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b/docs/.doctrees/plugins/pymol/tutorial/cage-cavity-detection.doctree index cafa57fe..0a414e56 100644 Binary files a/docs/.doctrees/plugins/pymol/tutorial/cage-cavity-detection.doctree and b/docs/.doctrees/plugins/pymol/tutorial/cage-cavity-detection.doctree differ diff --git a/docs/_sources/plugins/pymol/index.rst.txt b/docs/_sources/plugins/pymol/index.rst.txt index 875a4ec8..6e96ac99 100644 --- a/docs/_sources/plugins/pymol/index.rst.txt +++ b/docs/_sources/plugins/pymol/index.rst.txt @@ -9,19 +9,32 @@ Installation First, it is required to install Anaconda or Miniconda (Python 3.10 or later). If you do not have it installed, please refer to `Anaconda `_ or `Miniconda `_ websites. -In the `Anaconda Prompt`, create a new environment and install PyMOL: +In the `Anaconda Prompt`, create a new environment and activate it: .. code-block:: bash conda create -n pymol python=3.10 conda activate pymol - # PyMOL v3.0 - conda install -c conda-forge -c schrodinger pymol-bundle - # PyMOL v2.6 - conda install -c conda-forge -c schrodinger pymol-bundle=2.6 - # PyMOL Open-Source - conda install -c conda-forge pymol-open-source +Then, install **one** of the following versions of PyMOL: + +* PyMOL v3.0 (Schrodinger) + + .. code-block:: bash + + conda install -c conda-forge -c schrodinger pymol-bundle + +* PyMOL v2.6 (Schrodinger): + + .. code-block:: bash + + conda install -c conda-forge -c schrodinger pymol-bundle=2.6 + +* PyMOL Open-Source + + .. code-block:: bash + + conda install -c conda-forge pymol-open-source After installing one of the PyMOL versions (v3.0, v2.6 or Open-Source), you need to install the `pyKVFinder `_ package, if you have not done it yet: diff --git a/docs/package/api_reference/Molecule.html b/docs/package/api_reference/Molecule.html index 6bdd6d12..a23a6790 100644 --- a/docs/package/api_reference/Molecule.html +++ b/docs/package/api_reference/Molecule.html @@ -112,16 +112,16 @@

pyKVFinder.Molecule

-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]
+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]

A class for representing molecular structures.

Parameters:
    -

  • molecule (Union[str, pathlib.Path]) – A file path to the molecule in either PDB or XYZ format

    • -

  • radii (Union[str, pathlib.Path, Dict[str, Any]], optional) – A file path to a van der Waals radii file or a dictionary of VDW radii, by default None. If None, apply the built-in van der Waals radii file: vdw.dat.

    • -

  • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.

    • -

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • -

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • +

  • molecule (Union[str, pathlib.Path]) – A file path to the molecule in either PDB or XYZ format

    • +

  • radii (Union[str, pathlib.Path, Dict[str, Any]], optional) – A file path to a van der Waals radii file or a dictionary of VDW radii, by default None. If None, apply the built-in van der Waals radii file: vdw.dat.

    • +

  • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.

    • +

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • +

  • verbose (bool, optional) – Print extra information to standard output, by default False.

@@ -142,7 +142,7 @@

pyKVFinder.Molecule
Type:
-

tuple

+

tuple

@@ -171,7 +171,7 @@

pyKVFinder.Molecule
Type:
-

Union[str, pathlib.Path]

+

Union[str, pathlib.Path]

@@ -182,7 +182,7 @@

pyKVFinder.Molecule
Type:
-

float

+

float

@@ -193,7 +193,7 @@

pyKVFinder.Molecule
Type:
-

float

+

float

@@ -204,7 +204,7 @@

pyKVFinder.Molecule
Type:
-

Dict[str, Any]

+

Dict[str, Any]

@@ -215,7 +215,7 @@

pyKVFinder.Molecule
Type:
-

str, optional

+

str, optional

@@ -237,7 +237,7 @@

pyKVFinder.Molecule
Type:
-

float

+

float

@@ -259,7 +259,7 @@

pyKVFinder.Molecule
Type:
-

int

+

int

@@ -270,7 +270,7 @@

pyKVFinder.Molecule
Type:
-

bool

+

bool

@@ -327,20 +327,20 @@

pyKVFinder.Molecule
-property dim: Tuple[int, int, int]
+property dim: Tuple[int, int, int]

Get _dim attribute

-export(fn: str | Path = 'molecule.pdb') → None[source]
+export(fn: str | Path = 'molecule.pdb') → None[source]

Export molecule points (H) to a PDB-formatted file.

Parameters:
-

fn (Union[str, pathlib.Path], optional) – A file path to the molecular volume in the grid-based rerpesentation in PDB format, by default “molecule.pdb”.

+

fn (Union[str, pathlib.Path], optional) – A file path to the molecular volume in the grid-based rerpesentation in PDB format, by default “molecule.pdb”.

Raises:
-

TypeError – fn must be a string or a pathlib.Path.

+

TypeError – fn must be a string or a pathlib.Path.

Example

@@ -358,25 +358,25 @@

pyKVFinder.Molecule
-property molecule: str | Path
+property molecule: str | Path

Get _molecule attribute.

-property nx: int
+property nx: int

Get grid units in X-axis.

-property ny: int
+property ny: int

Get grid units in Y-axis.

-property nz: int
+property nz: int

Get grid units in Z-axis.

@@ -406,13 +406,13 @@

pyKVFinder.Molecule
-property padding: float
+property padding: float

Get _padding attribute.

-preview(**kwargs) → None[source]
+preview(**kwargs) → None[source]

Preview the molecular surface in the 3D grid.

Example

With the molecular surface modelled by Molecule.vdw() or Molecule.surface(), the modelled molecule in the 3D grid can be previewed by running:

@@ -423,19 +423,19 @@

pyKVFinder.Molecule
-property probe: float
+property probe: float

Get _probe attribute.

-property radii: Dict[str, Any]
+property radii: Dict[str, Any]

Get _radii attribute.

-property representation: str
+property representation: str

Get _representation attribute.

@@ -447,29 +447,29 @@

pyKVFinder.Molecule
-property step: float
+property step: float

Get _step attribute.

-surface(step: float = 0.6, probe: float = 1.4, surface: str = 'SES', padding: float | None = None) → None[source]
+surface(step: float = 0.6, probe: float = 1.4, surface: str = 'SES', padding: float | None = None) → None[source]

Fill the 3D grid with the molecule as the van der Waals surface representation.

Parameters:
    -

  • step (float, optional) – Grid spacing (A), by default 0.6.

    • -

  • probe (float, optional) – Spherical probe size to define the molecular surface based on a molecular representation, by default 1.4.

    • -

  • surface (str, optional) – Molecular surface representation. Keywords options are vdW (van der Waals surface), SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default “SES”.

    • -

  • padding (float, optional) – The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.

    • +

  • step (float, optional) – Grid spacing (A), by default 0.6.

    • +

  • probe (float, optional) – Spherical probe size to define the molecular surface based on a molecular representation, by default 1.4.

    • +

  • surface (str, optional) – Molecular surface representation. Keywords options are vdW (van der Waals surface), SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default “SES”.

    • +

  • padding (float, optional) – The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.

Raises:
    -

  • TypeError – step must be a positive real number.

    • -

  • ValueError – step must be a positive real number.

    • -

  • TypeError – probe_out must be a positive real number.

    • -

  • ValueError – probe_out must be a positive real number.

    • +

  • TypeError – step must be a positive real number.

    • +

  • ValueError – step must be a positive real number.

    • +

  • TypeError – probe_out must be a positive real number.

    • +

  • ValueError – probe_out must be a positive real number.

@@ -541,19 +541,19 @@

pyKVFinder.Molecule
-vdw(step: float = 0.6, padding: float | None = None) → None[source]
+vdw(step: float = 0.6, padding: float | None = None) → None[source]

Fill the 3D grid with the molecule as the van der Waals surface representation.

