Union[str, pathlib.Path] = "barplots.pdf",
         nthreads: Optional[int] = None,
     ) -> None:
-        """Exports cavities and characterization to PDB-formatted files,
+        """Exports cavities and characterization to PDB-formatted files,
         writes file paths and characterization to a TOML-formatted file, and
         optionally plot bar charts of frequencies (residues and classes of
         residues) in a PDF file.
@@ -737,10 +737,10 @@ 
Source code for pyKVFinder.main
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.export_all()
 
         Yet, we can set a ``include_frequencies_pdf`` flag to True to plot the bar charts of the frequencies in a PDF file.
@@ -776,7 +776,7 @@ 
Source code for pyKVFinder.main
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> pyKVFinderResults:
-    """Detects and characterizes cavities (volume, area, depth [optional],
+    """Detects and characterizes cavities (volume, area, depth [optional],
     hydropathy [optional] and interface residues).
 
     Parameters
@@ -1295,7 +1295,7 @@ 
Source code for pyKVFinder.main
 
 
 
[docs]class Molecule(object):
-    """A class for representing molecular structures.
+    """A class for representing molecular structures.
 
     Parameters
     ----------
@@ -1393,7 +1393,7 @@ 
Source code for pyKVFinder.main
         nthreads: Optional[int] = None,
         verbose: bool = False,
     ):
-        """Initialize the Molecule object with molecule, radii, model, nthreads and verbose.
+        """Initialize the Molecule object with molecule, radii, model, nthreads and verbose.
 
         Parameters
         ----------
@@ -1472,109 +1472,109 @@ 
Source code for pyKVFinder.main
 
     @property
     def atomic(self) -> numpy.ndarray:
-        """Get _atomic attribute."""
+        """Get _atomic attribute."""
         return self._atomic
 
     @property
     def dim(self) -> Tuple[int, int, int]:
-        """Get _dim attribute"""
+        """Get _dim attribute"""
         return self._dim
 
     @property
     def grid(self) -> numpy.ndarray:
-        """Get _grid attribute."""
+        """Get _grid attribute."""
         return self._grid
 
     @property
     def molecule(self) -> Union[str, pathlib.Path]:
-        """Get _molecule attribute."""
+        """Get _molecule attribute."""
         return self._molecule
 
     @property
     def nx(self) -> int:
-        """Get grid units in X-axis."""
+        """Get grid units in X-axis."""
         if self._dim is not None:
             return self._dim[0]
 
     @property
     def ny(self) -> int:
-        """Get grid units in Y-axis."""
+        """Get grid units in Y-axis."""
         if self._dim is not None:
             return self._dim[1]
 
     @property
     def nz(self) -> int:
-        """Get grid units in Z-axis."""
+        """Get grid units in Z-axis."""
         if self._dim is not None:
             return self._dim[2]
 
     @property
     def p1(self) -> numpy.ndarray:
-        """Get origin of the 3D grid."""
+        """Get origin of the 3D grid."""
         if self._vertices is not None:
             return self._vertices[0]
 
     @property
     def p2(self) -> numpy.ndarray:
-        """Get X-axis max of the 3D grid."""
+        """Get X-axis max of the 3D grid."""
         if self._vertices is not None:
             return self._vertices[1]
 
     @property
     def p3(self) -> numpy.ndarray:
-        """Get Y-axis max of the 3D grid."""
+        """Get Y-axis max of the 3D grid."""
         if self._vertices is not None:
             return self._vertices[2]
 
     @property
     def p4(self) -> numpy.ndarray:
-        """Get Z-axis max of the 3D grid."""
+        """Get Z-axis max of the 3D grid."""
         if self._vertices is not None:
             return self._vertices[3]
 
     @property
     def padding(self) -> float:
-        """Get _padding attribute."""
+        """Get _padding attribute."""
         return self._padding
 
     @property
     def probe(self) -> float:
-        """Get _probe attribute."""
+        """Get _probe attribute."""
         return self._probe
 
     @property
     def radii(self) -> Dict[str, Any]:
-        """Get _radii attribute."""
+        """Get _radii attribute."""
         return self._radii
 
     @property
     def representation(self) -> str:
-        """Get _representation attribute."""
+        """Get _representation attribute."""
         return self._representation
 
     @property
     def rotation(self) -> numpy.ndarray:
-        """Get _rotation attribute."""
+        """Get _rotation attribute."""
         return self._rotation
 
