MolecularDiffusion.data.component.pointcloud

Classes

Atom

PointCloud_Mol

Point Cloud representation of a molecule.

Functions

simple_idx_match_check(mol, ase_atoms)

Module Contents

class MolecularDiffusion.data.component.pointcloud.Atom
get_coord()
element: str
index: int
x: float
y: float
z: float
class MolecularDiffusion.data.component.pointcloud.PointCloud_Mol(_atoms)

Point Cloud representation of a molecule.

Parameters: _atoms: List of atoms in the molecule. Each atom is a list with the following elements:

  • Atomic symbol (str)

  • x coordinate (float)

  • y coordinate (float)

  • z coordinate (float)

classmethod from_arrays(zs: torch.Tensor, coords: torch.Tensor, with_hydrogen: bool = False, forbidden_atoms=[])

load arrays to mol representation

parameters: zs: Tensor with the atomic numbers. coords: Tensor with the atomic coordinates. with_hydrogen: Boolean to include Hydrogen atoms in the representation. forbidden_atoms: List of forbidden atoms to be excluded from the representation.

out: molrepr: Mol Object containing the molecular information (coordinates and elements).

classmethod from_xyz(_path: str, with_hydrogen: bool = False, forbidden_atoms=[])

load_xyz(_path: str) -> molrepr: Mol

Load molecule from an XYZ input file and initialize a Mol Object for it.

parameters: _path: String with the path of the input file. with_hydrogen: Boolean to include Hydrogen atoms in the representation. forbidden_atoms: List of forbidden atoms to be excluded from the representation.

out: molrepr: Mol Object containing the molecular information (coordinates and elements).

get_coord()
classmethod str_atom(_atom: int) → str

str_atom(_atom: int) -> atom: str

Convert integer atom to string atom.

in: _atom: Integer with the atomic number.

out: atom: String with the atomic element.

MolecularDiffusion.data.component.pointcloud.simple_idx_match_check(mol, ase_atoms)