Parameters:
    -

  • step (float, optional) – Grid spacing (A), by default 0.6.

    • -

  • padding (float, optional) – The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.

    • +

  • step (float, optional) – Grid spacing (A), by default 0.6.

    • +

  • padding (float, optional) – The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.

Raises:
    -

  • TypeError – step must be a positive real number.

    • -

  • ValueError – step must be a positive real number.

    • +

  • TypeError – step must be a positive real number.

    • +

  • ValueError – step must be a positive real number.

@@ -590,14 +590,14 @@

pyKVFinder.Molecule
-volume() → float[source]
+volume() → float[source]

Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.

Returns:

volume – Molecular volume (A³).

Return type:
-

float

+

float

Example

diff --git a/docs/package/api_reference/calculate_frequencies.html b/docs/package/api_reference/calculate_frequencies.html index 9b7aa547..11b2453e 100644 --- a/docs/package/api_reference/calculate_frequencies.html +++ b/docs/package/api_reference/calculate_frequencies.html @@ -128,12 +128,12 @@

pyKVFinder.calculate_frequencies

-pyKVFinder.calculate_frequencies(residues: Dict[str, List[List[str]]]) → Dict[str, Dict[str, Dict[str, int]]][source]
+pyKVFinder.calculate_frequencies(residues: Dict[str, List[List[str]]]) → Dict[str, Dict[str, Dict[str, int]]][source]

Calculate frequencies of residues and class of residues (R1, R2, R3, R4 and R5) for detected cavities.

Parameters:
-

residues (Dict[str, List[List[str]]]) – A dictionary with a list of interface residues for each detected +

residues (Dict[str, List[List[str]]]) – A dictionary with a list of interface residues for each detected cavity.

Returns:
@@ -141,7 +141,7 @@

pyKVFinder.calculate_frequenciesReturn type: -

Dict[str, Dict[str, Dict[str, int]]]

+

Dict[str, Dict[str, Dict[str, int]]]

diff --git a/docs/package/api_reference/constitutional.html b/docs/package/api_reference/constitutional.html index 2232bedc..ab022b4d 100644 --- a/docs/package/api_reference/constitutional.html +++ b/docs/package/api_reference/constitutional.html @@ -128,7 +128,7 @@

pyKVFinder.constitutional

-pyKVFinder.constitutional(cavities: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Dict[str, List[List[str]]][source]
+pyKVFinder.constitutional(cavities: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Dict[str, List[List[str]]][source]

Constitutional characterization (interface residues) of the detected cavities.

@@ -147,18 +147,18 @@

pyKVFinder.constitutionalstr, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates +

  • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

    • -

  • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, +

  • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

    • -

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • -

  • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

    • -

  • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface +

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • +

  • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

    • +

  • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface residues, by default False.

    • -

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selectedA list of integer labels of each cavity to be selected, by default None.

    • -

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selectedA list of integer labels of each cavity to be selected, by default None.

    • +

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • -

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • +

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • Returns:
    @@ -166,26 +166,26 @@

    pyKVFinder.constitutionalReturn type: -

    Dict[str, List[List[str]]]

    +

    Dict[str, List[List[str]]]

    Raises:
      -

    • TypeError – cavities must be a numpy.ndarray.

      • -

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – atomic must be a list or a numpy.ndarray.

      • -

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • -

    • TypeError – vertices must be a list or a numpy.ndarray.

      • -

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – probe_in must be a non-negative real number.

      • -

    • ValueError – probe_in must be a non-negative real number.

      • -

    • TypeError – ignore_backbone must be a boolean.

      • -

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • -

    • ValueError – Invalid selection: {selection}.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – verbose must be a boolean.

      • +

    • TypeError – cavities must be a numpy.ndarray.

      • +

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – atomic must be a list or a numpy.ndarray.

      • +

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • +

    • TypeError – vertices must be a list or a numpy.ndarray.

      • +

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – probe_in must be a non-negative real number.

      • +

    • ValueError – probe_in must be a non-negative real number.

      • +

    • TypeError – ignore_backbone must be a boolean.

      • +

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • +

    • ValueError – Invalid selection: {selection}.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – verbose must be a boolean.

    diff --git a/docs/package/api_reference/depth.html b/docs/package/api_reference/depth.html index 5812deee..16efa6b4 100644 --- a/docs/package/api_reference/depth.html +++ b/docs/package/api_reference/depth.html @@ -128,7 +128,7 @@

    pyKVFinder.depth

    -pyKVFinder.depth(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]
    +pyKVFinder.depth(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]

    Characterization of the depth of the detected cavities, including depth per cavity point and maximum and average depths of detected cavities.

    @@ -147,11 +147,11 @@

    pyKVFinder.depthfloat, int], optional) – Grid spacing (A).

    -

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • -

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

  • step (Union[float, int], optional) – Grid spacing (A).

    • +

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • +

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • -

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • +

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • Returns:
    @@ -164,15 +164,15 @@

    pyKVFinder.depthRaises:
      -

    • TypeError – cavities must be a numpy.ndarray.

      • -

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • -

    • ValueError – Invalid selection: {selection}.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – verbose must be a boolean.

      • +

    • TypeError – cavities must be a numpy.ndarray.

      • +

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • +

    • ValueError – Invalid selection: {selection}.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – verbose must be a boolean.

    diff --git a/docs/package/api_reference/detect.html b/docs/package/api_reference/detect.html index b9e3b824..94d7a4a6 100644 --- a/docs/package/api_reference/detect.html +++ b/docs/package/api_reference/detect.html @@ -128,32 +128,32 @@

    pyKVFinder.detect

    -pyKVFinder.detect(atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, latomic: ndarray | List[List[float]] | None = None, ligand_cutoff: float | int = 5.0, box_adjustment: bool = False, surface: str = 'SES', nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray][source]
    +pyKVFinder.detect(atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, latomic: ndarray | List[List[float]] | None = None, ligand_cutoff: float | int = 5.0, box_adjustment: bool = False, surface: str = 'SES', nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray][source]

    Detects biomolecular cavities.

    Cavity points that belongs to the same cavity are assigned with an integer in the grid.

    Parameters:
      -

    • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates +

    • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

      • -

    • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, +

    • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • -

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • -

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • -

    • removal_distance (Union[float, int], optional) – A length to be removed from the cavity-bulk frontier (A), by +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • +

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • +

    • removal_distance (Union[float, int], optional) – A length to be removed from the cavity-bulk frontier (A), by default 2.4.

      • -

    • volume_cutoff (Union[float, int], optional) – Volume filter for detected cavities (A3), by default 5.0.

      • -

    • latomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]], optional) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates +

    • volume_cutoff (Union[float, int], optional) – Volume filter for detected cavities (A3), by default 5.0.

      • +

    • latomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]], optional) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom of a target ligand, by default None.

      • -

    • ligand_cutoff (Union[float, int], optional) – A radius to limit a space around a ligand (A), by default 5.0.

      • -

    • box_adjustment (bool, optional) – Whether a custom 3D grid is applied, by default False.

      • -

    • surface (str, optional) – Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent +

    • ligand_cutoff (Union[float, int], optional) – A radius to limit a space around a ligand (A), by default 5.0.

      • +

    • box_adjustment (bool, optional) – Whether a custom 3D grid is applied, by default False.

      • +

    • surface (str, optional) – Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default SES.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

      • -

    • verbose (bool, optional) – Print extra information to standard output, by default False.

      • +

    • verbose (bool, optional) – Print extra information to standard output, by default False.

    Returns:
    @@ -177,30 +177,30 @@

    pyKVFinder.detectRaises:
      -

    • TypeError – atomic must be a list or a numpy.ndarray.

      • -

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • -

    • TypeError – vertices must be a list or a numpy.ndarray.

      • -

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – probe_in must be a non-negative real number.

      • -

    • ValueError – probe_in must be a non-negative real number.

      • -

    • TypeError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be greater than probe_in.

      • -

    • TypeError – removal_distance must be a non-negative real number.

      • -

    • ValueError – removal_distance must be a non-negative real number.