     @property
     def step(self) -> float:
-        """Get _step attribute."""
+        """Get _step attribute."""
         if self._step is not None:
             return self._step
 
     @property
     def vertices(self) -> numpy.ndarray:
-        """Get _vertices attribute."""
+        """Get _vertices attribute."""
         return self._vertices
 
     @property
     def xyzr(self) -> numpy.ndarray:
-        """Get xyz coordinates and radius of molecule atoms."""
+        """Get xyz coordinates and radius of molecule atoms."""
         return self._atomic[:, 4:].astype(numpy.float64)
 
     def _set_grid(self, padding: Optional[float] = None) -> None:
-        """Define the 3D grid for the target molecule.
+        """Define the 3D grid for the target molecule.
 
         Parameters
         ----------
@@ -1614,7 +1614,7 @@ 
Source code for pyKVFinder.main
             print("sina: {}, sinb: {}, cosa: {}, cosb: {}".format(*self.rotation))
 
     def _get_padding(self) -> float:
-        """Automatically define the padding based on molecule coordinates, probe size, grid spacing and atom radii.
+        """Automatically define the padding based on molecule coordinates, probe size, grid spacing and atom radii.
 
         Returns
         -------
@@ -1627,7 +1627,7 @@ 
Source code for pyKVFinder.main
         return float(padding.round(decimals=1))
 
 
[docs]    def vdw(self, step: float = 0.6, padding: Optional[float] = None) -> None:
-        """Fill the 3D grid with the molecule as the van der Waals surface representation.
+        """Fill the 3D grid with the molecule as the van der Waals surface representation.
 
         Parameters
         ----------
@@ -1709,7 +1709,7 @@ 
Source code for pyKVFinder.main
         surface: str = "SES",
         padding: Optional[float] = None,
     ) -> None:
-        """Fill the 3D grid with the molecule as the van der Waals surface representation.
+        """Fill the 3D grid with the molecule as the van der Waals surface representation.
 
         Parameters
         ----------
@@ -1844,7 +1844,7 @@ 
Source code for pyKVFinder.main
         ).reshape(self.nx, self.ny, self.nz)

 
 
[docs]    def volume(self) -> float:
-        """Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.
+        """Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.
 
         Returns
         -------
@@ -1864,10 +1864,10 @@ 
Source code for pyKVFinder.main
             volume = _volume(
                 (self.grid == 0).astype(numpy.int32) * 2, self.step, 1, self.nthreads
             )
-            return float(volume.round(decimals=2))

+            return volume.round(decimals=2).item()

 
 
[docs]    def preview(self, **kwargs) -> None:
-        """Preview the molecular surface in the 3D grid.
+        """Preview the molecular surface in the 3D grid.
 
         Example
         -------
@@ -1891,7 +1891,7 @@ 
Source code for pyKVFinder.main
         self,
         fn: Union[str, pathlib.Path] = "molecule.pdb",
     ) -> None:
-        """Export molecule points (H) to a PDB-formatted file.
+        """Export molecule points (H) to a PDB-formatted file.
 
         Parameters
         ----------
diff --git a/docs/_modules/pyKVFinder/utils.html b/docs/_modules/pyKVFinder/utils.html
index 10db9a46..4a2a9318 100644
--- a/docs/_modules/pyKVFinder/utils.html
+++ b/docs/_modules/pyKVFinder/utils.html
@@ -3,7 +3,7 @@
 
   
   
-  pyKVFinder.utils — pyKVFinder 0.6.0 documentation
+  pyKVFinder.utils — pyKVFinder 0.6.7 documentation
       
       
     
@@ -128,7 +128,7 @@ 
Source code for pyKVFinder.utils
 
[docs]def read_vdw(
     fn: Optional[Union[str, pathlib.Path]] = None
 ) -> Dict[str, Dict[str, float]]:
-    """Reads van der Waals radii from .dat file.
+    """Reads van der Waals radii from .dat file.
 
     Parameters
     ----------
@@ -234,7 +234,7 @@ 
Source code for pyKVFinder.utils
 def _process_pdb_line(
     line: str, vdw: Dict[str, Dict[str, float]]
 ) -> List[Union[str, float, int]]:
-    """Extracts ATOM and HETATM information of PDB line.
+    """Extracts ATOM and HETATM information of PDB line.
 
