mol2grid

############################ Molecules to grid (mol2grid) ############################

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Python package to insert a molecule in a 3D grid, considering each atom type as an integer.

See also:

• GitHub repository <https://github.com/LBC-LNBio/mol2grid/>_

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Requirements

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• Python 3.7+
• NumPy 1.19.5+
• toml 0.10.2+

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Installation

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To install the latest release on PyPI <https://pypi.org/project/mol2grid>_, run:

.. code-block:: bash

pip install mol2grid

To install the latest developmental version, run:

.. code-block:: bash

git clone https://github.com/LBC-LNBio/mol2grid.git
pip install mol2grid

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Usage

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First, save the ligand and receptor structures to PDB-formatted files.

.. code-block:: python

>>> ligand = 'path/to/ligand.pdb' # path to a target ligand
>>> receptor = 'path/to/receptor.pdb' # path to a target receptor

The lig2grid function takes a ligand and a receptor PDB-formatted files and inserts this ligand to a 3D grid created based on the receptor, a padding and a grid spacing (step).

.. code-block:: python

>>> from mol2grid import lig2grid
>>> lig = lig2grid(ligand, receptor, padding=4.0, step=0.6, file=None, vdw=None, catalog=None, ignore_h=True)

The rec2grid function takes a receptor PDB-formatted file and inserts this receptor to a 3D grid created based on the receptor, a padding and a grid spacing (step).

.. code-block:: python

>>> from mol2grid import rec2grid
>>> rec = rec2grid(receptor, padding=4.0, step=0.6, file=None, vdw=None, catalog=None, ignore_h=True)

The pair2grid function takes a ligand and a receptor PDB-formatted files and inserts this ligand and receptor to 3D grids created based on the receptor, a padding and a grid spacing (step).

.. code-block:: python

>>> from mol2grid import pair2grid
>>> lig, rec = pair2grid(ligand, receptor, padding=4.0, step=0.6, file=None, vdw=None, catalog=None, ignore_h=True)

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API

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mol2grid.lig2grid

Inserts a target receptor to a 3D grid, created based on the receptor, a padding and a grid spacing (step).

.. code-block:: python

mol2grid.lig2grid(ligand: str, receptor: str, padding: float, step: float = 0.6, file: Optional[str] = None, vdw: Optional[str] = None, catalog: Optional[str] = None, ignore_h: bool = True, nthreads: int = os.cpu_count() - 1, verbose: bool = False) → numpy.ndarray

:Args:

-  **ligand** (*str*) – A path to a PDB-formatted file of a target ligand

-  **receptor** (*str*) – A path to a PDB-formatted file of a target receptor

-  **padding** (*float*) – A length to be added in each direction of the 3D grid

-  **step** (*float*, *optional*) – Grid spacing (A), by default 0.6

-  **file** (*str*, *optional*) – A path to a PDB-formatted file to write the grid points where atoms lay on and the barcodes are mapped on the B-values, by default None

-  **vdw** (*str*, *optional*) – A path to a custom van der Waals radii file, by default None

-  **catalog** (*str*, *optional*) – A path to a custom catalog file, by default None

-  **ignore_h** (*bool*, *optional*) – Whether to ignore hydrogen atoms, by default True

-  **nthreads** (*int*, *optional*) – Number of threads, by default {os.cpu_count()-1}

-  **verbose** (*bool*, *optional*) – Whether to print extra information to standard output, by default False

:Returns: A numpy.ndarray with grid points corresponding to the atom barcodes of the receptor

:Return type: numpy.ndarray

:Note: Greater barcodes have priority in the 3D grid when atoms overlap

mol2grid.rec2grid

Inserts a target receptor to a 3D grid, created based on the receptor, a padding and a grid spacing (step).

.. code-block:: python

mol2grid.rec2grid(receptor: str, padding: float, step: float = 0.6, file: Optional[str] = None, vdw: Optional[str] = None, catalog: Optional[str] = None, ignore_h: bool = True, nthreads: int = os.cpu_count() - 1, verbose: bool = False) → numpy.ndarray

:Args:

-  **receptor** (*str*) – A path to a PDB-formatted file of a target receptor

-  **padding** (*float*) – A length to be added in each direction of the 3D grid

-  **step** (*float*, *optional*) – Grid spacing (A), by default 0.6

-  **file** (*str*, *optional*) – A path to a PDB-formatted file to write the grid points where atoms lay on and the barcodes are mapped on the B-values, by default None

-  **vdw** (*str*, *optional*) – A path to a custom van der Waals radii file, by default None

-  **catalog** (*str*, *optional*) – A path to a custom catalog file, by default None

-  **ignore_h** (*bool*, *optional*) – Whether to ignore hydrogen atoms, by default True

-  **nthreads** (*int*, *optional*) – Number of threads, by default {os.cpu_count()-1}

-  **verbose** (*bool*, *optional*) – Whether to print extra information to standard output, by default False

:Returns: A numpy.ndarray with grid points corresponding to the atom barcodes of the ligand

:Return type: numpy.ndarray

:Note: Greater barcodes have priority in the 3D grid when atoms overlap

mol2grid.pair2grid

Inserts a target receptor to a 3D grid, created based on the receptor, a padding and a grid spacing (step).

.. code-block:: python

mol2grid.pair2grid(ligand: str, receptor: str, padding: float, step: float = 0.6, ligfile: Optional[str] = None, recfile: Optional[str] = None, vdw: Optional[str] = None, catalog: Optional[str] = None, ignore_h: bool = True, nthreads: int = os.cpu_count() - 1, verbose: bool = False) → Tuple[numpy.ndarray,numpy.ndarray]

:Args:

-  **ligand** (*str*) – A path to a PDB-formatted file of a target ligand

-  **receptor** (*str*) – A path to a PDB-formatted file of a target receptor

-  **padding** (*float*) – A length to be added in each direction of the 3D grid

-  **step** (*float*, *optional*) – Grid spacing (A), by default 0.6

-  **ligfile** (*str*, *optional*) – A path to a PDB-formatted file to write the grid points where atoms of the ligand lay on and the barcodes are mapped on the B-values, by default None

-  **recfile** (*str*, *optional*) – A path to a PDB-formatted file to write the grid points where atoms of the receptor lay on and the barcodes are mapped on the B-values, by default None

-  **vdw** (*str*, *optional*) – A path to a custom van der Waals radii file, by default None

-  **catalog** (*str*, *optional*) – A path to a custom catalog file, by default None

-  **ignore_h** (*bool*, *optional*) – Whether to ignore hydrogen atoms, by default True

-  **nthreads** (*int*, *optional*) – Number of threads, by default {os.cpu_count()-1}

-  **verbose** (*bool*, *optional*) – Whether to print extra information to standard output, by default False

:Returns: A tuple with numpy.ndarrays with grid points corresponding to the atom barcodes of the ligand and the receptor

:Return type: numpy.ndarray

:Note: Greater barcodes have priority in the 3D grid when atoms overlap

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License

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The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.