      • -

    • TypeError – volume_cutoff must be a non-negative real number.

      • -

    • ValueError – volume_cutoff must be a non-negative real number.

      • -

    • TypeError – latomic must be a list, a numpy.ndarray or None.

      • -

    • ValueError – latomic has incorrect shape. It must be (n, 8).

      • -

    • TypeError – ligand_cutoff must be a positive real number.

      • -

    • ValueError – ligand_cutoff must be a positive real number.

      • -

    • TypeError – box_adjustment must be a boolean.

      • -

    • TypeError – surface must be a string.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • ValueError – surface must be SAS or SES, not surface.

      • +

    • TypeError – atomic must be a list or a numpy.ndarray.

      • +

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • +

    • TypeError – vertices must be a list or a numpy.ndarray.

      • +

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – probe_in must be a non-negative real number.

      • +

    • ValueError – probe_in must be a non-negative real number.

      • +

    • TypeError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be greater than probe_in.

      • +

    • TypeError – removal_distance must be a non-negative real number.

      • +

    • ValueError – removal_distance must be a non-negative real number.

      • +

    • TypeError – volume_cutoff must be a non-negative real number.

      • +

    • ValueError – volume_cutoff must be a non-negative real number.

      • +

    • TypeError – latomic must be a list, a numpy.ndarray or None.

      • +

    • ValueError – latomic has incorrect shape. It must be (n, 8).

      • +

    • TypeError – ligand_cutoff must be a positive real number.

      • +

    • ValueError – ligand_cutoff must be a positive real number.

      • +

    • TypeError – box_adjustment must be a boolean.

      • +

    • TypeError – surface must be a string.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • ValueError – surface must be SAS or SES, not surface.

    diff --git a/docs/package/api_reference/export.html b/docs/package/api_reference/export.html index 9c910512..ceba56f3 100644 --- a/docs/package/api_reference/export.html +++ b/docs/package/api_reference/export.html @@ -128,14 +128,14 @@

    pyKVFinder.export

    -pyKVFinder.export(fn: str | Path | None, cavities: ndarray, surface: ndarray | None, vertices: ndarray | List[List[float]], step: float | int = 0.6, B: ndarray | None = None, Q: ndarray | None = None, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → str | None[source]
    +pyKVFinder.export(fn: str | Path | None, cavities: ndarray, surface: ndarray | None, vertices: ndarray | List[List[float]], step: float | int = 0.6, B: ndarray | None = None, Q: ndarray | None = None, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → str | None[source]

    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).

    Parameters:
      -

    • fn (Union[str, pathlib.Path], optional) – A path to PDB file for writing cavities. If None, return a raw string with the PDB-formatted file.

      • +

    • fn (Union[str, pathlib.Path], optional) – A path to PDB file for writing cavities. If None, return a raw string with the PDB-formatted file.

    • cavities (numpy.ndarray) –

      Cavity points in the 3D grid (cavities[nx][ny][nz]). Cavities array has integer labels in each position, that are:

      @@ -162,49 +162,49 @@

      pyKVFinder.exportfloat]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, +

    • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • B (numpy.ndarray, optional) – A numpy.ndarray with values to be mapped on B-factor column in cavity points (B[nx][ny][nz]), by default None.

    • Q (numpy.ndarray, optional) – A numpy.ndarray with hydrophobicity scale values to be mapped on B-factor column in surface points (Q[nx][ny][nz]), by default None.

      • -

    • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

      • +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

      • -

    • append (bool, optional) – Whether to append cavities to the PDB file, by default False.

      • -

    • model (int, optional) – Model number, by default 0.

      • +

    • append (bool, optional) – Whether to append cavities to the PDB file, by default False.

      • +

    • model (int, optional) – Model number, by default 0.

    Returns:

    A raw string with the PDB-formatted file.

    Return type:
    -

    Optional[str]

    +

    Optional[str]

    Raises:
      -

    • TypeError – “fn must be a string, a pathlib.Path or None. If None, return a raw string with the PDB-formatted file.”

      • -

    • TypeError – cavities must be a numpy.ndarray.

      • -

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – surface must be a numpy.ndarray.

      • -

    • ValueError – surface has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – vertices must be a list or a numpy.ndarray.

      • -

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – B must be a numpy.ndarray.

      • -

    • ValueError – B has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – Q must be a numpy.ndarray.

      • -

    • ValueError – Q has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • -

    • ValueError – Invalid selection: {selection}.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – append must be a boolean.

      • -

    • TypeError – model must be a integer.

      • -

    • RuntimeError – User must define surface when not defining cavities.

      • +

    • TypeError – “fn must be a string, a pathlib.Path or None. If None, return a raw string with the PDB-formatted file.”

      • +

    • TypeError – cavities must be a numpy.ndarray.

      • +

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – surface must be a numpy.ndarray.

      • +

    • ValueError – surface has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – vertices must be a list or a numpy.ndarray.

      • +

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – B must be a numpy.ndarray.

      • +

    • ValueError – B has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – Q must be a numpy.ndarray.

      • +

    • ValueError – Q has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • +

    • ValueError – Invalid selection: {selection}.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – append must be a boolean.

      • +

    • TypeError – model must be a integer.

      • +

    • RuntimeError – User must define surface when not defining cavities.

    diff --git a/docs/package/api_reference/export_openings.html b/docs/package/api_reference/export_openings.html index bccdf657..a1288146 100644 --- a/docs/package/api_reference/export_openings.html +++ b/docs/package/api_reference/export_openings.html @@ -128,12 +128,12 @@

    pyKVFinder.export_openings

    -pyKVFinder.export_openings(fn: str | Path, openings: ndarray, vertices: ndarray | List[List[float]], step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → None[source]
    +pyKVFinder.export_openings(fn: str | Path, openings: ndarray, vertices: ndarray | List[List[float]], step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → None[source]

    Export opening points (H) to a PDB-formatted file.

    Parameters:
      -

    • fn (Union[str, pathlib.Path]) – A path to PDB file for writing openings.

      • +

    • fn (Union[str, pathlib.Path]) – A path to PDB file for writing openings.

    • openings (numpy.ndarray) –

      Openings points in the 3D grid (openings[nx][ny][nz]). Openings array has integer labels in each position, that are:

      @@ -147,31 +147,31 @@

      pyKVFinder.export_openingsfloat]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, +

    • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • -

    • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of opening names to be selected, by default None.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of opening names to be selected, by default None.

      • +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

      • -

    • append (bool, optional) – Whether to append openings to the PDB file, by default False.

      • -

    • model (int, optional) – Model number, by default 0.

      • +

    • append (bool, optional) – Whether to append openings to the PDB file, by default False.

      • +

    • model (int, optional) – Model number, by default 0.

    Raises:
      -

    • TypeError – openings must be a numpy.ndarray.

      • -

    • ValueError – openings has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – vertices must be a list or a numpy.ndarray.

      • -

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – selection must be a list of strings (opening names) or integers (opening labels).

      • -

    • ValueError – Invalid selection: {selection}.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – append must be a boolean.

      • -

    • TypeError – model must be a integer.

      • -

    • TypeError – fn must be a string or pathlib.Path.

      • +

    • TypeError – openings must be a numpy.ndarray.

      • +

    • ValueError – openings has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – vertices must be a list or a numpy.ndarray.

      • +

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – selection must be a list of strings (opening names) or integers (opening labels).

      • +

    • ValueError – Invalid selection: {selection}.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – append must be a boolean.

      • +

    • TypeError – model must be a integer.

      • +

    • TypeError – fn must be a string or pathlib.Path.

    diff --git a/docs/package/api_reference/get_vertices.html b/docs/package/api_reference/get_vertices.html index b13224d1..3e5914ab 100644 --- a/docs/package/api_reference/get_vertices.html +++ b/docs/package/api_reference/get_vertices.html @@ -128,15 +128,15 @@

    pyKVFinder.get_vertices

    -pyKVFinder.get_vertices(atomic: ndarray | List[List[str | float | int]], probe_out: float | int = 4.0, step: float | int = 0.6) → ndarray[source]
    +pyKVFinder.get_vertices(atomic: ndarray | List[List[str | float | int]], probe_out: float | int = 4.0, step: float | int = 0.6) → ndarray[source]

    Gets 3D grid vertices.

