mol2grid 0.1.4

Python package to insert a ligand in a 3D grid, created based on its respective receptor, considering each atom type as an integer

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

See also:

• GitHub repository

Requirements

• Python 3.7+

• NumPy 1.19.5+

• toml 0.10.2+

Installation

To install the latest release on PyPI, run:

pip install mol2grid

To install the latest developmental version, run:

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

Usage

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

>>> 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).

>>> 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).

>>> 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).

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

API

mol2grid.lig2grid

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

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).

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).

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

License

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.