e3fp.fingerprint.structs module

Class for defining 3D atom environments.

Author: Seth Axen E-mail: seth.axen@gmail.com

exception FormatError[source]

Bases: Exception

class Shell(center_atom, shells={}, radius=None, last_shell=None, identifier=None)[source]

Bases: object

A container for other Shells centered on an atom.

Shells represent all atoms explicitly within a container. Atoms are represented by their ids. If atoms are provided instead of shells, they are converted to single-atom shells. A Substruct is generated from a Shell on the fly by recursion through member shells. An optional identifier may be set.

property atoms

Get all atoms explicitly within the shell.

property center_atom
classmethod from_substruct(substruct)[source]

Create shell with one shell for each atom in the substruct.

property shells
property substruct

Get substruct with all atoms implicitly within the shell.

class Substruct(center_atom=None, atoms={})[source]

Bases: object

A container for atoms optionally centered on an atom.

A Substruct represents all atoms implicitly within a Shell. Two Substructs are equal if they contain the same atoms.

property atoms
property center_atom
classmethod from_shell(shell)[source]
shell_to_pdb(mol, shell, atom_coords, bound_atoms_dict, out_file=None, reorient=True)[source]

Append substructure within shell to PDB.

Parameters:

  • mol (RDKit Mol) – Input mol

  • shell (Shell) – A shell

  • atom_coords (dict) – Dict matching atom id to coordinates.

  • bound_atoms_dict (dict) – Dict matching atom id to id of bound atoms.

  • out_file (str or None, optional) – File to which to append coordinates.

  • reorient (bool, optional) – Use the transformation matrix in the shell to align by the stereo quadrants. If no transformation matrix present, centers the center atom.

Returns:

list of str

Return type:

list of PDB file lines, if out_file not specified