    Parameters:
      -

    • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates +

    • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

      • -

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    Returns:
    @@ -148,12 +148,12 @@

    pyKVFinder.get_vertices
    Raises:
      -

    • TypeError – atomic must be a list or a numpy.ndarray.

      • -

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • -

    • TypeError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be a non-negative real number.

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • +

    • TypeError – atomic must be a list or a numpy.ndarray.

      • +

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • +

    • TypeError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be a non-negative real number.

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

    diff --git a/docs/package/api_reference/get_vertices_from_file.html b/docs/package/api_reference/get_vertices_from_file.html index 589a6ba0..2b494762 100644 --- a/docs/package/api_reference/get_vertices_from_file.html +++ b/docs/package/api_reference/get_vertices_from_file.html @@ -128,20 +128,20 @@

    pyKVFinder.get_vertices_from_file

    -pyKVFinder.get_vertices_from_file(fn: str | Path, atomic: ndarray | List[List[str | float | int]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, nthreads: int | None = None) → Tuple[ndarray, ndarray, ndarray][source]
    +pyKVFinder.get_vertices_from_file(fn: str | Path, atomic: ndarray | List[List[str | float | int]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, nthreads: int | None = None) → Tuple[ndarray, ndarray, ndarray][source]

    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.

    Parameters:
      -

    • fn (Union[str, pathlib.Path]) – A path to box configuration file (TOML-formatted).

      • -

    • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates +

    • fn (Union[str, pathlib.Path]) – A path to box configuration file (TOML-formatted).

      • +

    • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • -

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • -

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • +

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    @@ -156,19 +156,19 @@

    pyKVFinder.get_vertices_from_fileRaises:
      -

    • TypeError – fn must be a string or a pathlib.Path.

      • -

    • TypeError – atomic must be a list or a numpy.ndarray.

      • -

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – probe_in must be a non-negative real number.

      • -

    • ValueError – probe_in must be a non-negative real number.

      • -

    • TypeError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be greater than probe_in.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – You must define (p1, p2, p3, p4) or (residues, padding) keys in fn.

      • -

    • ValueError – Box not properly defined in fn.

      • +

    • TypeError – fn must be a string or a pathlib.Path.

      • +

    • TypeError – atomic must be a list or a numpy.ndarray.

      • +

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – probe_in must be a non-negative real number.

      • +

    • ValueError – probe_in must be a non-negative real number.

      • +

    • TypeError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be greater than probe_in.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – You must define (p1, p2, p3, p4) or (residues, padding) keys in fn.

      • +

    • ValueError – Box not properly defined in fn.

    diff --git a/docs/package/api_reference/hydropathy.html b/docs/package/api_reference/hydropathy.html index 9870dba6..caccb68c 100644 --- a/docs/package/api_reference/hydropathy.html +++ b/docs/package/api_reference/hydropathy.html @@ -128,7 +128,7 @@

    pyKVFinder.hydropathy

    -pyKVFinder.hydropathy(surface: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, hydrophobicity_scale: str | Path = 'EisenbergWeiss', ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float]][source]
    +pyKVFinder.hydropathy(surface: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, hydrophobicity_scale: str | Path = 'EisenbergWeiss', ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float]][source]

    Hydropathy characterization of the detected cavities.

    Map a target hydrophobicity scale per surface point and calculate average hydropathy of detected cavities.

    @@ -146,13 +146,13 @@

    pyKVFinder.hydropathyThe empty space points are regions that do not meet the chosen volume cutoff to be considered a cavity.

    -

  • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates +

  • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

    • -

  • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, +

  • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

    • -

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • -

  • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

    • -

  • hydrophobicity_scale (str, optional) –

    Name of a built-in hydrophobicity scale or a path to a +

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • +

  • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

    • +

  • hydrophobicity_scale (str, optional) –

    Name of a built-in hydrophobicity scale or a path to a TOML-formatted file with a custom hydrophobicity scale, by default EisenbergWeiss. The hydrophobicity scale file defines the name of the scale and the @@ -171,12 +171,12 @@

    pyKVFinder.hydropathy

    • -

  • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface +

  • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface residues, by default False.

    • -

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • -

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • +

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • -

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • +

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • Returns:
    @@ -190,23 +190,23 @@

    pyKVFinder.hydropathy
    Raises:
      -

    • TypeError – surface must be a numpy.ndarray.

      • -

    • ValueError – surface has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – atomic must be a list or a numpy.ndarray.

      • -

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • -

    • TypeError – vertices must be a list or a numpy.ndarray.

      • -

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – probe_in must be a non-negative real number.

      • -

    • ValueError – probe_in must be a non-negative real number.

      • -

    • TypeError – hydrophobicity_scale must be a string or a pathlib.Path.

      • -

    • TypeError – ignore_backbone must be a boolean.

      • -

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • -

    • ValueError – Invalid selection: {selection}.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – verbose must be a boolean.

      • +

    • TypeError – surface must be a numpy.ndarray.

      • +

    • ValueError – surface has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – atomic must be a list or a numpy.ndarray.

      • +

    • ValueError – atomic has incorrect shape. It must be (n, 8).

      • +

    • TypeError – vertices must be a list or a numpy.ndarray.

      • +

    • ValueError – vertices has incorrect shape. It must be (4, 3).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – probe_in must be a non-negative real number.

      • +

    • ValueError – probe_in must be a non-negative real number.

      • +

    • TypeError – hydrophobicity_scale must be a string or a pathlib.Path.

      • +

    • TypeError – ignore_backbone must be a boolean.

      • +

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • +

    • ValueError – Invalid selection: {selection}.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – verbose must be a boolean.

    diff --git a/docs/package/api_reference/openings.html b/docs/package/api_reference/openings.html index 933e9dc6..77032ad1 100644 --- a/docs/package/api_reference/openings.html +++ b/docs/package/api_reference/openings.html @@ -128,7 +128,7 @@

    pyKVFinder.openings

    -pyKVFinder.openings(cavities: ndarray, depths: ndarray | None = None, step: float | int = 0.6, openings_cutoff: int = 1, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray, Dict[str, Dict[str, float]]][source]
    +pyKVFinder.openings(cavities: ndarray, depths: ndarray | None = None, step: float | int = 0.6, openings_cutoff: int = 1, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray, Dict[str, Dict[str, float]]][source]

    [WIP] Identify openings of the detected cavities and calculate their areas.

    Parameters:
    @@ -145,12 +145,12 @@

    pyKVFinder.openingsfloat, int], optional) – Grid spacing (A), by default 0.6.

    -

  • openings_cutoff (int, optional) – The minimum number of voxels an opening must have, by default 1.

    • -

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • -

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • +

  • openings_cutoff (int, optional) – The minimum number of voxels an opening must have, by default 1.

    • +

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • +

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • -

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • +

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • Returns:
    @@ -175,19 +175,19 @@

    pyKVFinder.openingsRaises:
      -

    • TypeError – cavities must be a numpy.ndarray.

      • -

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – depths must be a numpy.ndarray.

      • -

    • ValueError – depths has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – openings_cutoff must be an integer.

      • -

    • ValueError – openings_cutoff must be a positive integer.

      • -

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • -

    • ValueError – Invalid selection: selection.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – verbose must be a boolean

      • +

    • TypeError – cavities must be a numpy.ndarray.

      • +

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – depths must be a numpy.ndarray.

      • +

    • ValueError – depths has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – openings_cutoff must be an integer.

      • +

    • ValueError – openings_cutoff must be a positive integer.

