polymerist.rdutils.rdcoords.tiling
For generating periodically-tiled topologies from RDKit Mols
Functions
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Determine an effective radius of influence of a molecule such that all atoms are within this radius |
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Generate a tiled topology of copies of an RDKit molecule, transformed to occupy the same relative positions as points on the given lattice with unit dimensions |
Module Contents
- polymerist.rdutils.rdcoords.tiling.rdmol_effective_radius(rdmol: rdkit.Chem.Mol, conf_id: int = 0) float[source]
Determine an effective radius of influence of a molecule such that all atoms are within this radius
- polymerist.rdutils.rdcoords.tiling.tile_lattice_with_rdmol(rdmol: rdkit.Chem.Mol, lattice_points: numpy.ndarray[polymerist.genutils.typetools.numpytypes.Shape[polymerist.genutils.typetools.numpytypes.N, 3], float], rotate_randomly: bool = True, conf_id: int = 0) rdkit.Chem.Mol[source]
Generate a tiled topology of copies of an RDKit molecule, transformed to occupy the same relative positions as points on the given lattice with unit dimensions if “random_rotations” is True, each occurrence of the molecule will also have a random rotation applied to it. Mol is NOT modified at any point in the procedure