     Parameters
     ----------
@@ -283,7 +283,7 @@ 
Source code for pyKVFinder.utils
     vdw: Optional[Dict[str, Dict[str, float]]] = None,
     model: Optional[int] = None,
 ) -> numpy.ndarray:
-    """Reads PDB file into numpy.ndarrays.
+    """Reads PDB file into numpy.ndarrays.
 
     Parameters
     ----------
@@ -375,7 +375,7 @@ 
Source code for pyKVFinder.utils
 
[docs]def read_xyz(
     fn: Union[str, pathlib.Path], vdw: Optional[Dict[str, Dict[str, float]]] = None
 ) -> numpy.ndarray:
-    """Reads XYZ file into numpy.ndarrays.
+    """Reads XYZ file into numpy.ndarrays.
 
     Parameters
     ----------
@@ -473,7 +473,7 @@ 
Source code for pyKVFinder.utils
 
 
 def _read_cavity(cavity: Union[str, pathlib.Path]) -> numpy.ndarray:
-    """Reads xyz coordinates and labels of a cavities file into numpy.ndarray.
+    """Reads xyz coordinates and labels of a cavities file into numpy.ndarray.
 
     Parameters
     ----------
@@ -514,7 +514,7 @@ 
Source code for pyKVFinder.utils
     nthreads: Optional[int] = None,
     verbose: bool = False,
 ) -> numpy.ndarray:
-    """Read cavities and receptor inside a 3D grid.
+    """Read cavities and receptor inside a 3D grid.
 
     Parameters
     ----------
@@ -745,7 +745,7 @@ 
Source code for pyKVFinder.utils
 
 
 def _process_box(args: argparse.Namespace) -> Dict[str, List[float]]:
-    """Gets xyz coordinates of 3D grid vertices.
+    """Gets xyz coordinates of 3D grid vertices.
 
     Parameters
     ----------
@@ -834,7 +834,7 @@ 
Source code for pyKVFinder.utils
 
 
 def _write_parameters(args: argparse.Namespace) -> None:
-    """Writes parameters used in cavity detection and characterization of
+    """Writes parameters used in cavity detection and characterization of
     pyKVFinder to TOML-formatted file.
 
     Parameters
@@ -886,7 +886,7 @@ 
Source code for pyKVFinder.utils
 
[docs]def calculate_frequencies(
     residues: Dict[str, List[List[str]]]
 ) -> Dict[str, Dict[str, Dict[str, int]]]:
-    """Calculate frequencies of residues and class of residues
+    """Calculate frequencies of residues and class of residues
     (R1, R2, R3, R4 and R5) for detected cavities.
 
     Parameters
@@ -999,7 +999,7 @@ 
Source code for pyKVFinder.utils
     frequencies: Dict[str, Dict[str, Dict[str, int]]],
     fn: Union[str, pathlib.Path] = "barplots.pdf",
 ) -> None:
-    """Plot bar charts of calculated frequencies (residues and classes of
+    """Plot bar charts of calculated frequencies (residues and classes of
     residues) for each detected cavity in a target PDF file.
 
     Parameters
@@ -1213,7 +1213,7 @@ 
Source code for pyKVFinder.utils
     frequencies: Optional[Dict[str, Dict[str, Dict[str, int]]]] = None,
     step: Union[float, int] = 0.6,
 ) -> None:
-    """Writes file paths and cavity characterization to TOML-formatted file.
+    """Writes file paths and cavity characterization to TOML-formatted file.
 
     Parameters
     ----------
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 4b35c471..e5ac2122 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.6.0',
+    VERSION: '0.6.7',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/_tutorial/index.html b/docs/_tutorial/index.html
index 8accf2ef..68acab35 100644
--- a/docs/_tutorial/index.html
+++ b/docs/_tutorial/index.html
@@ -4,7 +4,7 @@
   
 
   
-  Cavity detection and characterization — pyKVFinder 0.6.0 documentation
+  Cavity detection and characterization — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/genindex.html b/docs/genindex.html
index 1b21fc85..c26d734e 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Index — pyKVFinder 0.6.0 documentation
+  Index — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/index.html b/docs/index.html
index e63028fd..4b2c0711 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,7 +4,7 @@
   
 
   