      • +

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • +

    • ValueError – Invalid selection: selection.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – verbose must be a boolean

    diff --git a/docs/package/api_reference/plot_frequencies.html b/docs/package/api_reference/plot_frequencies.html index 6f6d97a1..1c0e8cb7 100644 --- a/docs/package/api_reference/plot_frequencies.html +++ b/docs/package/api_reference/plot_frequencies.html @@ -128,20 +128,20 @@

    pyKVFinder.plot_frequencies

    -pyKVFinder.plot_frequencies(frequencies: Dict[str, Dict[str, Dict[str, int]]], fn: str | Path = 'barplots.pdf') → None[source]
    +pyKVFinder.plot_frequencies(frequencies: Dict[str, Dict[str, Dict[str, int]]], fn: str | Path = 'barplots.pdf') → None[source]

    Plot bar charts of calculated frequencies (residues and classes of residues) for each detected cavity in a target PDF file.

    Parameters:
      -

    • frequencies (Dict[str, Dict[str, Dict[str, int]]]) – A dictionary with frequencies of residues and class for +

    • frequencies (Dict[str, Dict[str, Dict[str, int]]]) – A dictionary with frequencies of residues and class for residues of each detected cavity.

      • -

    • fn (Union[str, pathlib.Path], optional) – A path to PDF file for plotting bar charts of frequencies, by +

    • fn (Union[str, pathlib.Path], optional) – A path to PDF file for plotting bar charts of frequencies, by default barplots.pdf.

    Raises:
    -

    TypeError – fn must be a string or a pathlib.Path.

    +

    TypeError – fn must be a string or a pathlib.Path.

    diff --git a/docs/package/api_reference/pyKVFinderResults.html b/docs/package/api_reference/pyKVFinderResults.html index 4359033d..d85de52c 100644 --- a/docs/package/api_reference/pyKVFinderResults.html +++ b/docs/package/api_reference/pyKVFinderResults.html @@ -112,7 +112,7 @@

    pyKVFinder.pyKVFinderResults

    -class pyKVFinder.pyKVFinderResults(cavities: ndarray, surface: ndarray, depths: ndarray | None, scales: ndarray | None, volume: Dict[str, float], area: Dict[str, float], max_depth: Dict[str, float] | None, avg_depth: Dict[str, float] | None, avg_hydropathy: Dict[str, float] | None, residues: Dict[str, List[List[str]]], frequencies: Dict[str, Dict[str, Dict[str, int]]] | None, _vertices: ndarray, _step: float | int, _input: str | Path | None = None, _ligand: str | Path | None = None)[source]
    +class pyKVFinder.pyKVFinderResults(cavities: ndarray, surface: ndarray, depths: ndarray | None, scales: ndarray | None, volume: Dict[str, float], area: Dict[str, float], max_depth: Dict[str, float] | None, avg_depth: Dict[str, float] | None, avg_hydropathy: Dict[str, float] | None, residues: Dict[str, List[List[str]]], frequencies: Dict[str, Dict[str, Dict[str, int]]] | None, _vertices: ndarray, _step: float | int, _input: str | Path | None = None, _ligand: str | Path | None = None)[source]

    A class containing pyKVFinder detection and characterization results.

    Parameters:
    @@ -145,21 +145,21 @@

    pyKVFinder.pyKVFinderResultsstr, float]) – A dictionary with volume of each detected cavity.

    -

  • area (Dict[str, float]) – A dictionary with area of each detected cavity.

    • -

  • max_depth (Dict[str, float], optional) – A dictionary with maximum depth of each detected cavity.

    • -

  • avg_depth (Dict[str, float], optional) – A dictionary with average depth of each detected cavity.

    • -

  • avg_hydropathy (Dict[str, float], optional) – A dictionary with average hydropathy for each detected cavity and +

  • volume (Dict[str, float]) – A dictionary with volume of each detected cavity.

    • +

  • area (Dict[str, float]) – A dictionary with area of each detected cavity.

    • +

  • max_depth (Dict[str, float], optional) – A dictionary with maximum depth of each detected cavity.

    • +

  • avg_depth (Dict[str, float], optional) – A dictionary with average depth of each detected cavity.

    • +

  • avg_hydropathy (Dict[str, float], optional) – A dictionary with average hydropathy for each detected cavity and the range of the hydrophobicity scale (min, max).

    • -

  • residues (Dict[str, List[List[str]]]) – A dictionary with a list of interface residues for each detected +

  • residues (Dict[str, List[List[str]]]) – A dictionary with a list of interface residues for each detected cavity.

    • -

  • frequencies (Dict[str, Dict[str, Dict[str, int]]], optional) – A dictionary with frequencies of residues and class for +

  • frequencies (Dict[str, Dict[str, Dict[str, int]]], optional) – A dictionary with frequencies of residues and class for residues of each detected cavity.

  • _vertices (numpy.ndarray) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

    • -

  • _step (float) – Grid spacing (A).

    • -

  • _input (Union[str, pathlib.Path], optional) – A path to input PDB or XYZ file, by default None.

    • -

  • _ligand (Union[str, pathlib.Path], optional) – A path to ligand PDB or XYZ file, by default None.

    • +

  • _step (float) – Grid spacing (A).

    • +

  • _input (Union[str, pathlib.Path], optional) – A path to input PDB or XYZ file, by default None.

    • +

  • _ligand (Union[str, pathlib.Path], optional) – A path to ligand PDB or XYZ file, by default None.

    • @@ -235,7 +235,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    int

    +

    int

    @@ -246,7 +246,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, float]

    +

    Dict[str, float]

    @@ -257,7 +257,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, float]

    +

    Dict[str, float]

    @@ -268,7 +268,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, float], optional

    +

    Dict[str, float], optional

    @@ -279,7 +279,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, float], optional

    +

    Dict[str, float], optional

    @@ -291,7 +291,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, float], optional

    +

    Dict[str, float], optional

    @@ -303,7 +303,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, List[List[str]]]

    +

    Dict[str, List[List[str]]]

    @@ -315,7 +315,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Dict[str, Dict[str, Dict[str, int]]], optional

    +

    Dict[str, Dict[str, Dict[str, int]]], optional

    @@ -338,7 +338,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    float

    +

    float

    @@ -349,7 +349,7 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Union[str, pathlib.Path], optional

    +

    Union[str, pathlib.Path], optional

    @@ -360,22 +360,22 @@

    pyKVFinder.pyKVFinderResults
    Type:
    -

    Union[str, pathlib.Path], optional

    +

    Union[str, pathlib.Path], optional

    -export(output: str | Path = 'cavity.pdb', nthreads: int | None = None) → str | None[source]
    +export(output: str | Path = 'cavity.pdb', nthreads: int | None = None) → str | None[source]

    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).

    Parameters:
      -

    • output (Union[str, pathlib.Path]), optional) – A path to PDB file for writing cavities, by default cavity.pdb.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • output (Union[str, pathlib.Path]), optional) – A path to PDB file for writing cavities, by default cavity.pdb.

      • +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    @@ -383,7 +383,7 @@

    pyKVFinder.pyKVFinderResults

    A raw string with the PDB-formatted file.

    Return type:
    -

    Optional[str]

    +

    Optional[str]

    @@ -405,7 +405,7 @@

    pyKVFinder.pyKVFinderResults
    -export_all(fn: str | Path = 'results.toml', output: str | Path = 'cavity.pdb', include_frequencies_pdf: bool = False, pdf: str | Path = 'barplots.pdf', nthreads: int | None = None) → None[source]
    +export_all(fn: str | Path = 'results.toml', output: str | Path = 'cavity.pdb', include_frequencies_pdf: bool = False, pdf: str | Path = 'barplots.pdf', nthreads: int | None = None) → None[source]

    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 @@ -413,14 +413,14 @@

    pyKVFinder.pyKVFinderResults
    Parameters:
      -

    • fn (Union[str, pathlib.Path], optional) – A path to TOML-formatted file for writing file paths and +

    • fn (Union[str, pathlib.Path], optional) – A path to TOML-formatted file for writing file paths and cavity characterization (volume, area and interface residues) per cavity detected, by default results.toml.

      • -

    • output (Union[str, pathlib.Path], optional) – A path to PDB file for writing cavities, by default cavity.pdb.

