Molecules to grid (mol2grid)
Python package to insert a molecule in a 3D grid, considering each atom type as an integer.
See also:
Requirements
Python 3.7+
NumPy 1.19.5+
toml 0.10.2+
Installation
To install the latest release on PyPI, run:
pip install mol2gridTo install the latest developmental version, run:
git clone https://github.com/LBC-LNBio/mol2grid.git
pip install mol2gridUsage
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 receptorThe 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.
1 maintainer
Metadata
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Release files for mol2grid 0.1.4
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Release files / mol2grid-0.1.4-cp39-cp39-win_amd64.whl
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Release files / mol2grid-0.1.4-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
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Release files / mol2grid-0.1.4-cp39-cp39-macosx_10_14_x86_64.whl
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Release files / mol2grid-0.1.4-cp38-cp38-win_amd64.whl
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Release files / mol2grid-0.1.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
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Release files / mol2grid-0.1.4-cp38-cp38-macosx_10_14_x86_64.whl
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Release files / mol2grid-0.1.4-cp37-cp37m-win_amd64.whl
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Release files / mol2grid-0.1.4-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
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Release files / mol2grid-0.1.4-cp37-cp37m-macosx_10_14_x86_64.whl
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