Stereodescriptors#

Stereodescriptors are standardized notations that precisely define the 3D spatial arrangement of atoms around a molecular center. These descriptors combine three key aspects of molecular geometry:

Hybridization state
Stereochemical configuration
Relative positioning of substituents

They serve as fundamental building blocks for representing molecular stereochemical perception in algorithms.

Order Sensitivity Stereodescriptor assignments depend critically on the input order of ligand atoms.

Permutation Invariance Within their defined symmetry group, stereodescriptors are invariant to permitted atom permutations.

Chiral Centers Tetrahedral atoms and other chiral elements use 1/-1 parity to distinguish enantiomers.

Achiral Centers Use parity 0

Special Case: ``None`` The None parity is used for: 1. Represents unknown or unspecified stereochemistry 2. Allows non-enantiomeric rearrangements (e.g., square planar ligand exchange) 3. Functions as a stereochemical wildcard in substructure searching

When using stereodescriptors, remember they encode local configuration. Global molecular chirality emerges from combinations of local descriptors and molecular topology.

class stereomolgraph.stereodescriptors.Stereo(atoms: A, parity: P = None)#

Protocol to represent the orientation of a group of atoms in space. This is used to represent local stereochemistry and simultaneously the hybridization of atoms.

atoms: TypeVar(A, bound= tuple[None | int, ...], covariant=True)#: Atoms are a order dependent tuple of integers.

parity: TypeVar(P, bound= Optional[Literal[1, 0, -1]], covariant=True)#: parity is a number that defines the orientation of the atoms. If None, the relative orientation of the atoms is not defined. If 0 the orientation is defined and part of a achiral stereochemistry. If 1 or -1 the orientation is defined and part of a chiral stereochemistry.

property PERMUTATION_GROUP: Iterable[A]#: Defines all allowed permutations defined by the symmetry group under which the stereochemistry is invariant.

invert() → Self#

Inverts the stereo. If the stereo is achiral, it returns itself.

Return type:: Self

get_isomers() → Set[Self]#

Returns all stereoisomers of the stereochemistry. Not just the inverted ones, but all possible stereoisomers.

Return type:: Set[Self]

class stereomolgraph.stereodescriptors.AtomStereo(atoms: A, parity: P = None)#: Bases: Stereo[A, P], Protocol, Generic[A, P]

class stereomolgraph.stereodescriptors.BondStereo(atoms: A, parity: P = None)#: Bases: Stereo[A, P], Protocol, Generic[A, P]

class stereomolgraph.stereodescriptors.Tetrahedral(atoms: A, parity: P = None)#

Represents all possible configurations of atoms for a Tetrahedral Stereochemistry:

parity = 1      parity = -1
    4                4
    |                |
    0                0
 /  ¦  \          /  ¦  \
2   1   3        3   1   2

Atoms of the tetrahedral stereochemistry are ordered in a way that when the first atom is rotated to the back, the other atoms in order are rotated in the direction defined by the stereo.

Variables:

atoms – Atoms of the stereochemistry
parity – Stereochemistry
PERMUTATION_GROUP – Permutations allowed by the stereochemistry

class stereomolgraph.stereodescriptors.SquarePlanar(atoms: A, parity: P = None)#

Represents all possible configurations of atoms for a SquarePlanar Stereochemistry:

Atoms of the Square Planar stereochemistry are ordered in a way that

Variables:

atoms – Atoms of the stereochemistry
parity – Stereochemistry

class stereomolgraph.stereodescriptors.TrigonalBipyramidal(atoms: A, parity: P = None)#

Represents all possible configurations of atoms for a TrigonalBipyramidal Stereochemistry:

parity = 1             parity = -1
 3   1                     1   3
  ◁  ¦                    ¦  ▷
     0  — 5           5 —  0
  ◀  ¦                    ¦  ▶
 4   2                     2   4

Atoms of the trigonal bipyramidal stereochemistry are ordered in a way that when the first two atoms are the top and bottom of the bipyramid. The last three equatorial atoms are ordered in a way that when the first atom is rotated to the back, the other atoms in order are rotated in the direction defined by the stereo.

Variables:

atoms – Atoms of the stereochemistry
parity – Stereochemistry

class stereomolgraph.stereodescriptors.Octahedral(atoms: A, parity: P = None)#

Represents all possible configurations of atoms for a Octahedral Stereochemistry:

parity = 1             parity = -1
 3  1   6                3  2  6
  ◁ ¦ /                  ◁ ¦ /
    0                       0
  / ¦ ▶                  / ¦  ▶
 4  2  5                4   1  5

class stereomolgraph.stereodescriptors.PlanarBond(atoms: A, parity: P = None)#

Represents all possible configurations of atoms for a Planar Structure and should be used for aromatic and double bonds:

All atoms of the double bond are in one plane. Atoms 2 and 3 are the center Atoms 0 and 1 are bonded to 2 and atoms 4 and 5 are bonded to 3. The stereochemistry is defined by the relative orientation of the atoms 0, 1, 4 and 5.

Variables:

atoms – Atoms of the stereochemistry
parity – Stereochemistry
PERMUTATION_GROUP – Permutations allowed by the stereochemistry

class stereomolgraph.stereodescriptors.AtropBond(atoms: A, parity: P = None)#

Represents all possible configurations of atoms for a Atropostereoisomer bond:

parity = 1          parity = -1
1       5           1        5
 \     /            ◀      /
  2 - 3               2 - 3
◀      \            /      \
0        4         0         4

Stereodescriptors#

This Page