      • -

    • include_frequencies_pdf (bool, optional) – Whether to plot frequencies (residues and classes of residues) +

    • output (Union[str, pathlib.Path], optional) – A path to PDB file for writing cavities, by default cavity.pdb.

      • +

    • include_frequencies_pdf (bool, optional) – Whether to plot frequencies (residues and classes of residues) to PDF file, by default False.

      • -

    • pdf (Union[str, pathlib.Path], optional) – A path to a PDF file, by default barplots.pdf.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • pdf (Union[str, pathlib.Path], optional) – A path to a PDF file, by default barplots.pdf.

      • +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    @@ -460,12 +460,12 @@

    pyKVFinder.pyKVFinderResults
    -plot_frequencies(pdf: str | Path = 'barplots.pdf')[source]
    +plot_frequencies(pdf: str | Path = 'barplots.pdf')[source]

    Plot bar charts of frequencies (residues and classes of residues) in a PDF file.

    Parameters:
    -

    pdf (Union[str, pathlib.Path], optional) – A path to a PDF file, by default barplots.pdf.

    +

    pdf (Union[str, pathlib.Path], optional) – A path to a PDF file, by default barplots.pdf.

    @@ -499,15 +499,15 @@

    pyKVFinder.pyKVFinderResults
    -write(fn: str | Path = 'results.toml', output: str | Path | None = None) → None[source]
    +write(fn: str | Path = 'results.toml', output: str | Path | None = None) → None[source]

    Writes file paths and cavity characterization to TOML-formatted file

    Parameters:
      -

    • fn (Union[str, pathlib.Path], optional) – A path to TOML-formatted file for writing file paths and cavity +

    • fn (Union[str, pathlib.Path], optional) – A path to TOML-formatted file for writing file paths and cavity characterization (volume, area, depth and interface residues) per cavity detected, by default results.toml.

      • -

    • output (Union[str, pathlib.Path], optional) – A path to a cavity PDB file, by default None.

      • +

    • output (Union[str, pathlib.Path], optional) – A path to a cavity PDB file, by default None.

    diff --git a/docs/package/api_reference/read_cavity.html b/docs/package/api_reference/read_cavity.html index dd86827c..db729dc7 100644 --- a/docs/package/api_reference/read_cavity.html +++ b/docs/package/api_reference/read_cavity.html @@ -128,22 +128,22 @@

    pyKVFinder.read_cavity

    -pyKVFinder.read_cavity(cavity: str | Path, receptor: str | Path, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, surface: str = 'SES', vdw: Dict[str, Dict[str, float]] | None = None, nthreads: int | None = None, verbose: bool = False) → ndarray[source]
    +pyKVFinder.read_cavity(cavity: str | Path, receptor: str | Path, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, surface: str = 'SES', vdw: Dict[str, Dict[str, float]] | None = None, nthreads: int | None = None, verbose: bool = False) → ndarray[source]

    Read cavities and receptor inside a 3D grid.

    Parameters:
      -

    • cavity (Union[str, pathlib.Path]) – A path to a PDB file of cavities.

      • -

    • receptor (Union[str, pathlib.Path]) – A path to a PDB or XYZ file of the receptor.

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • -

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • -

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • -

    • surface (str, optional) – Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent +

    • cavity (Union[str, pathlib.Path]) – A path to a PDB file of cavities.

      • +

    • receptor (Union[str, pathlib.Path]) – A path to a PDB or XYZ file of the receptor.

      • +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • +

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • +

    • surface (str, optional) – Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default “SES”.

      • -

    • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

      • -

    • nthreads (Optional[int], optional) – Number of threads, by default None. If None, the number of threads is +

    • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

      • +

    • nthreads (Optional[int], optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

      • -

    • verbose (bool, optional) – Print extra information to standard output, by default False.

      • +

    • verbose (bool, optional) – Print extra information to standard output, by default False.

    Returns:
    @@ -163,21 +163,21 @@

    pyKVFinder.read_cavity
    Raises:
      -

    • TypeError – cavity must be a string or a pathlib.Path.

      • -

    • TypeError – receptor must be a string or a pathlib.Path.

      • -

    • TypeError – target must have .pdb or .xyz extension.

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – probe_in must be a non-negative real number.

      • -

    • ValueError – probe_in must be a non-negative real number.

      • -

    • TypeError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be a non-negative real number.

      • -

    • ValueError – probe_out must be greater than probe_in.

      • -

    • TypeError – surface must be a str.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – verbose must be a boolean.

      • -

    • ValueError – surface must be SAS or SES, not {surface}.

      • +

    • TypeError – cavity must be a string or a pathlib.Path.

      • +

    • TypeError – receptor must be a string or a pathlib.Path.

      • +

    • TypeError – target must have .pdb or .xyz extension.

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – probe_in must be a non-negative real number.

      • +

    • ValueError – probe_in must be a non-negative real number.

      • +

    • TypeError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be a non-negative real number.

      • +

    • ValueError – probe_out must be greater than probe_in.

      • +

    • TypeError – surface must be a str.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – verbose must be a boolean.

      • +

    • ValueError – surface must be SAS or SES, not {surface}.

    diff --git a/docs/package/api_reference/read_pdb.html b/docs/package/api_reference/read_pdb.html index e6e7a8c8..dddca2a4 100644 --- a/docs/package/api_reference/read_pdb.html +++ b/docs/package/api_reference/read_pdb.html @@ -128,14 +128,14 @@

    pyKVFinder.read_pdb

    -pyKVFinder.read_pdb(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None, model: int | None = None) → ndarray[source]
    +pyKVFinder.read_pdb(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None, model: int | None = None) → ndarray[source]

    Reads PDB file into numpy.ndarrays.

    Parameters:
      -

    • fn (Union[str, pathlib.Path]) – A path to PDB file.

      • -

    • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

      • -

    • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.

      • +

    • fn (Union[str, pathlib.Path]) – A path to PDB file.

      • +

    • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

      • +

    • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.

    Returns:
    @@ -146,7 +146,7 @@

    pyKVFinder.read_pdb

    numpy.ndarray

    Raises:
    -

    TypeError – fn must be a string or a pathlib.Path.

    +

    TypeError – fn must be a string or a pathlib.Path.

    diff --git a/docs/package/api_reference/read_vdw.html b/docs/package/api_reference/read_vdw.html index 100ef698..5040ff51 100644 --- a/docs/package/api_reference/read_vdw.html +++ b/docs/package/api_reference/read_vdw.html @@ -128,25 +128,25 @@

    pyKVFinder.read_vdw

    -pyKVFinder.read_vdw(fn: str | Path | None = None) → Dict[str, Dict[str, float]][source]
    +pyKVFinder.read_vdw(fn: str | Path | None = None) → Dict[str, Dict[str, float]][source]

    Reads van der Waals radii from .dat file.

    Parameters:
    -

    fn (Optional[Union[str, pathlib.Path]], optional) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der +

    fn (Optional[Union[str, pathlib.Path]], optional) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der Waals radii file: vdw.dat.

    Returns:

    vdw – A dictionary containing radii values.

    Return type:
    -

    Dict[str, Dict[str, float]]

    +

    Dict[str, Dict[str, float]]

    Raises:
      -

    • TypeError – fn must be a string or a pathlib.Path.

      • -

    • ValueError – A line in vdw has incorrect format. The values must be double +

    • TypeError – fn must be a string or a pathlib.Path.

      • +

    • ValueError – A line in vdw has incorrect format. The values must be double tab-separated.

      • -

    • ValueError – A line in vdw has an incorrect radius type for an atom.

      • +

    • ValueError – A line in vdw has an incorrect radius type for an atom.

    diff --git a/docs/package/api_reference/read_xyz.html b/docs/package/api_reference/read_xyz.html index 811b0b9e..3741f0f4 100644 --- a/docs/package/api_reference/read_xyz.html +++ b/docs/package/api_reference/read_xyz.html @@ -128,13 +128,13 @@

    pyKVFinder.read_xyz

    -pyKVFinder.read_xyz(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None) → ndarray[source]
    +pyKVFinder.read_xyz(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None) → ndarray[source]

    Reads XYZ file into numpy.ndarrays.