-  Welcome to pyKVFinder’s documentation! — pyKVFinder 0.6.0 documentation
+  Welcome to pyKVFinder’s documentation! — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/search.html b/docs/search.html
index ddb73f21..7da232f2 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -3,7 +3,7 @@
 
   
   
-  Search — pyKVFinder 0.6.0 documentation
+  Search — pyKVFinder 0.6.7 documentation
       
       
     
diff --git a/docs/searchindex.js b/docs/searchindex.js
index d53b66c6..524b96ca 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["_about/index", "_api_reference/Molecule", "_api_reference/calculate_frequencies", "_api_reference/constitutional", "_api_reference/depth", "_api_reference/detect", "_api_reference/export", "_api_reference/export_openings", "_api_reference/get_vertices", "_api_reference/get_vertices_from_file", "_api_reference/hydropathy", "_api_reference/index", "_api_reference/openings", "_api_reference/plot_frequencies", "_api_reference/pyKVFinderResults", "_api_reference/read_cavity", "_api_reference/read_pdb", "_api_reference/read_vdw", "_api_reference/read_xyz", "_api_reference/run_workflow", "_api_reference/spatial", "_api_reference/write_results", "_cfg_files/box_file_template", "_cfg_files/hydrophobicity_scale_file_template", "_cfg_files/vdw_file_template", "_cli/index", "_installation/index", "_tutorial/index", "index"], "filenames": ["_about/index.rst", "_api_reference/Molecule.rst", "_api_reference/calculate_frequencies.rst", "_api_reference/constitutional.rst", "_api_reference/depth.rst", "_api_reference/detect.rst", "_api_reference/export.rst", "_api_reference/export_openings.rst", "_api_reference/get_vertices.rst", "_api_reference/get_vertices_from_file.rst", "_api_reference/hydropathy.rst", "_api_reference/index.rst", "_api_reference/openings.rst", "_api_reference/plot_frequencies.rst", "_api_reference/pyKVFinderResults.rst", "_api_reference/read_cavity.rst", "_api_reference/read_pdb.rst", "_api_reference/read_vdw.rst", "_api_reference/read_xyz.rst", "_api_reference/run_workflow.rst", "_api_reference/spatial.rst", "_api_reference/write_results.rst", "_cfg_files/box_file_template.rst", "_cfg_files/hydrophobicity_scale_file_template.rst", "_cfg_files/vdw_file_template.rst", "_cli/index.rst", "_installation/index.rst", "_tutorial/index.rst", "index.rst"], "titles": ["Issues", "pyKVFinder.Molecule", "pyKVFinder.calculate_frequencies", "pyKVFinder.constitutional", "pyKVFinder.depth", "pyKVFinder.detect", 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(pykvfinder.molecule attribute)": [[1, "pyKVFinder.Molecule._step"]], "_vertices (pykvfinder.molecule attribute)": [[1, "pyKVFinder.Molecule._vertices"]], "atomic (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.atomic"]], "dim (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.dim"]], "export() (pykvfinder.molecule method)": [[1, "pyKVFinder.Molecule.export"]], "grid (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.grid"]], "molecule (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.molecule"]], "nthreads (pykvfinder.molecule attribute)": [[1, "pyKVFinder.Molecule.nthreads"]], "nx (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.nx"]], "ny (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.ny"]], "nz (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.nz"]], "p1 (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.p1"]], "p2 (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.p2"]], "p3 (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.p3"]], "p4 (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.p4"]], "padding (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.padding"]], "preview() (pykvfinder.molecule method)": [[1, "pyKVFinder.Molecule.preview"]], "probe (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.probe"]], "radii (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.radii"]], "representation (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.representation"]], "rotation (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.rotation"]], "step (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.step"]], "surface() (pykvfinder.molecule method)": [[1, "pyKVFinder.Molecule.surface"]], "vdw() (pykvfinder.molecule method)": [[1, "pyKVFinder.Molecule.vdw"]], "verbose (pykvfinder.molecule attribute)": [[1, "pyKVFinder.Molecule.verbose"]], "vertices (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.vertices"]], "volume() (pykvfinder.molecule method)": [[1, "pyKVFinder.Molecule.volume"]], "xyzr (pykvfinder.molecule