e3fp.fingerprint.structs module¶
Class for defining 3D atom environments.
Author: Seth Axen E-mail: seth.axen@gmail.com
- 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¶
- 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