    Parameters:
      -

    • fn (Union[str, pathlib.Path]) – A path to XYZ file.

      • -

    • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

      • +

    • fn (Union[str, pathlib.Path]) – A path to XYZ file.

      • +

    • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().

    Returns:
    @@ -145,7 +145,7 @@

    pyKVFinder.read_xyz

    numpy.ndarray

    Raises:
    -

    TypeError – fn must be a string or a pathlib.Path.

    +

    TypeError – fn must be a string or a pathlib.Path.

    diff --git a/docs/package/api_reference/run_workflow.html b/docs/package/api_reference/run_workflow.html index a9671681..75b49ccc 100644 --- a/docs/package/api_reference/run_workflow.html +++ b/docs/package/api_reference/run_workflow.html @@ -128,39 +128,39 @@

    pyKVFinder.run_workflow

    -pyKVFinder.run_workflow(input: str | pathlib.Path, ligand: str | pathlib.Path | None = None, vdw: str | pathlib.Path | None = None, box: str | pathlib.Path | None = None, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, ligand_cutoff: float | int = 5.0, include_depth: bool = False, include_hydropathy: bool = False, hydrophobicity_scale: str | pathlib.Path = 'EisenbergWeiss', surface: str = 'SES', ignore_backbone: bool = False, model: int | None = None, nthreads: int | None = None, verbose: bool = False) → pyKVFinder.pyKVFinderResults[source]
    +pyKVFinder.run_workflow(input: str | pathlib.Path, ligand: str | pathlib.Path | None = None, vdw: str | pathlib.Path | None = None, box: str | pathlib.Path | None = None, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, ligand_cutoff: float | int = 5.0, include_depth: bool = False, include_hydropathy: bool = False, hydrophobicity_scale: str | pathlib.Path = 'EisenbergWeiss', surface: str = 'SES', ignore_backbone: bool = False, model: int | None = None, nthreads: int | None = None, verbose: bool = False) → pyKVFinder.pyKVFinderResults[source]

    Detects and characterizes cavities (volume, area, depth [optional], hydropathy [optional] and interface residues).

    Parameters:
      -

    • input (Union[str, pathlib.Path]) – A path to a target structure file, in PDB or XYZ format, to detect and characterize cavities.

      • -

    • ligand (Union[str, pathlib.Path], optional) – A path to ligand file, in PDB or XYZ format, by default None.

      • -

    • vdw (Union[str, pathlib.Path], optional) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der +

    • input (Union[str, pathlib.Path]) – A path to a target structure file, in PDB or XYZ format, to detect and characterize cavities.

      • +

    • ligand (Union[str, pathlib.Path], optional) – A path to ligand file, in PDB or XYZ format, by default None.

      • +

    • vdw (Union[str, pathlib.Path], optional) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der Waals radii file: vdw.dat.

      • -

    • box (Union[str, pathlib.Path], optional) – A path to box configuration file (TOML-formatted), by default None.

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • -

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • -

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • -

    • removal_distance (Union[float, int], optional) – Length to be removed from the cavity-bulk frontier (A), by default 2.4.

      • -

    • volume_cutoff (Union[float, int], optional) – Cavities volume filter (A3), by default 5.0.

      • -

    • ligand_cutoff (Union[float, int], optional) – Radius value to limit a space around a ligand (A), by default 5.0.

      • -

    • include_depth (bool, optional) – Whether to characterize the depth of the detected cavities, by +

    • box (Union[str, pathlib.Path], optional) – A path to box configuration file (TOML-formatted), by default None.

      • +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

      • +

    • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.

      • +

    • removal_distance (Union[float, int], optional) – Length to be removed from the cavity-bulk frontier (A), by default 2.4.

      • +

    • volume_cutoff (Union[float, int], optional) – Cavities volume filter (A3), by default 5.0.

      • +

    • ligand_cutoff (Union[float, int], optional) – Radius value to limit a space around a ligand (A), by default 5.0.

      • +

    • include_depth (bool, optional) – Whether to characterize the depth of the detected cavities, by default False.

      • -

    • include_hydropathy (bool, optional) – Whether to characterize the hydropathy of the detected cavities, by +

    • include_hydropathy (bool, optional) – Whether to characterize the hydropathy of the detected cavities, by default False.

      • -

    • hydrophobicity_scale (Union[str, pathlib.Path], optional) – Name of a built-in hydrophobicity scale (EisenbergWeiss, HessaHeijne, +

    • hydrophobicity_scale (Union[str, pathlib.Path], optional) – Name of a built-in hydrophobicity scale (EisenbergWeiss, HessaHeijne, KyteDoolitte, MoonFleming, RadzickaWolfenden, WimleyWhite, ZhaoLondon) or a path to a TOML-formatted file with a custom hydrophobicity scale, by default EisenbergWeiss.

      • -

    • surface (str, optional) – Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent +

    • surface (str, optional) – Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default SES.

      • -

    • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface +

    • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface residues, by default False.

      • -

    • model (int, optional) – Model number, by default None. If None, keep atoms from all models.

      • -

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

    • model (int, optional) – Model number, by default None. If None, keep atoms from all models.

      • +

    • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

      • -

    • verbose (bool, optional) – Print extra information to standard output, by default False.

      • +

    • verbose (bool, optional) – Print extra information to standard output, by default False.

    Returns:
    @@ -279,8 +279,8 @@

    pyKVFinder.run_workflow
    Raises:
      -

    • TypeError – input must have .pdb or .xyz extension.

      • -

    • TypeError – ligand must have .pdb or .xyz extension.

      • +

    • TypeError – input must have .pdb or .xyz extension.

      • +

    • TypeError – ligand must have .pdb or .xyz extension.

    diff --git a/docs/package/api_reference/spatial.html b/docs/package/api_reference/spatial.html index 8d54f3b5..f105db35 100644 --- a/docs/package/api_reference/spatial.html +++ b/docs/package/api_reference/spatial.html @@ -128,7 +128,7 @@

    pyKVFinder.spatial

    -pyKVFinder.spatial(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]
    +pyKVFinder.spatial(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]

    Spatial characterization (volume and area) of the detected cavities.

    Parameters:
    @@ -146,11 +146,11 @@

    pyKVFinder.spatialfloat, int], optional) – Grid spacing (A), by default 0.6.

    -

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • -

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is +

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    • +

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.

    • +

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

    • -

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • +

  • verbose (bool, optional) – Print extra information to standard output, by default False.

    • Returns:
    @@ -182,15 +182,15 @@

    pyKVFinder.spatial
    Raises:
      -

    • TypeError – cavities must be a numpy.ndarray.

      • -

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • -

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • -

    • ValueError – Invalid selection: {selection}.

      • -

    • TypeError – nthreads must be a positive integer.

      • -

    • ValueError – nthreads must be a positive integer.

      • -

    • TypeError – verbose must be a boolean.

      • +

    • TypeError – cavities must be a numpy.ndarray.

      • +

    • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

      • +

    • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

      • +

    • ValueError – Invalid selection: {selection}.

      • +

    • TypeError – nthreads must be a positive integer.

      • +

    • ValueError – nthreads must be a positive integer.

      • +

    • TypeError – verbose must be a boolean.

    diff --git a/docs/package/api_reference/write_results.html b/docs/package/api_reference/write_results.html index c28ba807..192999a3 100644 --- a/docs/package/api_reference/write_results.html +++ b/docs/package/api_reference/write_results.html @@ -128,47 +128,47 @@

    pyKVFinder.write_results

    -pyKVFinder.write_results(fn: str | Path, input: str | Path | None, ligand: str | Path | None, output: str | Path | None, volume: Dict[str, float] | None = None, area: Dict[str, float] | None = None, max_depth: Dict[str, float] | None = None, avg_depth: Dict[str, float] | None = None, avg_hydropathy: Dict[str, float] | None = None, residues: Dict[str, List[List[str]]] | None = None, frequencies: Dict[str, Dict[str, Dict[str, int]]] | None = None, step: float | int = 0.6) → None[source]
    +pyKVFinder.write_results(fn: str | Path, input: str | Path | None, ligand: str | Path | None, output: str | Path | None, volume: Dict[str, float] | None = None, area: Dict[str, float] | None = None, max_depth: Dict[str, float] | None = None, avg_depth: Dict[str, float] | None = None, avg_hydropathy: Dict[str, float] | None = None, residues: Dict[str, List[List[str]]] | None = None, frequencies: Dict[str, Dict[str, Dict[str, int]]] | None = None, step: float | int = 0.6) → None[source]

    Writes file paths and cavity characterization to TOML-formatted file.