property)": [[1, "pyKVFinder.Molecule.xyzr"]], "calculate_frequencies() (in module pykvfinder)": [[2, "pyKVFinder.calculate_frequencies"]], "constitutional() (in module pykvfinder)": [[3, "pyKVFinder.constitutional"]], "depth() (in module pykvfinder)": [[4, "pyKVFinder.depth"]], "detect() (in module pykvfinder)": [[5, "pyKVFinder.detect"]], "export() (in module pykvfinder)": [[6, "pyKVFinder.export"]], "export_openings() (in module pykvfinder)": [[7, "pyKVFinder.export_openings"]], "get_vertices() (in module pykvfinder)": [[8, "pyKVFinder.get_vertices"]], "get_vertices_from_file() (in module pykvfinder)": [[9, "pyKVFinder.get_vertices_from_file"]], "hydropathy() (in module pykvfinder)": [[10, "pyKVFinder.hydropathy"]], "openings() (in module pykvfinder)": [[12, "pyKVFinder.openings"]], "plot_frequencies() (in module pykvfinder)": [[13, "pyKVFinder.plot_frequencies"]], "_input (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults._input"]], "_ligand (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults._ligand"]], "_step (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults._step"]], "_vertices (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults._vertices"]], "area (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.area"]], "avg_depth (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.avg_depth"]], "avg_hydropathy (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.avg_hydropathy"]], "cavities (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.cavities"]], "depths (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.depths"]], "export() (pykvfinder.pykvfinderresults method)": [[14, "pyKVFinder.pyKVFinderResults.export"]], "export_all() (pykvfinder.pykvfinderresults method)": [[14, "pyKVFinder.pyKVFinderResults.export_all"]], "frequencies (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.frequencies"]], "max_depth (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.max_depth"]], "ncav (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.ncav"]], "plot_frequencies() (pykvfinder.pykvfinderresults method)": [[14, "pyKVFinder.pyKVFinderResults.plot_frequencies"]], "pykvfinderresults (class in pykvfinder)": [[14, "pyKVFinder.pyKVFinderResults"]], "residues (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.residues"]], "scales (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.scales"]], "surface (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.surface"]], "volume (pykvfinder.pykvfinderresults attribute)": [[14, "pyKVFinder.pyKVFinderResults.volume"]], "write() (pykvfinder.pykvfinderresults method)": [[14, "pyKVFinder.pyKVFinderResults.write"]], "read_cavity() (in module pykvfinder)": [[15, "pyKVFinder.read_cavity"]], "read_pdb() (in module pykvfinder)": [[16, "pyKVFinder.read_pdb"]], "read_vdw() (in module pykvfinder)": [[17, "pyKVFinder.read_vdw"]], "read_xyz() (in module pykvfinder)": [[18, "pyKVFinder.read_xyz"]], "run_workflow() (in module pykvfinder)": [[19, "pyKVFinder.run_workflow"]], "spatial() (in module pykvfinder)": [[20, "pyKVFinder.spatial"]], "write_results() (in module pykvfinder)": [[21, "pyKVFinder.write_results"]]}})
\ No newline at end of file
diff --git a/pyKVFinder/__init__.py b/pyKVFinder/__init__.py
index 947e85cd..ee0469d6 100644
--- a/pyKVFinder/__init__.py
+++ b/pyKVFinder/__init__.py
@@ -31,7 +31,7 @@
 """
 
 __name__ = "pyKVFinder"
-__version__ = "0.6.6"
+__version__ = "0.6.7"
 license = "GNU GPL-3.0 License"
 
 from .utils import *
diff --git a/pyKVFinder/main.py b/pyKVFinder/main.py
index 551505e6..863c6340 100644
--- a/pyKVFinder/main.py
+++ b/pyKVFinder/main.py
@@ -469,10 +469,10 @@ def export(
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.export()
         """
         export(
@@ -513,10 +513,10 @@ def write(
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.write()
         """
         write_results(
@@ -568,10 +568,10 @@ def plot_frequencies(self, pdf: Union[str, pathlib.Path] = "barplots.pdf"):
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.plot_frequencies()
         """
         plot_frequencies(self.frequencies, pdf)
@@ -631,10 +631,10 @@ def export_all(
 
         Example
         -------
-        >>> from pyKVFinder import pyKVFinder
         >>> import os
+        >>> import pyKVFinder
         >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
+        >>> results = pyKVFinder.run_workflow(pdb)
         >>> results.export_all()
 
         Yet, we can set a ``include_frequencies_pdf`` flag to True to plot the bar charts of the frequencies in a PDF file.