e3fp.fingerprint.structs module¶
Class for defining 3D atom environments.
Author: Seth Axen E-mail: seth.axen@gmail.com
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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.
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property
atoms
¶ Get all atoms explicitly within the shell.
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property
center_atom
¶
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classmethod
from_substruct
(substruct)[source]¶ Create shell with one shell for each atom in the substruct.
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property
shells
¶
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property
substruct
¶ Get substruct with all atoms implicitly within the shell.
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property
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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.
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property
atoms
¶
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property
center_atom
¶
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property
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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