    Parameters:
      -

    • fn (Union[str, pathlib.Path]) – A path to TOML-formatted file for writing file paths and +

    • fn (Union[str, pathlib.Path]) – A path to TOML-formatted file for writing file paths and cavity characterization (volume, area, depth [optional] and interface residues) per cavity detected.

      • -

    • input (Union[str, pathlib.Path], optional) – A path to input PDB or XYZ file.

      • -

    • ligand (Union[str, pathlib.Path], optional) – A path to ligand PDB or XYZ file.

      • -

    • output (Union[str, pathlib.Path], optional) – A path to cavity PDB file.

      • -

    • volume (Dict[str, float], optional) – A dictionary with volume of each detected cavity, by default None.

      • -

    • area (Dict[str, float], optional) – A dictionary with area of each detected cavity, by default None.

      • -

    • max_depth (Dict[str, float], optional) – A dictionary with maximum depth of each detected cavity, by default +

    • input (Union[str, pathlib.Path], optional) – A path to input PDB or XYZ file.

      • +

    • ligand (Union[str, pathlib.Path], optional) – A path to ligand PDB or XYZ file.

      • +

    • output (Union[str, pathlib.Path], optional) – A path to cavity PDB file.

      • +

    • volume (Dict[str, float], optional) – A dictionary with volume of each detected cavity, by default None.

      • +

    • area (Dict[str, float], optional) – A dictionary with area of each detected cavity, by default None.

      • +

    • max_depth (Dict[str, float], optional) – A dictionary with maximum depth of each detected cavity, by default None.

      • -

    • avg_depth (Dict[str, float], optional) – A dictionary with average depth of each detected cavity, by default +

    • avg_depth (Dict[str, float], optional) – A dictionary with average depth of each detected cavity, by default None.

      • -

    • avg_hydropapthy (Dict[str, float], optional) – A dictionary with average hydropathy of each detected cavity and range +

    • avg_hydropapthy (Dict[str, float], optional) – A dictionary with average hydropathy of each detected cavity and range of the hydrophobicity scale mapped, by default None.

      • -

    • residues (Dict[str, List[List[str]]], optional) – A dictionary with interface residues of each detected cavity, by +

    • residues (Dict[str, List[List[str]]], optional) – A dictionary with interface residues of each detected cavity, by default None.

      • -

    • frequencies (Dict[str, Dict[str, Dict[str, int]]], optional) – A dictionary with frequencies of interface residues and classes of +

    • frequencies (Dict[str, Dict[str, Dict[str, int]]], optional) – A dictionary with frequencies of interface residues and classes of residues of each detected cavity, by default None.

      • -

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

      • +

    • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

    Raises:
      -

    • TypeError – fn must be a string or a pathlib.Path.

      • -

    • TypeError – input must be a string or a pathlib.Path.

      • -

    • TypeError – ligand must be a string or a pathlib.Path.

      • -

    • TypeError – output must be a string or a pathlib.Path.

      • -

    • TypeError – volume must be a dictionary.

      • -

    • TypeError – area must be a dictionary.

      • -

    • TypeError – max_depth must be a dictionary.

      • -

    • TypeError – avg_depth must be a dictionary.

      • -

    • TypeError – avg_hydropathy must be a dictionary.

      • -

    • TypeError – residues must be a dictionary.

      • -

    • TypeError – frequencies must be a dictionary.

      • -

    • TypeError – step must be a positive real number.

      • -

    • ValueError – step must be a positive real number.

      • +

    • TypeError – fn must be a string or a pathlib.Path.

      • +

    • TypeError – input must be a string or a pathlib.Path.

      • +

    • TypeError – ligand must be a string or a pathlib.Path.

      • +

    • TypeError – output must be a string or a pathlib.Path.

      • +

    • TypeError – volume must be a dictionary.

      • +

    • TypeError – area must be a dictionary.

      • +

    • TypeError – max_depth must be a dictionary.

      • +

    • TypeError – avg_depth must be a dictionary.

      • +

    • TypeError – avg_hydropathy must be a dictionary.

      • +

    • TypeError – residues must be a dictionary.

      • +

    • TypeError – frequencies must be a dictionary.

      • +

    • TypeError – step must be a positive real number.

      • +

    • ValueError – step must be a positive real number.

    diff --git a/docs/plugins/pymol/index.html b/docs/plugins/pymol/index.html index a5398a72..72482eb9 100644 --- a/docs/plugins/pymol/index.html +++ b/docs/plugins/pymol/index.html @@ -109,17 +109,35 @@

    PyMOL pyKVFinder Tools

    Installation

    First, it is required to install Anaconda or Miniconda (Python 3.10 or later). If you do not have it installed, please refer to Anaconda or Miniconda websites.

    -

    In the Anaconda Prompt, create a new environment and install PyMOL:

    +

    In the Anaconda Prompt, create a new environment and activate it:

    conda create -n pymol python=3.10
 conda activate pymol
-# PyMOL v3.0
-conda install -c conda-forge -c schrodinger pymol-bundle
-# PyMOL v2.6
-conda install -c conda-forge -c schrodinger pymol-bundle=2.6
-# PyMOL Open-Source
-conda install -c conda-forge pymol-open-source
    +

    Then, install one of the following versions of PyMOL:

    +
      +

    • PyMOL v3.0 (Schrodinger)

      +
      +
      conda install -c conda-forge -c schrodinger pymol-bundle
+
      +
      +
      +
      • +

    • PyMOL v2.6 (Schrodinger):

      +
      +
      conda install -c conda-forge -c schrodinger pymol-bundle=2.6
+
      +
      +
      +
      • +

    • PyMOL Open-Source

      +
      +
      conda install -c conda-forge pymol-open-source
+
      +
      +
      +
      • +

    After installing one of the PyMOL versions (v3.0, v2.6 or Open-Source), you need to install the pyKVFinder package, if you have not done it yet:

    pip install pyKVFinder
    diff --git a/docs/source/plugins/pymol/index.rst b/docs/source/plugins/pymol/index.rst index 875a4ec8..6e96ac99 100644 --- a/docs/source/plugins/pymol/index.rst +++ b/docs/source/plugins/pymol/index.rst @@ -9,19 +9,32 @@ Installation First, it is required to install Anaconda or Miniconda (Python 3.10 or later). If you do not have it installed, please refer to `Anaconda `_ or `Miniconda `_ websites. -In the `Anaconda Prompt`, create a new environment and install PyMOL: +In the `Anaconda Prompt`, create a new environment and activate it: .. code-block:: bash conda create -n pymol python=3.10 conda activate pymol - # PyMOL v3.0 - conda install -c conda-forge -c schrodinger pymol-bundle - # PyMOL v2.6 - conda install -c conda-forge -c schrodinger pymol-bundle=2.6 - # PyMOL Open-Source - conda install -c conda-forge pymol-open-source +Then, install **one** of the following versions of PyMOL: + +* PyMOL v3.0 (Schrodinger) + + .. code-block:: bash + + conda install -c conda-forge -c schrodinger pymol-bundle + +* PyMOL v2.6 (Schrodinger): + + .. code-block:: bash + + conda install -c conda-forge -c schrodinger pymol-bundle=2.6 + +* PyMOL Open-Source + + .. code-block:: bash + + conda install -c conda-forge pymol-open-source After installing one of the PyMOL versions (v3.0, v2.6 or Open-Source), you need to install the `pyKVFinder `_ package, if you have not done it yet: